0s autopkgtest [02:09:29]: starting date and time: 2024-03-18 02:09:29+0000 0s autopkgtest [02:09:29]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [02:09:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rzbwqz5n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade transdecoder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-23.secgroup --name adt-noble-arm64-transdecoder-20240318-020928-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 125s autopkgtest [02:11:34]: testbed dpkg architecture: arm64 125s autopkgtest [02:11:34]: testbed apt version: 2.7.12 125s autopkgtest [02:11:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 126s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 126s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 126s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 126s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 126s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 126s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 126s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 126s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 126s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 127s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 127s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 127s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 128s Fetched 9189 kB in 2s (5845 kB/s) 128s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s sh: Attempting to set up Debian/Ubuntu apt sources automatically 133s sh: Distribution appears to be Ubuntu 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s eatmydata is already the newest version (131-1). 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s dbus is already the newest version (1.14.10-4ubuntu1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s rng-tools-debian is already the newest version (2.4). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s The following packages will be REMOVED: 137s cloud-init* python3-configobj* python3-debconf* 137s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 137s After this operation, 3252 kB disk space will be freed. 138s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 138s Removing cloud-init (24.1.1-0ubuntu1) ... 138s Removing python3-configobj (5.0.8-3) ... 138s Removing python3-debconf (1.5.86) ... 138s Processing triggers for man-db (2.12.0-3) ... 139s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74369 files and directories currently installed.) 139s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 139s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 139s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 139s invoke-rc.d: policy-rc.d denied execution of try-restart. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s linux-generic is already the newest version (6.8.0-11.11+1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Reading package lists... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s autopkgtest [02:11:54]: rebooting testbed after setup commands that affected boot 402s autopkgtest [02:16:11]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 404s autopkgtest [02:16:13]: @@@@@@@@@@@@@@@@@@@@ apt-source transdecoder 408s Get:1 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (dsc) [2260 B] 408s Get:2 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (tar) [15.0 MB] 408s Get:3 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (diff) [5940 B] 408s gpgv: Signature made Thu Sep 14 10:39:31 2023 UTC 408s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 408s gpgv: Can't check signature: No public key 408s dpkg-source: warning: cannot verify inline signature for ./transdecoder_5.7.1-2.dsc: no acceptable signature found 409s autopkgtest [02:16:18]: testing package transdecoder version 5.7.1-2 409s autopkgtest [02:16:18]: build not needed 410s autopkgtest [02:16:19]: test run-tests: preparing testbed 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 412s Starting pkgProblemResolver with broken count: 0 412s Starting 2 pkgProblemResolver with broken count: 0 412s Done 413s The following additional packages will be installed: 413s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hmmer 413s libblas3 libcairo2 libdatrie1 libdeflate0 libdivsufsort3 libfontconfig1 413s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 413s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libmbedcrypto7 libmbedtls14 413s libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 413s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 413s libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 libxcb-render0 413s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ ncbi-data 413s r-base-core transdecoder transdecoder-doc unzip x11-common xdg-utils zip 413s Suggested packages: 413s hmmer-doc tcl8.6 tk8.6 libbusiness-isbn-perl libregexp-ipv6-perl libwww-perl 413s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 413s Recommended packages: 413s r-recommended r-base-dev r-doc-html r-cran-ggplot2 r-bioc-seqlogo 413s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 413s x11-xserver-utils 413s The following NEW packages will be installed: 413s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 413s fonts-dejavu-mono hmmer libblas3 libcairo2 libdatrie1 libdeflate0 413s libdivsufsort3 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 413s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 413s libmbedcrypto7 libmbedtls14 libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 413s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 413s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 413s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ 413s ncbi-data r-base-core transdecoder transdecoder-doc unzip x11-common 413s xdg-utils zip 413s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 413s Need to get 69.7 MB/69.7 MB of archives. 413s After this operation, 188 MB of additional disk space will be used. 413s Get:1 /tmp/autopkgtest.hmQi3d/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [732 B] 413s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 414s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 414s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 414s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 414s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 414s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 414s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 414s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 414s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 414s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 414s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 414s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 414s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 414s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 414s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 414s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 414s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 414s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 414s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 414s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 414s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 414s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 414s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 414s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 414s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 414s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 414s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 414s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 414s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 414s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 414s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 414s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 414s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 414s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 414s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 414s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 414s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 414s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 414s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 414s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 414s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 414s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 414s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 414s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 liburi-perl all 5.27-1 [88.0 kB] 414s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 414s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 414s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 415s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 415s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 415s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 415s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 415s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder all 5.7.1-2 [204 kB] 415s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder-doc all 5.7.1-2 [14.9 MB] 416s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 416s Preconfiguring packages ... 416s Fetched 69.7 MB in 3s (27.2 MB/s) 416s Selecting previously unselected package fonts-dejavu-mono. 416s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74314 files and directories currently installed.) 416s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 416s Unpacking fonts-dejavu-mono (2.37-8) ... 417s Selecting previously unselected package fonts-dejavu-core. 417s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 417s Unpacking fonts-dejavu-core (2.37-8) ... 417s Selecting previously unselected package fontconfig-config. 417s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 417s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 417s Selecting previously unselected package libfontconfig1:arm64. 417s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 417s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 417s Selecting previously unselected package fontconfig. 417s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 417s Unpacking fontconfig (2.15.0-1ubuntu1) ... 417s Selecting previously unselected package libblas3:arm64. 417s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 417s Unpacking libblas3:arm64 (3.12.0-3) ... 417s Selecting previously unselected package libpixman-1-0:arm64. 417s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_arm64.deb ... 417s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 417s Selecting previously unselected package libxcb-render0:arm64. 417s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ... 417s Unpacking libxcb-render0:arm64 (1.15-1) ... 417s Selecting previously unselected package libxcb-shm0:arm64. 417s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ... 417s Unpacking libxcb-shm0:arm64 (1.15-1) ... 417s Selecting previously unselected package libxrender1:arm64. 417s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 417s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 417s Selecting previously unselected package libcairo2:arm64. 417s Preparing to unpack .../10-libcairo2_1.18.0-1_arm64.deb ... 417s Unpacking libcairo2:arm64 (1.18.0-1) ... 417s Selecting previously unselected package libdatrie1:arm64. 417s Preparing to unpack .../11-libdatrie1_0.2.13-3_arm64.deb ... 417s Unpacking libdatrie1:arm64 (0.2.13-3) ... 417s Selecting previously unselected package libdeflate0:arm64. 417s Preparing to unpack .../12-libdeflate0_1.19-1_arm64.deb ... 417s Unpacking libdeflate0:arm64 (1.19-1) ... 417s Selecting previously unselected package libdivsufsort3:arm64. 417s Preparing to unpack .../13-libdivsufsort3_2.0.1-6_arm64.deb ... 417s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 417s Selecting previously unselected package libgfortran5:arm64. 417s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 417s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 417s Selecting previously unselected package libgomp1:arm64. 417s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 417s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 417s Selecting previously unselected package libgraphite2-3:arm64. 417s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 417s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 417s Selecting previously unselected package libharfbuzz0b:arm64. 417s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 417s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 418s Selecting previously unselected package x11-common. 418s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 418s Unpacking x11-common (1:7.7+23ubuntu2) ... 418s Selecting previously unselected package libice6:arm64. 418s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 418s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 418s Selecting previously unselected package libjpeg-turbo8:arm64. 418s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 418s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 418s Selecting previously unselected package libjpeg8:arm64. 418s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 418s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 418s Selecting previously unselected package liblapack3:arm64. 418s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 418s Unpacking liblapack3:arm64 (3.12.0-3) ... 418s Selecting previously unselected package liblerc4:arm64. 418s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 418s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 418s Selecting previously unselected package libmbedcrypto7:arm64. 418s Preparing to unpack .../24-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 418s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 418s Selecting previously unselected package libmbedx509-1:arm64. 418s Preparing to unpack .../25-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 418s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 418s Selecting previously unselected package libmbedtls14:arm64. 418s Preparing to unpack .../26-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 418s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 418s Selecting previously unselected package libthai-data. 418s Preparing to unpack .../27-libthai-data_0.1.29-2_all.deb ... 418s Unpacking libthai-data (0.1.29-2) ... 418s Selecting previously unselected package libthai0:arm64. 418s Preparing to unpack .../28-libthai0_0.1.29-2_arm64.deb ... 418s Unpacking libthai0:arm64 (0.1.29-2) ... 418s Selecting previously unselected package libpango-1.0-0:arm64. 418s Preparing to unpack .../29-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 418s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 418s Selecting previously unselected package libpangoft2-1.0-0:arm64. 418s Preparing to unpack .../30-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 418s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 418s Selecting previously unselected package libpangocairo-1.0-0:arm64. 418s Preparing to unpack .../31-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 418s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 418s Selecting previously unselected package libpaper1:arm64. 418s Preparing to unpack .../32-libpaper1_1.1.29_arm64.deb ... 418s Unpacking libpaper1:arm64 (1.1.29) ... 418s Selecting previously unselected package libpaper-utils. 418s Preparing to unpack .../33-libpaper-utils_1.1.29_arm64.deb ... 418s Unpacking libpaper-utils (1.1.29) ... 418s Selecting previously unselected package libsharpyuv0:arm64. 418s Preparing to unpack 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man-db (2.12.0-3) ... 429s Processing triggers for install-info (7.1-3) ... 429s Processing triggers for libc-bin (2.39-0ubuntu2) ... 433s (Reading database ... 76813 files and directories currently installed.) 433s Removing autopkgtest-satdep (0) ... 434s autopkgtest [02:16:43]: test run-tests: [----------------------- 434s Running example in $... 434s make[1]: Entering directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 434s ./runMe.sh incl_pfam_n_blast 434s 434s export PERL_HASH_SEED=0 434s 434s if [ ! -e test.genome.fasta ]; then 434s gunzip -c test.genome.fasta.gz > test.genome.fasta 434s fi 434s 434s 434s if [ ! -e transcripts.gtf ]; then 434s gunzip -c transcripts.gtf.gz > transcripts.gtf 434s fi 434s 434s if [ ! -e mini_Pfam-A.hmm ]; then 434s gunzip -c mini_Pfam-A.hmm.gz > mini_Pfam-A.hmm 434s fi 434s 434s if [ ! -e mini_sprot.db.pep ]; then 434s gunzip -c mini_sprot.db.pep.gz > mini_sprot.db.pep 434s fi 434s 434s 434s ## generate alignment gff3 formatted output 434s ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 434s 434s ## generate transcripts fasta file 434s ../../util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta 434s -parsing cufflinks output: transcripts.gtf 434s -parsing genome fasta: test.genome.fasta 434s -done parsing genome. 434s // processing 7000000090838467 434s 434s ## Extract the long ORFs 434s ../../TransDecoder.LongOrfs -t transcripts.fasta 434s CMD: mkdir -p /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir 434s * [Mon Mar 18 02:16:43 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 434s 434s 434s -first extracting base frequencies, we'll need them later. 434s 434s 434s - extracting ORFs from transcripts. 434s -total transcripts to examine: 64 435s CMD: touch /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 435s 435s 435s ################################# 435s ### Done preparing long ORFs. ### 435s ################################## 435s 435s Use file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. 435s 435s Then, run TransDecoder.Predict for your final coding region predictions. 435s 435s 435s 435s cmd="" 435s ## Predict likely ORFs 435s if [ "$1" == "" ]; then # always doing this now. 435s # just coding metrics 435s cmd="../../TransDecoder.Predict -t transcripts.fasta" 435s 435s else 435s 435s # this is how I would have run blast and pfam but I'm using precomputed results for ease of demonstration. 435s #BLASTDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/uniprot_sprot.pep 435s #PFAMDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/Pfam-A.hmm 435s # 435s ## run blast 435s #blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db $BLASTDB -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 435s 435s makeblastdb -in mini_sprot.db.pep -dbtype prot 435s blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db mini_sprot.db.pep -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 435s 435s # 435s ## run pfam 435s #hmmsearch --domtblout pfam.domtblout $PFAMDB transcripts.fasta.transdecoder_dir/longest_orfs.pep > pfam.log 435s 435s hmmpress -f mini_Pfam-A.hmm 435s hmmsearch --domtblout pfam.domtblout mini_Pfam-A.hmm transcripts.fasta.transdecoder_dir/longest_orfs.pep 435s 435s ## use pfam and blast results: 435s cmd="../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v" 435s 435s fi 435s 435s 435s Building a new DB, current time: 03/18/2024 02:16:44 435s New DB name: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/mini_sprot.db.pep 435s New DB title: mini_sprot.db.pep 435s Sequence type: Protein 435s Keep MBits: T 435s Maximum file size: 1000000000B 435s Adding sequences from FASTA; added 240 sequences in 0.013397 seconds. 435s 435s 435s Warning: [blastp] Examining 5 or more matches is recommended 436s Working... done. 436s Pressed and indexed 118 HMMs (118 names and 118 accessions). 436s Models pressed into binary file: mini_Pfam-A.hmm.h3m 436s SSI index for binary model file: mini_Pfam-A.hmm.h3i 436s Profiles (MSV part) pressed into: mini_Pfam-A.hmm.h3f 436s Profiles (remainder) pressed into: mini_Pfam-A.hmm.h3p 436s # hmmsearch :: search profile(s) against a sequence database 436s # HMMER 3.4 (Aug 2023); http://hmmer.org/ 436s # Copyright (C) 2023 Howard Hughes Medical Institute. 436s # Freely distributed under the BSD open source license. 436s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s # query HMM file: mini_Pfam-A.hmm 436s # target sequence database: transcripts.fasta.transdecoder_dir/longest_orfs.pep 436s # per-dom hits tabular output: pfam.domtblout 436s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s 436s Query: AA_permease [M=479] 436s Accession: PF00324.20 436s Description: Amino acid permease 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.5e-25 80.4 51.2 7.3e-25 80.0 51.2 1.0 1 CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 80.0 51.2 7.7e-27 7.3e-25 19 463 .. 70 500 .. 53 509 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 80.0 bits; conditional E-value: 7.7e-27 436s AA_permease 19 lgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpe....lGfviGlnylfswitvlaleltaasiliqfwelvtdlp 111 436s + + ++G++g++ ++++++++++ v +slge+a+ +p sgg y+++ +p+ l +v+G+ ++ ++t +a + as+++q + + + + 436s CUFF.38.1.p2 70 SLIFSMNCGGGGMVWSWIIGCICLIPVSISLGELASSMPTSGGLYFWIFTLASPSsrafLCWVCGYVSVLGYATIYASTVYSASSMVQALAVIGSPS 166 436s 44455689999************************************99999987222255555555555566666666666666666664444333 PP 436s 436s AA_permease 112 kawvt..........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkga..gfrflgdngsifknnlppgfakeeeg 196 436s + a +l+v+++++ + +v +++ +i + + ++ i++ii ++ ++ + +n g ++ f++++g n+ 436s CUFF.38.1.p2 167 ----YsptkyeqygiYAALLFVISAMTAIPSRVIAKVNIINITFQFLVSIILIIALAAGSDSTTRNSGSfiFGDFTNYSGW---SNM---------- 246 436s ....02345666666999**********************99999999999999996555555555553333333333333...111.......... PP 436s 436s AA_permease 197 afknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplin 293 436s +fi f + v +G+e+ a++a+E+ + +k+ P a+++ + ti+ +++++++++++ + +l +s+ + + ++ g++++ ++ 436s CUFF.38.1.p2 247 -GWAFILSFTTPVWVVSGFESSAAVAEESTNAAKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSSLGQ-PVAQVLVNNVGNKGALGIFS 341 436s .246888888899999*******************************************************99966.7888889999********** PP 436s 436s AA_permease 294 aviltaalssansslysasRvlyslakdglaP..kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388 436s +++++ +l++ +s+l++asR ++++++dg +P ++l+ ++k++vPl+aill+++ sll+ ll +n+ ais + +l++ l i+ + 436s CUFF.38.1.p2 342 LLVIALCLNC-ISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILVNVT---------AISSVFNLAIIALYIAYSG 428 436s *999999998.79************************************************99999999.........4444444444444444444 PP 436s 436s AA_permease 389 rfRkalkyqgrsieelgfkaallplgvi..lvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463 436s +++ + y++ + + + + p ++ +++ ++i++ll+ + ++ + + +++a +++ +++v++++ ++ 436s CUFF.38.1.p2 429 PLMCRFVYNKFQPGVFYVGKWSKPAALWslVWMWFMILMLLFPQYQKPNQ-----DEMNWAIVVLGFVMVFCVVYYY 500 436s 55555555555555555555666555540045555555555555555555.....6788888899999998888777 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (479 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1980.66 436s // 436s Query: AA_permease_2 [M=425] 436s Accession: PF13520.5 436s Description: Amino acid permease 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.1e-56 184.1 57.6 2.6e-56 183.8 57.6 1.0 1 CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 183.8 57.6 2.7e-58 2.6e-56 1 425 [] 48 491 .. 48 491 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: 183.8 bits; conditional E-value: 2.7e-58 436s AA_permease_2 1 lsllsafalvigsv......igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf....gkkvaflsawfnwf 86 436s +s++s f+ ++gs+ +gs if +++ gg +++++i+++++ ++v++ + El+s +p+sgG+y + + ++ +++++ +++ 436s CUFF.38.1.p2 48 FSYVSIFGQSFGSMglcpamAGSLIF---SMNCGGGGMVWSWIIGCICL-IPVSISLGELASSMPTSGGLYFWIFTLAspssRAFLCWVCGYVSVL 139 436s 799***********777755555555...57888888888888888888.9*********888***********8886333356666********* PP 436s 436s AA_permease_2 87 ayvpvlasilsvaasyl..lnalg.pdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfssl.ste 178 436s +y+ as++++a s+ l ++g p++ ++++ +y+i++a+l ++ +++++ + +ak++ i +++ +l + iili ++l++++ ++ ++ s++ 436s CUFF.38.1.p2 140 GYATIYASTVYSASSMVqaLAVIGsPSYSPTKYEQYGIYAALLFVISAMTAIPSRVIAKVNIINITFQFL-VSIILI-IALAAGSDSTTRNSgSFI 233 436s ****9999888777777433345547*******************************************5.555454.566666555444334444 PP 436s 436s AA_permease_2 179 tdtffpn.gwp..g..vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsn.lgs.vaalffe 265 436s + f++ gw+ g ++l++++ +w+++Gfes+a v+ee + k +p+a++++l+++++l++ + i++++ ++ d a l++ lg+ va+++++ 436s CUFF.38.1.p2 234 FGDFTNYsGWSnmGwaFILSFTTPVWVVSGFESSAAVAEESTNaaKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSsLGQpVAQVLVN 329 436s 4444444477743133699*********************8887789*****************************999887773444569***** PP 436s 436s AA_permease_2 266 avggkvvaiivvilialsllgaintavigssrvlealardgvlP..rffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgli 359 436s +vg+k + +i++ l++++l+++ ++++i++sr ++a++rdg++P r+++ k++ p++ai l++++sl+++ll+l+ + +a++ +++++ ++l+ 436s CUFF.38.1.p2 330 NVGNKGALGIFS-LLVIALCLNCISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILV-NVTAISSVFNLAIIALY 423 436s ***999999999.8999****************************************************888877765.69*************** PP 436s 436s AA_permease_2 360 isyllliigalilrkkrphl...krpgkilvaiigalfllfllvalffppkgpatqssliytiiltval 425 436s i y ++ +++++ k +p +++ + a+ ++++ f++ +l fp+ + +q++++++i++++++ 436s CUFF.38.1.p2 424 IAYSGPLMCRFVYNKFQPGVfyvGKW-SKPAALWSLVWMWFMILMLLFPQYQKPNQDEMNWAIVVLGFV 491 436s **********9999999977444444.468**********************************99875 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (425 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1876.09 436s // 436s Query: Acetyltransf_1 [M=117] 436s Accession: PF00583.24 436s Description: Acetyltransferase (GNAT) family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.8e-15 48.5 0.0 5.6e-15 48.3 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 5.3e-15 48.4 0.0 6.2e-15 48.1 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 48.3 0.0 1.2e-16 5.6e-15 18 117 .] 35 129 .. 16 129 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 48.3 bits; conditional E-value: 1.2e-16 436s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 436s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 436s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 436s CUFF.34.1.p2 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 436s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 436s 436s HHHHH.TTE CS 436s Acetyltransf_1 110 rlYek.lGF 117 436s +lY + +GF 436s CUFF.34.1.p2 122 PLY-RsVGF 129 436s ***.65**9 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 48.1 0.0 1.3e-16 6.2e-15 18 117 .] 35 129 .. 16 129 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 48.1 bits; conditional E-value: 1.3e-16 436s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 436s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 436s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 436s CUFF.35.1.p1 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 436s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 436s 436s HHHHH.TTE CS 436s Acetyltransf_1 110 rlYek.lGF 117 436s +lY + +GF 436s CUFF.35.1.p1 122 PLY-RsVGF 129 436s ***.65**9 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (117 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 2279.54 436s // 436s Query: Acetyltransf_10 [M=127] 436s Accession: PF13673.6 436s Description: Acetyltransferase (GNAT) domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.5e-22 71.0 0.0 5.3e-22 70.8 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 1.7e-20 65.9 0.0 2e-20 65.7 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 70.8 0.0 1.1e-23 5.3e-22 32 127 .] 50 150 .. 28 150 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 70.8 bits; conditional E-value: 1.1e-23 436s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 436s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 436s CUFF.35.1.p1 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 436s 67888899*******9986666799***************************98888888888889999************************* PP 436s 436s Acetyltransf_10 121 vpMekel 127 436s v+M++el 436s CUFF.35.1.p1 144 VEMRLEL 150 436s ****986 PP 436s 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 65.7 0.0 4.1e-22 2e-20 32 123 .. 50 146 .] 28 146 .] 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 65.7 bits; conditional E-value: 4.1e-22 436s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 436s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 436s CUFF.34.1.p2 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 436s 67888899*******9986666799***************************98888888888889999************************* PP 436s 436s Acetyltransf_10 121 vpM 123 436s v+M 436s CUFF.34.1.p2 144 VEM 146 436s **9 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (127 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1697.48 436s // 436s Query: Acetyltransf_15 [M=210] 436s Accession: PF17013.4 436s Description: Putative acetyl-transferase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1e-06 21.0 0.1 3e-06 19.4 0.1 1.7 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 4.7e-06 18.8 0.1 1.2e-05 17.4 0.1 1.7 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 19.4 0.1 6.3e-08 3e-06 28 154 .. 5 149 .. 1 150 [. 0.84 436s 436s Alignments for each domain: 436s == domain 1 score: 19.4 bits; conditional E-value: 6.3e-08 436s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 436s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 436s CUFF.35.1.p1 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 436s 5578888888888888888888999999988734444479999999999999999999987777889999************************ PP 436s 436s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksgPeelkkrle 154 436s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g ++++ rle 436s CUFF.35.1.p1 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDGIPHVEMRLE 149 436s **********9888774........6789999*******99744499999998888876 PP 436s 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 17.4 0.1 2.6e-07 1.2e-05 28 145 .. 5 140 .. 1 146 [] 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 17.4 bits; conditional E-value: 2.6e-07 436s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 436s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 436s CUFF.34.1.p2 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 436s 5678888888888888888888999999988734444479999999999999999999987777889999************************ PP 436s 436s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksg 145 436s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g 436s CUFF.34.1.p2 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDG 140 436s *********99887774........5677888888888887633366655 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (210 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 865.70 436s // 436s Query: Acetyltransf_5 [M=101] 436s Accession: PF13444.5 436s Description: Acetyltransferase (GNAT) domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.2e-07 23.3 0.0 9.5e-07 22.2 0.0 1.7 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 4.6e-07 23.2 0.0 1.3e-06 21.7 0.0 1.7 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 22.2 0.0 2e-08 9.5e-07 1 82 [. 25 102 .. 25 123 .. 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 22.2 bits; conditional E-value: 2e-08 436s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 436s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 436s CUFF.34.1.p2 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 436s 7888888888888777......*************988889*********9999987777776666665555443555666666 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 21.7 0.0 2.7e-08 1.3e-06 1 82 [. 25 102 .. 25 106 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 21.7 bits; conditional E-value: 2.7e-08 436s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 436s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 436s CUFF.35.1.p1 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 436s 7888888888888777......*************988889*********9999877777776666665555443555677666 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (101 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 715.26 436s // 436s Query: Acetyltransf_7 [M=76] 436s Accession: PF13508.6 436s Description: Acetyltransferase (GNAT) domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.1e-13 42.3 0.0 5.6e-13 41.8 0.0 1.2 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 4.6e-13 42.1 0.0 6.2e-13 41.7 0.0 1.2 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 41.8 0.0 1.2e-14 5.6e-13 5 76 .] 29 131 .. 25 131 .. 0.68 436s 436s Alignments for each domain: 436s == domain 1 score: 41.8 bits; conditional E-value: 1.2e-14 436s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 436s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 436s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 436s CUFF.34.1.p2 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 436s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 436s 436s HHHHHTTEEE CS 436s Acetyltransf_7 67 kfYeklGFee 76 436s ++Y++ GF++ 436s CUFF.34.1.p2 122 PLYRSVGFKK 131 436s ********95 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 41.7 0.0 1.3e-14 6.2e-13 5 76 .] 29 131 .. 25 131 .. 0.68 436s 436s Alignments for each domain: 436s == domain 1 score: 41.7 bits; conditional E-value: 1.3e-14 436s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 436s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 436s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 436s CUFF.35.1.p1 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 436s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 436s 436s HHHHHTTEEE CS 436s Acetyltransf_7 67 kfYeklGFee 76 436s ++Y++ GF++ 436s CUFF.35.1.p1 122 PLYRSVGFKK 131 436s ********95 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (76 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2150.08 436s // 436s Query: Acetyltransf_9 [M=128] 436s Accession: PF13527.6 436s Description: Acetyltransferase (GNAT) domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.3e-07 23.6 0.0 8.3e-07 21.8 0.0 1.8 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 2.6e-07 23.4 0.0 9.2e-07 21.6 0.0 1.8 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 21.8 0.0 1.7e-08 8.3e-07 72 127 .. 72 131 .. 11 132 .. 0.71 436s 436s Alignments for each domain: 436s == domain 1 score: 21.8 bits; conditional E-value: 1.7e-08 436s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 436s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 436s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 436s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 436s 4567999*************************9986556666667566669******975 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 21.6 0.0 1.9e-08 9.2e-07 72 127 .. 72 131 .. 11 132 .. 0.71 436s 436s Alignments for each domain: 436s == domain 1 score: 21.6 bits; conditional E-value: 1.9e-08 436s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 436s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 436s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 436s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 436s 4567999*************************9986556666667566669******975 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (128 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 770.89 436s // 436s Query: Acetyltransf_CG [M=80] 436s Accession: PF14542.5 436s Description: GCN5-related N-acetyl-transferase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.2e-05 18.0 0.0 2.3e-05 17.2 0.0 1.4 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 1.3e-05 17.9 0.0 2.5e-05 17.1 0.0 1.4 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 17.2 0.0 4.8e-07 2.3e-05 8 56 .. 57 105 .. 50 108 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 17.2 bits; conditional E-value: 4.8e-07 436s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 436s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 436s CUFF.34.1.p2 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 436s 5677888888778999***************************998875 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 17.1 0.0 5.2e-07 2.5e-05 8 56 .. 57 105 .. 50 108 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 17.1 bits; conditional E-value: 5.2e-07 436s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 436s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 436s CUFF.35.1.p1 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 436s 5677888888778999***************************998875 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (80 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2356.01 436s // 436s Query: Aldo_ket_red [M=292] 436s Accession: PF00248.20 436s Description: Aldo/keto reductase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.9e-69 225.5 0.0 4.6e-69 225.3 0.0 1.0 1 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 225.3 0.0 4.8e-71 4.6e-69 1 289 [. 21 340 .. 21 342 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 225.3 bits; conditional E-value: 4.8e-71 436s .EEEE-SSS-ST.......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..................... CS 436s Aldo_ket_red 1 elglGtwqlgsk......eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..................... 70 436s +l+lG +++g k ++ee+++++++a++aGi++fDtA+ Y g seel+G++++k++ +r +++i +K+ 436s CUFF.17.1.p1 21 KLILGCMSYGKKeywedwVLEDEEEVFKIMKAAYDAGIRTFDTANCYSAGVSEELVGKFIRKYEIPRSSIVILSKCffpvrkdlikifgdlssrgvh 117 436s 689999999999888663334678999*********************************************************************9 PP 436s 436s ..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH....HHTTT--EEEEE- CS 436s Aldo_ket_red 71 ..dkrdaeiksglskenieesleeslkrLgtdyvDllllHrpdpslpieevldaleelvkeGkiraiGvSnfsveqleka....kkkkkvkivavqv 161 436s d +++ gls+++i ++e+s+krLgt y+D+l++Hr dp ++ eev++al+++v++Gk+r+iG S q ++ +k++ +k+++ q+ 436s CUFF.17.1.p1 118 flDSPELANQCGLSRKHIFDAVEDSVKRLGT-YIDVLQIHRYDPHVSAEEVMRALNDVVESGKVRYIGASTMRCYQFIELqntaEKHGWHKFISMQN 213 436s 998888889999******************6.**************************************88866655566778************* PP 436s 436s B-BTTB-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------....S-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT CS 436s Aldo_ket_red 162 eynllkreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr....rtsknqdaaeelselakehgvsiaqvalryalsqpa 254 436s +nll ++ee++++++c+k gv+li++spl++Gllt+ + +e++ + +++ ++ + +++++elak+++vs+a++a ++ l + 436s CUFF.17.1.p1 214 YHNLL-YREEEREMIPYCQKTGVGLIPWSPLARGLLTRSIDANEETIRSKTD-LY-TraleFGAGYKAILSRVEELAKKYNVSMATLATAWSL--HK 305 436s *****.*******************************999988887743332.33.2479555556666799*********************..9* PP 436s 436s -SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS 436s Aldo_ket_red 255 vgivipgasnieqlednldalelklseeevaelde 289 436s + +i+g s++e+l+d l+a+elklsee++++l+e 436s CUFF.17.1.p1 306 GDYPIVGISKVERLKDALAAVELKLSEEDIKYLEE 340 436s *******************************9986 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (292 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2581.18 436s // 436s Query: Amidohydro_1 [M=344] 436s Accession: PF01979.19 436s Description: Amidohydrolase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.4e-82 268.7 0.4 5.3e-82 268.4 0.4 1.1 1 CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-13 436s 4.5e-82 268.6 0.4 5.4e-82 268.4 0.4 1.1 1 CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 268.4 0.4 1.1e-83 5.3e-82 1 343 [. 55 420 .. 55 421 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 436s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 436s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 436s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 436s CUFF.26.1.p1 55 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 149 436s 79************************************************************************************9..******** PP 436s 436s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 436s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 436s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 436s CUFF.26.1.p1 150 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 238 436s ******************9988899999999999999....*******************************************9999996....67 PP 436s 436s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 436s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 436s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 436s CUFF.26.1.p1 239 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 332 436s 76.6677.8*************.************************************************************************** PP 436s 436s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 436s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 436s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 436s CUFF.26.1.p1 333 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 420 436s ***99998888.6677.89999***************6.******************972255668888********************97 PP 436s 436s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 268.4 0.4 1.1e-83 5.4e-82 1 343 [. 57 422 .. 57 423 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 436s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 436s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 436s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 436s CUFF.27.1.p1 57 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 151 436s 79************************************************************************************9..******** PP 436s 436s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 436s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 436s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 436s CUFF.27.1.p1 152 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 240 436s ******************9988899999999999999....*******************************************9999996....67 PP 436s 436s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 436s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 436s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 436s CUFF.27.1.p1 241 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 334 436s 76.6677.8*************.************************************************************************** PP 436s 436s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 436s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 436s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 436s CUFF.27.1.p1 335 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 422 436s ***99998888.6677.89999***************6.******************972255668888********************97 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (344 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 2003.90 436s // 436s Query: Amidohydro_3 [M=473] 436s Accession: PF07969.10 436s Description: Amidohydrolase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.6e-17 55.5 0.1 1.6e-13 43.4 0.0 2.2 2 CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-13 436s 3.6e-17 55.5 0.1 1.6e-13 43.4 0.0 2.2 2 CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.0 0.1 4.8e-05 0.0023 5 25 .. 51 71 .. 50 82 .. 0.86 436s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 211 421 .. 163 422 .. 0.75 436s 436s Alignments for each domain: 436s == domain 1 score: 10.0 bits; conditional E-value: 4.8e-05 436s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 436s ++G +v+PG++ H Hla 436s CUFF.26.1.p1 51 LEGHIVMPGLISLHVHLAQSL 71 436s 89**************99865 PP 436s 436s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 436s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 436s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 436s CUFF.26.1.p1 211 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 298 436s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 436s 436s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 436s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 436s CUFF.26.1.p1 299 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 389 436s 9******************.....4444444444433333333666999***************************8.***************9555 PP 436s 436s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 436s l ++p ++ v +v+dG+ + 436s CUFF.26.1.p1 390 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 421 436s 55555443333346666888899999999876 PP 436s 436s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.0 0.1 4.9e-05 0.0023 5 25 .. 53 73 .. 52 84 .. 0.86 436s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 213 423 .. 165 424 .. 0.75 436s 436s Alignments for each domain: 436s == domain 1 score: 10.0 bits; conditional E-value: 4.9e-05 436s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 436s ++G +v+PG++ H Hla 436s CUFF.27.1.p1 53 LEGHIVMPGLISLHVHLAQSL 73 436s 89**************99865 PP 436s 436s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 436s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 436s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 436s CUFF.27.1.p1 213 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 300 436s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 436s 436s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 436s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 436s CUFF.27.1.p1 301 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 391 436s 9******************.....4444444444433333333666999***************************8.***************9555 PP 436s 436s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 436s l ++p ++ v +v+dG+ + 436s CUFF.27.1.p1 392 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 423 436s 55555443333346666888899999999876 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (473 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2275.84 436s // 436s Query: Aminotran_1_2 [M=363] 436s Accession: PF00155.20 436s Description: Aminotransferase class I and II 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4e-06 18.7 0.0 7.3e-06 17.9 0.0 1.4 1 CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 17.9 0.0 7.6e-08 7.3e-06 48 334 .. 65 357 .. 61 375 .. 0.71 436s 436s Alignments for each domain: 436s == domain 1 score: 17.9 bits; conditional E-value: 7.6e-08 436s HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHH...HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS 436s Aminotran_1_2 48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyk...nilrlsggevvryplyseedfhldlealeealk 140 436s e ++ lak+l+ ++++++++ +++++++++ + lk pgd++++ d +++ +l++ g+ev+ +p +e ++h ++ + ++ 436s CUFF.40.1.p1 65 ETRSLLAKLLN------ASTKDSITFTRDTTEGLNLFQRSLKWKPGDNVVILDNEHPNQGfgwIALQNDGLEVRLVP--NEGQYHANASTFAPYVD 152 436s 778999*****......45555***********************************987333568999********..77999999999*99999 PP 436s 436s THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTTSGGG-EEEEEEE CS 436s Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgn 236 436s + +tk i + s+ +G+ +++++++++ + ++++++ D + +++ ++ +v++ +++ s+ K +G++ +G ++++ 436s CUFF.40.1.p1 153 S------RTKAIGLSSVMFHSGQ---KNDVKDIANAFRPKGIHVLADLTQQVGLSK--------IDVQDLNVSACAFSCHKGLGCPT-GLGVLYVS 230 436s 9......9***********9*97...5677777777*************9999998........55555544688889999999975.58999998 PP 436s 436s H.........................HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHS.....TEEE CS 436s Aminotran_1_2 237 a.........................avvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLael.....glkv 299 436s + +++ ++ ++++ + + ++++ +al++ l+ +++ + lq + k l +eL++l g k 436s CUFF.40.1.p1 231 PlaiselrstppfvgggavedfkedlKLKLNAKYHQSALRYeHTNNAYMLITALRAYLKFLLkvGISNVERYLQGLGKDLIKELESLnvsviGYKD 326 436s 866666666666666666666666555555555555555555555666666666666555554434444444555555666666555444444444 PP 436s 436s ECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEE CS 436s Aminotran_1_2 300 lasq.sgmflltdlsaetakelskkLleevgvyvtp 334 436s ++++ s+ ++l l++e ++ L+++ gv v++ 436s CUFF.40.1.p1 327 FDKHsSHSYVLKILNPE----WFDFLRQQ-GVCVSR 357 436s 44444555555555555....44445555.666655 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (363 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1242.02 436s // 436s Query: Aminotran_5 [M=371] 436s Accession: PF00266.18 436s Description: Aminotransferase class-V 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.1e-47 153.1 0.0 8.8e-47 152.3 0.0 1.3 1 CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 152.3 0.0 9.2e-49 8.8e-47 41 369 .. 59 376 .. 25 378 .. 0.89 436s 436s Alignments for each domain: 436s == domain 1 score: 152.3 bits; conditional E-value: 9.2e-49 436s HHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCHHH-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS 436s Aminotran_5 41 atkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137 436s ++ ee+r+ +a+l+na++++ i ft+ tte++nl+ +sl ++kpgd++v+ ++eh + w +l+ g++v+ +p + + + + ++++ +++ 436s CUFF.40.1.p1 59 WKERTEETRSLLAKLLNASTKDSITFTRDTTEGLNLFQRSL--KWKPGDNVVILDNEHPNQGFGWIALQ-NDGLEVRLVPNEGQYHANASTFAPYVD 152 436s 56789************************************..59***********************8.67************************* PP 436s 436s TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHHS.....SS.STTS CS 436s Aminotran_5 138 ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl...eplllggem 230 436s +tk++ ++ v +G ++v++i+++++ kg+ vl+D +q+vg +idv++l+v afs hK l PtG+Gvlyv++ ++ +l +p+ +gg+ 436s CUFF.40.1.p1 153 SRTKAIGLSSVMFHSGQKNDVKDIANAFRPKGIHVLADLTQQVGLSKIDVQDLNVSACAFSCHKgLGCPTGLGVLYVSPLAISELrstPPF-VGGGA 248 436s ****************************************************************8888*************9999774455.55555 PP 436s 436s EEEEET.....TEEEEHHTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTSSHH CS 436s Aminotran_5 231 veevsl.....eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhae 322 436s ve+ + +++++++ ++e+ + i +l+a l++l ++g++++e++ + l + l ++l+sl+ + g k+ ++s s ++k +++e 436s CUFF.40.1.p1 249 VEDFKEdlklkLNAKYHQSALRYEHTNNAYMLITALRAYLKFLLKVGISNVERYLQGLGKDLIKELESLNVSVI-G-YKDFDKHSSHSYVLKILNPE 343 436s 665554110044555999*******555578899***********************************98766.8.67899999999999999998 PP 436s 436s HHHHHHHHTTEEEEEE-TTTHHHHHHHT.S-EEEEE--TTS-HHHHH CS 436s Aminotran_5 323 dvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369 436s + +L+++g++v+ e+++R+S+++ynt++++ 436s CUFF.40.1.p1 344 WF-DFLRQQGVCVSR-------------FESGIRVSFGLYNTSKDII 376 436s 65.79******9974.............45999***********996 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (371 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1281.09 436s // 436s Query: Arginase [M=280] 436s Accession: PF00491.20 436s Description: Arginase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.9e-91 298.4 0.0 3.4e-91 298.2 0.0 1.0 1 CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 298.2 0.0 3.6e-93 3.4e-91 2 277 .. 75 373 .. 74 374 .] 0.93 436s 436s Alignments for each domain: 436s == domain 1 score: 298.2 bits; conditional E-value: 3.6e-93 436s EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE...SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEE......... CS 436s Arginase 2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv...leelkivdlgdvavtpvdneevleqieeavaeilkagklp......... 86 436s d+a+lG+Pfd+++s+rpGarfGP+ ire+s+rl+ + +yn+ ++ +++kivd+gd+++t +dn+ +++qie+ e+l+++ + 436s CUFF.38.1.p4 75 DIAFLGAPFDTGTSYRPGARFGPSGIREGSRRLNLYGGYNVPMETnpfNNWAKIVDCGDIPLTSYDNAVAIKQIENGHFELLTRKPTSysekdgyal 171 436s 89********************************8778888887788999******************9***************4444555555555 PP 436s 436s ........EEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSC......TTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH..HHHH CS 436s Arginase 87 ........ivlGGDHsialgilralaekygkplgvihfDAHaDlrtpe......tegsgnshGtpfrraaeegllkpkklvqiGirsvdne..eyel 167 436s i+lGGDH+i l+ilr+++++yg p+++ihfD+H+D ++p+ ++ +++hGt+f++a++egl+++++ +++Gir++ ++ +y+ 436s CUFF.38.1.p4 172 dgsvlprvITLGGDHTIVLPILRSVSRAYG-PVSIIHFDSHLDSWKPKvfgggkSSVGSINHGTYFYHASQEGLVSNDSNIHAGIRTTLSGlsDYDN 267 436s 55555666********************99.6****************99988877778********************************999999 PP 436s 436s HHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTT CS 436s Arginase 168 akelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteae 264 436s ++++g+++i++reid +g++a++++i++rvg ++ ylS+DiDvlDpa+aP+tGtpe G+t+rel+++lr+l + +lvgaD+vEv+Pa+d ae 436s CUFF.38.1.p4 268 DADCGFEIIEAREIDTIGIDAIIKRIRDRVG--DGIAYLSIDIDVLDPAYAPATGTPESAGWTTRELRTILRGLDG-IKLVGADIVEVAPAYDF-AE 360 436s 999***************************8..57***************************************99.*****************.67 PP 436s 436s HHHHHHHHHHHHH CS 436s Arginase 265 qtarlaarlvrel 277 436s t+++aa++++e+ 436s CUFF.38.1.p4 361 VTTLAAADILFEV 373 436s ***********95 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (280 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 3281.16 436s // 436s Query: Asparaginase [M=191] 436s Accession: PF00710.19 436s Description: Asparaginase, N-terminal 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.1e-54 176.5 0.6 2.9e-54 176.1 0.6 1.2 1 CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-11 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-1103(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 176.1 0.6 3.1e-56 2.9e-54 1 182 [. 47 233 .. 47 241 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 176.1 bits; conditional E-value: 3.1e-56 436s EEEEEEEESGGGBB-SSSS--SS-B...S-HHHHHTTSTTHHHHSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHH.HT.--EEEEE--STTHHHHH CS 436s Asparaginase 1 kvlvlatGGTiasekdesggalapa...lsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee.ydgfVvlhGTDTlaytA 92 436s +v v a+GGTia +++s + +++ + +e+l+ea+p+++ ia+++ q++n+ S+n+tpad+lkla+ i +++ + ++g+V++hGTD+l++tA 436s CUFF.15.1.p1 47 NVTVFAMGGTIAGCANSSLEIVNYIpgsVGIEKLIEAVPAIKAIANINGVQVTNMGSENLTPADVLKLAKLILAEVaKPnVHGIVITHGTDSLEETA 143 436s 599***************99999878899***********************************************7669***************** PP 436s 436s HHHHHH---.-S-EEEE--SS-TTSTT-SHHHHHHHHHHHHHSGG.TTS-SEEEETTEEEETTT-EE-BSSSSS-EE-TTT--SEEEETTE CS 436s Asparaginase 93 saLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasse.riagvlvvfngkllranrvtKvhtssldaFespnlgplaevegsk 182 436s ++L+l++ + +kp+v++G++rp++++++Dgp+Nll+A++va+s++ ++g lv +n+++ +a ++tK++ ++ld+F+s ++g+l+ v ++k 436s CUFF.15.1.p1 144 MFLDLTIST-AKPIVVVGAMRPSTAIGADGPMNLLNAVAVASSNQsMGRGTLVLLNDRIGSAFYTTKTNGNTLDTFKSYEAGSLGIVLNQK 233 436s *******99.***************************************************************************986655 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (191 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 436s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2744.56 436s // 436s Query: Asp_Glu_race [M=224] 436s Accession: PF01177.21 436s Description: Asp/Glu/Hydantoin racemase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.1e-06 19.8 0.0 5.8e-06 18.9 0.0 1.4 1 CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722- 436s 3.6e-06 19.6 0.0 6.9e-06 18.6 0.0 1.4 1 CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 18.9 0.0 1.2e-07 5.8e-06 49 98 .. 157 205 .. 141 211 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 18.9 bits; conditional E-value: 1.2e-07 436s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 436s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 436s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 436s CUFF.52.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 436s 34455667**********************99.****************7 PP 436s 436s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 18.6 0.0 1.4e-07 6.9e-06 49 98 .. 157 205 .. 141 212 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 18.6 bits; conditional E-value: 1.4e-07 436s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 436s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 436s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 436s CUFF.50.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 436s 34455667**********************99.****************7 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (224 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3322.13 436s // 436s Query: Beta_elim_lyase [M=293] 436s Accession: PF01212.20 436s Description: Beta-eliminating lyase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.2e-06 19.7 0.0 4.2e-06 18.8 0.0 1.4 1 CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 18.8 0.0 4.4e-08 4.2e-06 29 201 .. 619 786 .. 611 886 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 18.8 bits; conditional E-value: 4.4e-08 436s T--HHHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT........-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS 436s Beta_elim_lyase 29 gedktvnrLedavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep........ahihfdetgaiaelagvklrdlknkeaGkmdlek 113 436s g + +++L+ ++ ++g++aa f p +G a++ l+++ + ++ +++ ah+ ++ a a++ag +++++k ++G++d+++ 436s CUFF.57.1.p1 619 GYRHVIEDLQLMLTTITGFDAACFQPnSGAAGEYTGLSVIRAYQRSIGQGHRniclipvsAHG---TNPASAAMAGFTVIPVKCLNNGYLDMQD 709 436s 555667788999999*********9956*******9977765555555555445444344443...55677889*********9999******* PP 436s 436s HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH...HHHTS-CHHHHTTSSEEEEESSSTT- CS 436s Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa...kslgeivkemfsyvDsvtmslkKdll 201 436s l+++ + h++k ++ ++t G ++e+ ++ +++g ++ +DgA +na+ ++ ++ ++D++ + l K + 436s CUFF.57.1.p1 710 LKEKASK---HADKLAAFMVTYPSTF--GI--FEPDVKEALEVIHEHGGQVYFDGAN-MNAMvglC----KAGDI--GADVCHLNLHKTFC 786 436s ***9999...8889999999888887..54..44579*******************5.45552332....33333..23444444444444 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (293 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2384.42 436s // 436s Query: Chitin_synth_1 [M=163] 436s Accession: PF01644.16 436s Description: Chitin synthase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.9e-83 270.9 0.2 3.3e-83 270.1 0.2 1.4 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 1.9e-83 270.9 0.2 3.3e-83 270.1 0.2 1.4 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 436s 436s Alignments for each domain: 436s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 436s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 436s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 436s CUFF.60.1.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 436s 9********************************************************************************************** PP 436s 436s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 436s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 436s CUFF.60.1.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 436s ******************************************************************98 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 436s 436s Alignments for each domain: 436s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 436s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 436s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 436s CUFF.60.2.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 436s 9********************************************************************************************** PP 436s 436s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 436s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 436s CUFF.60.2.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 436s ******************************************************************98 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (163 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1799.94 436s // 436s Query: Chitin_synth_1N [M=73] 436s Accession: PF08407.10 436s Description: Chitin synthase N-terminal 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5e-29 92.8 0.1 1.2e-28 91.6 0.1 1.7 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 5e-29 92.8 0.1 1.2e-28 91.6 0.1 1.7 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 436s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 436s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 436s CUFF.60.1.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 436s 89***********************65..9******************************8779*********9 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 436s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 436s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 436s CUFF.60.2.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 436s 89***********************65..9******************************8779*********9 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (73 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1597.50 436s // 436s Query: Chitin_synth_2 [M=527] 436s Accession: PF03142.14 436s Description: Chitin synthase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.3e-24 77.5 9.9 2.7e-21 68.3 0.0 2.7 4 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 4.3e-24 77.5 9.9 2.7e-21 68.3 0.0 2.7 4 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 436s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 436s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 436s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: -3.5 bits; conditional E-value: 0.33 436s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 436s + + +t y ede + +t+ s+ 436s CUFF.60.1.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 436s 3446999*****99999999986 PP 436s 436s == domain 2 score: -3.2 bits; conditional E-value: 0.27 436s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 436s G tki ++ ++++ai v++ i+++++ 436s CUFF.60.1.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 436s 38899999999999999999988887776 PP 436s 436s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 436s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 436s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 436s CUFF.60.1.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 436s 8899********************************9876543244222225789************************************9886 PP 436s 436s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 436s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 436s CUFF.60.1.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 436s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 436s 436s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 436s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 436s CUFF.60.1.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 436s 4445556778888887776522256665111344556666666666655555555 PP 436s 436s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 436s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 436s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 436s CUFF.60.1.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 436s 34558999*************************************************6 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 436s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 436s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 436s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: -3.5 bits; conditional E-value: 0.33 436s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 436s + + +t y ede + +t+ s+ 436s CUFF.60.2.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 436s 3446999*****99999999986 PP 436s 436s == domain 2 score: -3.2 bits; conditional E-value: 0.27 436s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 436s G tki ++ ++++ai v++ i+++++ 436s CUFF.60.2.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 436s 38899999999999999999988887776 PP 436s 436s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 436s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 436s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 436s CUFF.60.2.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 436s 8899********************************9876543244222225789************************************9886 PP 436s 436s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 436s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 436s CUFF.60.2.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 436s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 436s 436s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 436s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 436s CUFF.60.2.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 436s 4445556778888887776522256665111344556666666666655555555 PP 436s 436s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 436s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 436s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 436s CUFF.60.2.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 436s 34558999*************************************************6 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (527 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 436s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 1418.96 436s // 436s Query: CO_dh [M=168] 436s Accession: PF02552.15 436s Description: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.4e-07 22.4 0.0 2.4e-06 20.0 0.0 2.1 2 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.3 0.0 0.091 8.6 18 41 .. 130 154 .. 125 156 .. 0.80 436s 2 ! 20.0 0.0 2.5e-08 2.4e-06 14 78 .. 194 257 .. 175 297 .. 0.74 436s 436s Alignments for each domain: 436s == domain 1 score: -1.3 bits; conditional E-value: 0.091 436s --EEE--SHHHHHHHHHS.SSEEEE CS 436s CO_dh 18 katleealkvvakmikka.krPlli 41 436s + ++ ++l+ +a +ik+a + P++i 436s CUFF.32.1.p1 130 QMEIAKKLTCAAVAIKRAeDAPVMI 154 436s 6788899999*******93468877 PP 436s 436s == domain 2 score: 20.0 bits; conditional E-value: 2.5e-08 436s XXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G. CS 436s CO_dh 14 anskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkd 78 436s s k +le+a +a++i+k ++P+l+ Gp+++ a e a++k + + + + +g + 436s CUFF.32.1.p1 194 EISDKESLEKATDIAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMP-AAKGFYS 257 436s 455677899999*******************************99887776654444.3555554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (168 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2717.97 436s // 436s Query: CRCB [M=95] 436s Accession: PF02537.14 436s Description: CrcB-like protein, Camphor Resistance (CrcB) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.2e-32 104.7 23.7 4.8e-18 58.0 3.7 2.5 3 CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 56.7 7.3 1.2e-19 1.2e-17 3 92 .. 8 118 .. 6 123 .. 0.83 436s 2 ? -2.4 0.1 0.33 32 44 56 .. 166 180 .. 143 183 .. 0.58 436s 3 ! 58.0 3.7 5e-20 4.8e-18 3 93 .. 190 296 .. 188 299 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: 56.7 bits; conditional E-value: 1.2e-19 436s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHH.. CS 436s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkal.. 77 436s +++++lG+l+R++l ++ln+ + g l+v ++G++++g++ + ++ttGf+G+lTTfS+++l++++ +++ + ++ + 436s CUFF.14.1.p1 8 FCIMSMLGTLARLGL-TALNTYpgapFSGLLWVQFVGCVIMGFCQTesvffprpkhnatfllAITTGFCGSLTTFSSWMLQMFTGMANLDPFERRgr 103 436s 6899***********.7677777997569**************99988887777777777666*********************8877665555566 PP 436s 436s HHHHHHHHHHHHHHH CS 436s CRCB 78 lyvllsvvlgllavv 92 436s y +lsvv +++++ 436s CUFF.14.1.p1 104 GYSFLSVVSDFMVTM 118 436s 999999998887665 PP 436s 436s == domain 2 score: -2.4 bits; conditional E-value: 0.33 436s H..HHTTTHHHHH-- CS 436s CRCB 44 a..llttGflGglTT 56 436s +++ f ++TT 436s CUFF.14.1.p1 166 IcfFVGAAFYTAYTT 180 436s 122455555555555 PP 436s 436s == domain 3 score: 58.0 bits; conditional E-value: 5e-20 436s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHHHH CS 436s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkally 79 436s ++++++ al+R++l++ ln+ p+gtl++Nv++++ll ++++ +++Gf+ l+T Stf++el+++ + +a +y 436s CUFF.14.1.p1 190 SLIFSPFAALTRLYLARFLNSPqyfiPYGTLCANVFATLLLSIMYMipqithctpvsrsvmyGIQNGFCAVLSTLSTFSNELHTMP----IKRAYIY 282 436s 689************9988888***999***************99977766666655555555*********************96....4458999 PP 436s 436s HHHHHHHHHHHHHH CS 436s CRCB 80 vllsvvlgllavvl 93 436s +++sv++++ ++v+ 436s CUFF.14.1.p1 283 CIISVAISFSICVI 296 436s 9****999987765 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (95 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2276.08 436s // 436s Query: CTP_transf_like [M=143] 436s Accession: PF01467.25 436s Description: Cytidylyltransferase-like 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00037 13.3 0.0 0.00069 12.4 0.0 1.4 1 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.4 0.0 7.3e-06 0.00069 9 43 .. 33 66 .. 29 73 .. 0.88 436s 436s Alignments for each domain: 436s == domain 1 score: 12.4 bits; conditional E-value: 7.3e-06 436s --HHHHHHHHHHHHHSSESEEEEEESSTHCCST-S CS 436s CTP_transf_like 9 iHlGHlrlleqakklleedlivgvpsdeppkkkkk 43 436s +H GH l+++ak++ e+ ++v + ++ ++ + 436s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAEK-VVVSIFVNPMQFNNPQ 66 436s 7*****************.9999999988887754 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (143 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4527.61 436s // 436s Query: Dak1 [M=307] 436s Accession: PF02733.16 436s Description: Dak1 domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.1e-110 360.0 0.4 6.1e-110 359.4 0.4 1.3 1 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ 436s 1.4e-52 171.0 1.0 1.7e-52 170.8 1.0 1.1 1 CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 359.4 0.4 1.3e-111 6.1e-110 2 304 .. 75 396 .. 74 399 .. 0.92 436s 436s Alignments for each domain: 436s == domain 1 score: 359.4 bits; conditional E-value: 1.3e-111 436s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 436s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 436s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 436s CUFF.19.1.p1 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 436s 899*****************94444666779****************************************************************** PP 436s 436s HHHHHHHHHHHHTT--EEEEEE--B-SSS.SSTTCSSSB--THHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTEEEEEEEEE--B-TTTSSBSS-- CS 436s Dak1 95 lnfglAaekakaegikvetvvvdDDvave.dseekagrRGvagtvlveKiaGaaaeegasLeevaelaekvnenlrsigvalsactvpgagkpsfel 190 436s ++fglAae+aka g++ve v v+DDv+v+ +++ +grRG+++tvlv+KiaG aa+ g +L++va++a++v++n ++i+++l++c vpg++ +++ l 436s CUFF.19.1.p1 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGkKRGALVGRRGLGATVLVHKIAGSAAALGLDLHQVAQVAQSVIDNAATIAASLDHCAVPGRKFETN-L 267 436s ****************************9799999********************************************************8886.* PP 436s 436s -TTEEEETE-TTS---SEEEE.---HHHHHHHHHHHHHH............TT-EEEEEEEE-BSS-HHHHHHHHHHHHHHHHHTT-EEEEEEEESS CS 436s Dak1 191 eedemelGvGiHgEpGverek.lksadelveelleklled...........kgdevvllvnglGgtsllelyivarevaelleekgikvvrvlvGey 275 436s ++de+e+G+GiH+EpG+ +++ l s+ elv+e+l+ l+ + ++d+v+llvn++Gg+s+lel ++ v e+l+++gi ++r+++G++ 436s CUFF.19.1.p1 268 GPDEYEIGMGIHNEPGTFKSSpLPSIPELVTEMLSILFGEknpdnsfvefsSKDDVILLVNNMGGMSNLELGYATEVVSEQLAKRGIIPKRTMSGTF 364 436s ****************977651566789**********64356666666655********************************************* PP 436s 436s S--TTBEEEEEEEEEE-...HHHHHHHHS-EE CS 436s Dak1 276 vTsldmaGfsitllkld...dellelldapve 304 436s vT+l+++Gf itl++++ ++ +++d p++ 436s CUFF.19.1.p1 365 VTALNGPGFGITLVNASkatPDIFKYFDLPTT 396 436s ***************98444566667776665 PP 436s 436s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 170.8 1.0 3.5e-54 1.7e-52 2 125 .. 75 202 .. 74 204 .] 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: 170.8 bits; conditional E-value: 3.5e-54 436s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 436s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 436s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 436s CUFF.20.1.p2 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 436s 899*****************94444666779****************************************************************** PP 436s 436s HHHHHHHHHHHHTT--EEEEEE--B-SSSSS CS 436s Dak1 95 lnfglAaekakaegikvetvvvdDDvaveds 125 436s ++fglAae+aka g++ve v v+DDv+v+++ 436s CUFF.20.1.p2 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGKK 202 436s ****************************876 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (307 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1875.93 436s // 436s Query: Dak2 [M=174] 436s Accession: PF02734.16 436s Description: DAK2 domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.9e-45 146.9 3.1 4.9e-45 146.1 2.0 2.0 2 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -2.4 0.0 0.22 21 70 88 .. 437 455 .. 422 460 .. 0.64 436s 2 ! 146.1 2.0 5.2e-47 4.9e-45 2 173 .. 467 642 .. 466 643 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: -2.4 bits; conditional E-value: 0.22 436s TT---HHHHHHHHHHHHHH CS 436s Dak2 70 ldaedlaaalkaaleaiqa 88 436s +d + + ++lkaa++ai++ 436s CUFF.19.1.p1 437 ADPKMFTKILKAAVDAINE 455 436s 5666677777777777765 PP 436s 436s == domain 2 score: 146.1 bits; conditional E-value: 5.2e-47 436s TS-S-HHHHHHHHHHHHHHHHHC-..--SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.......TT---HHHHHHHHHHHHHHHH---T CS 436s Dak2 2 vGDGDtGtnmargaeavlkaleel..eeaslaevlkalakallsgagGtsGvlysqflralakalke..keeldaedlaaalkaaleaiqavgkarp 94 436s +GDGD+Gt++ +g ea++ka++++ + ++ + +++la ++++++gGtsG lys++l+alak ++e +el++ ++a a k al+a+ ++++ar+ 436s CUFF.19.1.p1 467 AGDGDCGTTLVNGGEAITKAINDKsiRLDDGVNGIDDLAYIVEDSMGGTSGGLYSIYLSALAKGVHEsgDSELSVHTFAFASKYALDALFKYTRARK 563 436s 8***********************9****************************************8865777************************* PP 436s 436s TSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSGGGGGGGGGTT.......S--HHHHHHHHHHHHHH CS 436s Dak2 95 gdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgrAsylgerslg.......vvDpGAvglalileala 173 436s g +T++D+++p+ve+l++ k l++aakaa++g e+T+++ a++grAsy+++++l+ +DpGA +la+il+a++ 436s CUFF.19.1.p1 564 GFRTLIDAIQPFVETLNEGKG-------LDAAAKAATEGSEQTRKMDAVVGRASYVAKEELHkldseggLPDPGAFALAAILNAIV 642 436s ******************999.......*******************************9966999999**************997 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (174 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2843.23 436s // 436s Query: DJ-1_PfpI [M=165] 436s Accession: PF01965.23 436s Description: DJ-1/PfpI family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 8.2e-16 50.8 0.0 3e-15 49.0 0.0 1.9 1 CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028( 436s 3e-15 49.0 0.0 4.5e-15 48.4 0.0 1.2 1 CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 436s 3.7e-10 32.4 0.0 6.7e-10 31.6 0.0 1.5 1 CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 49.0 0.0 9.5e-17 3e-15 12 125 .. 30 168 .. 26 239 .. 0.74 436s 436s Alignments for each domain: 436s == domain 1 score: 49.0 bits; conditional E-value: 9.5e-17 436s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 436s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 436s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 436s CUFF.46.1.p1 30 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 126 436s 5579**************************955554433134444444444444666666667777******************************* PP 436s 436s HHHHHHTT-EEEEETTTHHHHHHTT...TTTTSEE--SGGGH CS 436s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag...vlkgrrvTsypavk 125 436s ++e++++g+++ a+C+gp+lLa+ + ++g++v ++ v+ 436s CUFF.46.1.p1 127 AREVFTNGGVLSAVCHGPVLLANVKnpqSVEGKTVVYHKHVT 168 436s **********************87512245555554444443 PP 436s 436s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 48.4 0.0 1.4e-16 4.5e-15 12 111 .. 51 172 .. 47 198 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 48.4 bits; conditional E-value: 1.4e-16 436s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 436s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 436s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 436s CUFF.47.1.p1 51 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 147 436s 5579**************************955554433134444444444444666666667777******************************* PP 436s 436s HHHHHHTT-EEEEETTTHHHHHHTT CS 436s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag 111 436s ++e++++g+++ a+C+gp+lLa+ + 436s CUFF.47.1.p1 148 AREVFTNGGVLSAVCHGPVLLANVK 172 436s *********************9865 PP 436s 436s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 31.6 0.0 2.1e-11 6.7e-10 52 161 .. 75 215 .. 15 219 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 31.6 bits; conditional E-value: 2.1e-11 436s EEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH......HHTTTTTTSEE--SGGGH.HHH............. CS 436s DJ-1_PfpI 52 aslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL......aaagvlkgrrvTsypavk.dkl............. 128 436s + +d++ ++y + GG+ ++ + + + + + ++ g+++aa+C+gp++L +++kg++vT++ + +++ 436s CUFF.42.1.p2 75 KNASDINFSDYSIFFAAGGHGTLFDFPSATNLHKGAAKIYSMGGVIAAVCHGPVILpcikdsTGFSIVKGKTVTAFNEIAeQQMnlmptfekyhfkt 171 436s 445699***************9999999999999999****************99955332223469***********995556999*9*9999999 PP 436s 436s .....HHTTSEE-SS......SEEEETTEEEESSGGGHHHHHHH CS 436s DJ-1_PfpI 129 .....ekagakyvdk......rvvvdgnlvTsrgpgaaiefale 161 436s ++ag+++vd v +dg+lvT ++p +a a++ 436s CUFF.42.1.p2 172 lnklfQEAGSNFVDPqepfddFVKTDGKLVTGANPASAASTAKA 215 436s 9999999999999999***977889*********9998776665 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (165 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 3 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 620.79 436s // 436s Query: DLH [M=217] 436s Accession: PF01738.17 436s Description: Dienelactone hydrolase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.1e-11 35.4 0.0 4.8e-11 35.2 0.0 1.1 1 CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-77 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-771(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 35.2 0.0 5e-13 4.8e-11 3 215 .. 41 254 .. 39 256 .. 0.72 436s 436s Alignments for each domain: 436s == domain 1 score: 35.2 bits; conditional E-value: 5e-13 436s DLH 3 aylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa........ldpndeaeaaraldelvskvaeekvlddlkaavaylks 91 436s +y ++ ++ k v + + ++fG+ ++ik+ +++la+ + +Pd++ ++ + + e+++a ++ ++k ++ +l ++ ++ 436s CUFF.18.1.p1 41 TYFTGKRSS-KVVLIGFMDVFGLSKQIKEGADQLANHELAIYLPDFLNGETasiemidpK----TIEQKEARSKFMEKISSPLHWPKLTKVIEDIER 132 436s 555566666.4455559**********************************898863332....333344444555555555566677777888888 PP 436s 436s DLH 92 vpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188 436s ++ k+g+ GfC+G+++ + + ++ ++ + ++ s+ ++ +a+++ +p+ +l + + + d+ +k e+ + + ++ + H+ 436s CUFF.18.1.p1 133 IH-GQDVKIGAYGFCWGAKVLITYPNKE-RFLRIGCAHP-SLLDPV-DAKHVHCPVCFLCSKDEDPEEVDAWKKSFENS-PYFSESYFETFGKMHHG 224 436s 88.44589****************9999.5667777899.555555.578999***99998766665555544433333.46677778888888888 PP 436s 436s DLH 189 Fandsre...syneeaaedawervlelfkq 215 436s ++++++ +n + +++ +l++fk+ 436s CUFF.18.1.p1 225 WMAARANlsdPENRKYFDLGYQIFLKFFKE 254 436s 888888766677777777778888888776 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (217 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 4078.53 436s // 436s Query: DsrD [M=64] 436s Accession: PF08679.10 436s Description: Dissimilatory sulfite reductase D (DsrD) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.0008 12.3 0.0 0.0023 10.9 0.0 1.8 2 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -4.1 0.0 1 95 21 33 .. 102 114 .. 97 116 .. 0.82 436s 2 ! 10.9 0.0 2.4e-05 0.0023 2 58 .. 132 188 .. 131 192 .. 0.80 436s 436s Alignments for each domain: 436s == domain 1 score: -4.1 bits; conditional E-value: 1 436s HHHHHH-TTS-HH CS 436s DsrD 21 kDlekalPdakpr 33 436s kDl k++ d ++r 436s CUFF.17.1.p1 102 KDLIKIFGDLSSR 114 436s 7999999888877 PP 436s 436s == domain 2 score: 10.9 bits; conditional E-value: 2.4e-05 436s HHHHHHHHSSCCCSS-EEHH..HHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETTEEE CS 436s DsrD 2 kkaiveflekkkkKskfYfk..DlekalPdakpreiKkvvneLVnegkLeywSsGSTtm 58 436s +k+i + +e + k+ Y+ +++ +P +++ e+ +++n+ V+ gk+ y G +tm 436s CUFF.17.1.p1 132 RKHIFDAVEDSVKRLGTYIDvlQIHRYDPHVSAEEVMRALNDVVESGKVRYI--GASTM 188 436s 578899999999877788762245567***********************95..66666 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (64 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2400.46 436s // 436s Query: DUF1129 [M=206] 436s Accession: PF06570.10 436s Description: Protein of unknown function (DUF1129) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.0012 10.9 1.9 0.0033 9.5 0.7 2.2 2 CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 9.5 0.7 3.4e-05 0.0033 88 189 .. 128 229 .. 124 236 .. 0.73 436s 2 ? -1.5 0.0 0.083 7.9 119 133 .. 451 465 .. 423 478 .. 0.59 436s 436s Alignments for each domain: 436s == domain 1 score: 9.5 bits; conditional E-value: 3.4e-05 436s DUF1129 88 llalfallfgilalfskkkqtasiGlitl.llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvl 183 436s +la++++ ++ lfs ++++ Gli+ l+++l+ G+++ ++ +lt + +k++ + + +l+++++l ++ lf+ + + N ++++ 436s CUFF.45.1.p2 128 MLAFISFAWSMTVLFSG-FMSSYGGLIATrLILGLLEGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEQVHAGNKEGWQWIY 223 436s 67778888889999998.777787988543899****************997788877777777777777777666665544444555555555555 PP 436s 436s DUF1129 184 iiigvi 189 436s i+ g + 436s CUFF.45.1.p2 224 IVEGLV 229 436s 555555 PP 436s 436s == domain 2 score: -1.5 bits; conditional E-value: 0.083 436s DUF1129 119 valvgGlamvlvyrl 133 436s + +vgGla+v++ 436s CUFF.45.1.p2 451 CVIVGGLAYVVMFFS 465 436s 345555555554332 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (206 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3399.02 436s // 436s Query: DUF1989 [M=167] 436s Accession: PF09347.9 436s Description: Domain of unknown function (DUF1989) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.5e-57 186.4 0.0 2e-57 186.1 0.0 1.1 1 CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 186.1 0.0 2.1e-59 2e-57 2 167 .] 58 231 .. 57 231 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 186.1 bits; conditional E-value: 2.1e-59 436s DUF1989 2 tiparsgravevkaGqvlriidleGnqvvdllafnaddprerlsaadTrklqesahlttgdrlysnl..grplltiveDtv.........gvHDtlg 87 436s ++++r+g av++++ +++ i+ +eG+qv+dl+++n ++prer++aa+Tr+++ sah++t+drl+s+l rpl+ti+ D++ +vHDtlg 436s CUFF.34.1.p1 58 VCQPRTGLAVKIPQKSIFSIVVPEGPQVCDLNIWNFHNPRERFWAARTRQIH-SAHVSTYDRLWSTLpyLRPLVTIIGDSLqarhdewggRVHDTLG 153 436s 6899************************************************.************************************99****** PP 436s 436s DUF1989 88 gacdpevnellygegkeyhrnCrdnllralakyglterdvpdvlNlFmnvgvdedgrlfmeespskpGdyvelraemDll 167 436s ++cdp++ +l + gk+++ +C++nl+ra+ yglte+dv+dvlN+F+++g++e +++fme++p++ dy++++ae+Dll 436s CUFF.34.1.p1 154 TRCDPYIDKLIS--GKDNDLHCHSNLTRAIMPYGLTEFDVHDVLNVFQVTGLNEYDQYFMETCPATSKDYFQCFAEQDLL 231 436s *********999..678*************99**********************************************97 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (167 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4103.22 436s // 436s Query: DUF2157 [M=147] 436s Accession: PF09925.8 436s Description: Predicted membrane protein (DUF2157) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s ------ inclusion threshold ------ 436s 0.023 7.1 8.8 0.0029 10.0 3.5 2.1 2 CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -0.5 0.2 0.055 5.2 109 109 .. 75 75 .. 10 128 .. 0.54 436s 2 ? 10.0 3.5 3.1e-05 0.0029 34 120 .. 156 243 .. 142 265 .. 0.89 436s 436s Alignments for each domain: 436s == domain 1 score: -0.5 bits; conditional E-value: 0.055 436s DUF2157 109 a 109 436s + 436s CUFF.14.1.p1 75 C 75 436s 1 PP 436s 436s == domain 2 score: 10.0 bits; conditional E-value: 3.1e-05 436s DUF2157 34 fleallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifqls 120 436s +++ll+l ++++ +G + A+ + +r + f l+++++++ l a++++ ++ + g + + + a+ll+ + ++ qi + + 436s CUFF.14.1.p1 156 VVRVLLLLLSICFFVGAAFYTAYTTNVTHRGIGFSLIFSPFAALTRLYlARFLNSPQYFIPYGTLCANVFATLLLSIMYMIPQITHCT 243 436s 489999999***********************************99999***99999999999999999999********99997766 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (147 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1651.18 436s // 436s Query: DUF2868 [M=328] 436s Accession: PF11067.7 436s Description: Protein of unknown function (DUF2868) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00065 11.7 0.3 0.001 11.1 0.3 1.2 1 CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.1 0.3 1.1e-05 0.001 47 74 .. 97 123 .. 92 126 .. 0.94 436s 436s Alignments for each domain: 436s == domain 1 score: 11.1 bits; conditional E-value: 1.1e-05 436s DUF2868 47 fllGalltlllllatrdlaFgWetTLnl 74 436s +llGa++ l + ++r+l++gW+ TL l 436s CUFF.9.1.p1 97 LLLGAIFPLFAESLFRRLNYGWGCTL-L 123 436s 689***********************.6 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (328 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3906.24 436s // 436s Query: DUF2976 [M=88] 436s Accession: PF11190.7 436s Description: Protein of unknown function (DUF2976) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00011 14.6 4.9 0.00058 12.3 0.1 3.5 3 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.3 0.1 6.1e-06 0.00058 28 76 .. 120 168 .. 107 177 .. 0.90 436s 2 ! 2.3 0.1 0.0082 0.78 39 77 .. 307 348 .. 282 351 .. 0.68 436s 3 ? -1.6 0.1 0.13 13 58 75 .. 404 421 .. 371 425 .. 0.73 436s 436s Alignments for each domain: 436s == domain 1 score: 12.3 bits; conditional E-value: 6.1e-06 436s DUF2976 28 villgLvlaavaflaVakaalkkfnevregkaewgkfgltlvvGvvllv 76 436s ++ L +a++ + V+k +l kf+++ + +++ + l+ v+G++++ 436s CUFF.25.1.p1 120 SMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIGFIVVA 168 436s 678889999*************************************996 PP 436s 436s == domain 2 score: 2.3 bits; conditional E-value: 0.0082 436s DUF2976 39 aflaVaka.alkkfnevregkaewg..kfgltlvvGvvllvv 77 436s +l V ++ +l f+ + k+ w ++++++vvG v+l++ 436s CUFF.25.1.p1 307 ILLGVGWSiLLLPFSLTSYAKNGWKnpSMIAMMVVGGVILIA 348 436s 445555441345677777778888733588888999988876 PP 436s 436s == domain 3 score: -1.6 bits; conditional E-value: 0.13 436s DUF2976 58 kaewgkfgltlvvGvvll 75 436s +w+ f t+ ++ ++ 436s CUFF.25.1.p1 404 YRDWTYFNNTMTIALCVF 421 436s 567888888888888775 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (88 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1906.17 436s // 436s Query: DUF2997 [M=47] 436s Accession: PF11211.7 436s Description: Protein of unknown function (DUF2997) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00049 12.5 0.0 0.0011 11.5 0.0 1.5 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.5 0.0 1.1e-05 0.0011 10 25 .. 83 98 .. 83 103 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 11.5 bits; conditional E-value: 1.1e-05 436s DUF2997 10 rVeeeveGikGksCle 25 436s +V+ +ve+i+GksCl+ 436s CUFF.54.1.p1 83 KVKLRVEDIQGKSCLT 98 436s 79************96 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (47 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2042.19 436s // 436s Query: DUF3288 [M=89] 436s Accession: PF11691.7 436s Description: Protein of unknown function (DUF3288) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 8.3e-05 15.3 0.0 0.00013 14.6 0.0 1.2 1 CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 14.6 0.0 1.4e-06 0.00013 17 62 .. 72 117 .. 68 119 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 14.6 bits; conditional E-value: 1.4e-06 436s DUF3288 17 LlaeepedenlaelArLliRYegFpGardiqkdldkvlkkWqltee 62 436s L++++++ +l e++r l+R +F G +++++ l+ l +W+++++ 436s CUFF.32.1.p3 72 LIEGSANLLSLEEISRTLLRILDFVGNKNMRTYLEVPLCRWHISQA 117 436s 55667777899********************************986 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (89 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3941.17 436s // 436s Query: DUF4208 [M=96] 436s Accession: PF13907.5 436s Description: Domain of unknown function (DUF4208) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00081 12.5 0.4 0.0012 11.9 0.4 1.2 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 436s 0.00081 12.5 0.4 0.0012 11.9 0.4 1.2 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 436s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 436s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 436s CUFF.48.1.p3 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 436s 5567899**************99877***********999855576 PP 436s 436s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 436s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 436s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 436s CUFF.49.1.p2 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 436s 5567899**************99877***********999855576 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (96 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2842.31 436s // 436s Query: DUF705 [M=304] 436s Accession: PF05152.11 436s Description: Protein of unknown function (DUF705) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00044 12.4 0.0 0.00076 11.6 0.0 1.4 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.6 0.0 8e-06 0.00076 225 270 .. 70 116 .. 58 152 .. 0.73 436s 436s Alignments for each domain: 436s == domain 1 score: 11.6 bits; conditional E-value: 8e-06 436s DUF705 225 vlditnskrl..PksvkvvlkyLsdknleffksitLvDDladnninYD 270 436s + + n+++l Pks ++v+ sd n+ f+s L DD ++n i+Y 436s CUFF.52.1.p2 70 YTATVNHEDLnePKSHEIVMLLASDGNVGSFESN-LLDDCFKNRIEYA 116 436s 555566665333********************95.78*******9874 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (304 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 5114.48 436s // 436s Query: DUF999 [M=143] 436s Accession: PF06198.10 436s Description: Protein of unknown function (DUF999) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2e-94 305.8 5.8 2.4e-94 305.5 5.8 1.0 1 CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 436s 9.5e-91 293.9 4.2 1.5e-90 293.2 4.2 1.3 1 CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 305.5 5.8 5e-96 2.4e-94 1 143 [] 21 163 .. 21 163 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 305.5 bits; conditional E-value: 5e-96 436s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 436s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyypdgristrs++rw+lliiwsiiiv 436s CUFF.5.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPDGRISTRSNFRWPLLIIWSIIIV 118 436s 9************************************************************************************************* PP 436s 436s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 436s +a+dkkfev++flsiwinenrfyseiw+piaiyvcllvl+ll+li 436s CUFF.5.1.p1 119 FAVDKKFEVQKFLSIWINENRFYSEIWVPIAIYVCLLVLMLLSLI 163 436s ******************************************996 PP 436s 436s >> CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 293.2 4.2 3.2e-92 1.5e-90 1 143 [] 21 163 .. 21 163 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 293.2 bits; conditional E-value: 3.2e-92 436s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 436s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyyp+grist++k+rwvlliiwsii++ 436s CUFF.3.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPNGRISTQDKSRWVLLIIWSIITI 118 436s 9************************************************************************************************* PP 436s 436s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 436s l+idkkf++ke++++wi+en+++seiwgpi+iyv+l++lll+a++ 436s CUFF.3.1.p1 119 LTIDKKFKIKESYLEWIGENQSHSEIWGPIVIYVGLFILLLSAFN 163 436s ******************************************985 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (143 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2902.12 436s // 436s Query: FAD_syn [M=158] 436s Accession: PF06574.11 436s Description: FAD synthetase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00019 14.0 0.0 0.00065 12.2 0.0 1.8 2 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.2 0.0 6.8e-06 0.00065 18 82 .. 33 92 .. 22 109 .. 0.84 436s 2 ? -1.4 0.0 0.1 9.9 112 145 .. 141 174 .. 125 188 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 12.2 bits; conditional E-value: 6.8e-06 436s FAD_syn 18 vHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlv 82 436s +H GH +l+++a+++a+ ++vv +F + P+++ ++++ t+++ ++l++lgvd v+ 436s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAE----KVVVSIFVN-PMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYA 92 436s 7*******999998884....577888865.99999988888888899999**********9986 PP 436s 436s == domain 2 score: -1.4 bits; conditional E-value: 0.1 436s FAD_syn 112 vvGfdfrfGkkregdvellkelgaklgfevevvp 145 436s v + +fG+k +v+ +k++ + l+f +e+++ 436s CUFF.50.1.p2 141 VNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQ 174 436s 5555568999999999999999999997776654 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (158 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3093.07 436s // 436s Query: Fe-ADH [M=364] 436s Accession: PF00465.18 436s Description: Iron-containing alcohol dehydrogenase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.6e-127 415.8 1.9 7.6e-127 415.6 1.9 1.0 1 CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 415.6 1.9 8e-129 7.6e-127 1 364 [] 52 414 .. 52 414 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 415.6 bits; conditional E-value: 8e-129 436s -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHH CS 436s Fe-ADH 1 PtrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtA 97 436s P+ +fgkg+l+e ++ +k g+k+ livtd+g++ k gl+dkv++ lee+ i+v+++dgv+pnpt+ +v+++++++++e++d +++GGGs++D+A 436s CUFF.50.1.p1 52 PSFNLFGKGCLAEAAKQIKMSGFKNTLIVTDPGII-KVGLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCA 147 436s 56678****************************99.************************************************************* PP 436s 436s HHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHH CS 436s Fe-ADH 98 Kaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahal 193 436s K+iall++n++ ++dy+g++k+ k++lpliai TtaGt+se+t++a+it e ++ k++i d++++P l++ Dpe +++lP+++taatg+Dal+ha+ 436s CUFF.50.1.p1 148 KGIALLATNGGkIADYEGVDKS-SKPQLPLIAINTTAGTASEMTRFAIITEETRHIKMAIIDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAV 243 436s *********956*****99987.8999***********************99999****************************************** PP 436s 436s HHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH........ CS 436s Fe-ADH 194 EayvskkanplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaa. 289 436s Eayvs+ anp++da+a ++i+l+ k+l+rav++g+d ear +m++a +l+g+af+na+lg vHa+ah+lg+++giphg++na+ll++v +fn ++ 436s CUFF.50.1.p1 244 EAYVSTAANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFYGIPHGVCNAVLLAHVQKFNSRDPr 340 436s ***********************************************************************99********************5554 PP 436s 436s ....HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHHH CS 436s Fe-ADH 290 p.erlaqlaralggesdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkdrslannpreltaedv 364 436s + +rl ++a lg +e ae++++++ +l+ e+++ +L +lgv+e+d+d l+++a+kd + a+np ++t+++v 436s CUFF.50.1.p1 341 AnARLGDIAFHLGC--EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKDFDVLVDHAMKDACGATNPIQPTHDEV 414 436s 44888888888864..699*****************************************************9986 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (364 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2665.13 436s // 436s Query: Fe-ADH_2 [M=250] 436s Accession: PF13685.5 436s Description: Iron-containing alcohol dehydrogenase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 7.2e-23 74.1 4.0 2.3e-20 65.9 2.6 2.4 2 CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 65.9 2.6 2.4e-22 2.3e-20 2 245 .. 57 320 .. 56 323 .. 0.89 436s 2 ? -3.6 0.0 0.4 38 27 60 .. 355 388 .. 350 399 .. 0.70 436s 436s Alignments for each domain: 436s == domain 1 score: 65.9 bits; conditional E-value: 2.4e-22 436s Fe-ADH_2 2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvs.. 95 436s +g+g l + ++ +k ++k+ l+v+d ++ k+ + +kv+ l+e+ i+v++++ v++++++ +v++ +e ++++++d +v++GgG+++D ak ++ 436s CUFF.50.1.p1 57 FGKGCLAEAAKQIKMSGFKNTLIVTDPGIIKVgLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCAKGIAll 153 436s 57899999********************9999899*********************************************************98622 PP 436s 436s Fe-ADH_2 96 ................aklnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkl 173 436s +k ++p++++ T+a + +a ++++ + k + k ++P+ + D + + P +l+a+ D+l + + + + 436s CUFF.50.1.p1 154 atnggkiadyegvdksSKPQLPLIAINTTAGTASEMTRFAIITEEtrHIKMAIiDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAVEAYVSTA 250 436s 222222222222222256689*********9999999999999887788888888999*************************************** PP 436s 436s Fe-ADH_2 174 anevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalH 245 436s an +++ a + ++ v + ++++v+++k++ea +++ a l+g+++ ++ G H ++H l + H 436s CUFF.50.1.p1 251 ANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFY--GIPH 320 436s ************************************************************997666..5555 PP 436s 436s == domain 2 score: -3.6 bits; conditional E-value: 0.4 436s Fe-ADH_2 27 dentkkaagekveeslkeagikvevveeveeead 60 436s +e+t +aa +++++ + e +i++++v+ +e+d 436s CUFF.50.1.p1 355 EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKD 388 436s 5778888888888888888888887765555554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (250 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1111.97 436s // 436s Query: Fig1 [M=188] 436s Accession: PF12351.7 436s Description: Ca2+ regulator and membrane fusion protein Fig1 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00077 12.0 0.1 0.0012 11.4 0.1 1.2 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.4 0.1 1.2e-05 0.0012 73 147 .. 7 79 .. 2 95 .. 0.75 436s 436s Alignments for each domain: 436s == domain 1 score: 11.4 bits; conditional E-value: 1.2e-05 436s Fig1 73 sdnvvhpyllmvaiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalwqhvassaastl 147 436s ++++ +l+m a+++++ f + lyf +ei ++ fk a++ ++v+s ++l+ + ++l++ ++ + l 436s CUFF.52.1.p2 7 KNTLTKRKLIMLALAIVFTFFAFGLYFIPHDEISVFDFKLPALQYETTVTSLDNFLIGGSTTLYTATVN--HEDL 79 436s 5566677899999999999999999998899**********7777777777777888777777765543..3555 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (188 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4781.04 436s // 436s Query: Flavodoxin_2 [M=198] 436s Accession: PF02525.16 436s Description: Flavodoxin-like fold 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.4e-36 117.9 0.1 3.1e-36 117.5 0.1 1.1 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 436s 2.4e-36 117.9 0.1 3.1e-36 117.5 0.1 1.1 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 436s 436s Alignments for each domain: 436s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 436s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 436s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 436s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 436s CUFF.48.1.p3 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 436s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 436s 436s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 436s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 436s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 436s CUFF.48.1.p3 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 436s **************999999****97777778878888899******************999999****************************9644 PP 436s 436s CCCHHHHHHHHHH CS 436s Flavodoxin_2 180 gaedeealaeale 192 436s +++ ++ a+ 436s CUFF.48.1.p3 173 NPK----VDIAVC 181 436s 443....444444 PP 436s 436s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 436s 436s Alignments for each domain: 436s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 436s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 436s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 436s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 436s CUFF.49.1.p2 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 436s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 436s 436s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 436s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 436s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 436s CUFF.49.1.p2 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 436s **************999999****97777778878888899******************999999****************************9644 PP 436s 436s CCCHHHHHHHHHH CS 436s Flavodoxin_2 180 gaedeealaeale 192 436s +++ ++ a+ 436s CUFF.49.1.p2 173 NPK----VDIAVC 181 436s 443....444444 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (198 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3120.72 436s // 436s Query: FMN_red [M=155] 436s Accession: PF03358.14 436s Description: NADPH-dependent FMN reductase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00021 13.6 0.0 0.0029 10.0 0.0 2.2 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 436s 0.00021 13.6 0.0 0.0029 10.0 0.0 2.2 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 436s 436s Alignments for each domain: 436s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 436s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 436s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 436s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 436s CUFF.48.1.p3 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 436s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 436s 436s HCH CS 436s FMN_red 96 Drl 98 436s D + 436s CUFF.48.1.p3 82 DEV 84 436s 976 PP 436s 436s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 436s 436s Alignments for each domain: 436s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 436s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 436s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 436s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 436s CUFF.49.1.p2 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 436s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 436s 436s HCH CS 436s FMN_red 96 Drl 98 436s D + 436s CUFF.49.1.p2 82 DEV 84 436s 976 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (155 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 971.90 436s // 436s Query: FPP [M=866] 436s Accession: PF05911.10 436s Description: Filament-like plant protein, long coiled-coil 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00068 10.5 0.1 0.00099 9.9 0.1 1.2 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 436s 0.00085 10.2 0.1 0.0013 9.6 0.1 1.2 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 9.9 0.1 2.1e-05 0.00099 518 597 .. 171 250 .. 146 265 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 9.9 bits; conditional E-value: 2.1e-05 436s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 436s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 436s CUFF.60.1.p2 171 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 250 436s 333333333333333334444455778999************************9*******************999985 PP 436s 436s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 9.6 0.1 2.7e-05 0.0013 518 597 .. 222 301 .. 197 316 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 9.6 bits; conditional E-value: 2.7e-05 436s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 436s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 436s CUFF.60.2.p2 222 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 301 436s 333333333333333334444455778999************************9*******************999985 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (866 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2842.43 436s // 436s Query: FR47 [M=86] 436s Accession: PF08445.9 436s Description: FR47-like protein 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.2e-06 18.8 0.0 9e-06 18.3 0.0 1.2 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 6.7e-06 18.7 0.0 9.8e-06 18.2 0.0 1.2 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 18.3 0.0 1.9e-07 9e-06 18 81 .. 70 133 .. 53 137 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: 18.3 bits; conditional E-value: 1.9e-07 436s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 436s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 436s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 436s CUFF.34.1.p2 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 436s 455578********************999999899999999999999*************9975 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 18.2 0.0 2.1e-07 9.8e-06 18 81 .. 70 133 .. 53 137 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: 18.2 bits; conditional E-value: 2.1e-07 436s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 436s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 436s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 436s CUFF.35.1.p1 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 436s 455578********************999999899999999999999*************9975 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (86 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2885.96 436s // 436s Query: Fungal_trans [M=267] 436s Accession: PF04082.17 436s Description: Fungal specific transcription factor domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.6e-42 137.9 0.2 2.2e-42 137.5 0.2 1.1 1 CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759( 436s 1.6e-42 137.9 0.2 2.2e-42 137.5 0.2 1.1 1 CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+ 436s 4.1e-28 90.7 6.2 4.5e-27 87.3 5.9 2.2 2 CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772( 436s 2.5e-12 38.9 4.7 1e-11 36.9 4.7 1.9 1 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 436s 436s Alignments for each domain: 436s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 436s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 436s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 436s CUFF.40.1.p2 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 436s 799*********************.*****************************9998444444....66....******..*************** PP 436s 436s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 436s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 436s CUFF.40.1.p2 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 436s ****************************************999**********************************99********9999997776 PP 436s 436s Fungal_trans 191 dlwesddase 200 436s ++e +++ 436s CUFF.40.1.p2 303 -VNEYRVNNA 311 436s .777766665 PP 436s 436s >> CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 436s 436s Alignments for each domain: 436s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 436s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 436s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 436s CUFF.41.1.p1 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 436s 799*********************.*****************************9998444444....66....******..*************** PP 436s 436s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 436s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 436s CUFF.41.1.p1 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 436s ****************************************999**********************************99********9999997776 PP 436s 436s Fungal_trans 191 dlwesddase 200 436s ++e +++ 436s CUFF.41.1.p1 303 -VNEYRVNNA 311 436s .777766665 PP 436s 436s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 87.3 5.9 1.9e-28 4.5e-27 3 234 .. 203 429 .. 201 459 .. 0.81 436s 2 ? 1.2 0.0 0.035 0.82 1 23 [. 471 492 .. 471 504 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 87.3 bits; conditional E-value: 1.9e-28 436s Fungal_trans 3 rffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLll 99 436s ++f++++ ++p + +++f+++++ ++++ l+ +l+ ++ +++ + s++ ++s ++ ++ df+ +s + +q+L 436s CUFF.38.1.p1 203 SYFQHVNWWWPTFVYNDFMYEFERLYAFGFHSNNAWLISFYSILALSSIRKRLGNSKTLAESLF------STAWVFVQKSDFFLTPS-IDKVQALIV 292 436s 8999999999999999999999666666666677777766777777778888887766666643......34777666667777777.********* PP 436s 436s Fungal_trans 100 lelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddlwesd 196 436s + y +s+ +l+ ++g a+ +a++l Lhr++s +e+ aes++R++w++++lDk i+l++G p+ ++d +i+++LP++ +l + 436s CUFF.38.1.p1 293 MTQYAAYLSSSSLCRTLCGQACLMAQQLNLHRKQSTDV------EPEK-AESWKRIFWMCYILDKNISLIFGTPSVFNDKDIDCNLPDSKYELLFGV 382 436s **********************************9988......7777.**************************99**********9998887777 PP 436s 436s Fungal_trans 197 daseetlvetk.........lsneeksrkiasfllaLkkilskiags 234 436s + + + n+ s+k ++++ a ki+ i+ + 436s CUFF.38.1.p1 383 QSGGDLIFVPTvsltiiqseIRNRLYSVKSPTQMAAREKIIIPIHQK 429 436s 77666666544667777777777777777777777766666666554 PP 436s 436s == domain 2 score: 1.2 bits; conditional E-value: 0.035 436s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpk 23 436s ++++fs+++ ++ ilh+ps +++ 436s CUFF.38.1.p1 471 MEVYFSYLNTLI-ILHRPSSSTE 492 436s 679******998.****997665 PP 436s 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 36.9 4.7 4.3e-13 1e-11 4 197 .. 151 329 .. 148 351 .. 0.75 436s 436s Alignments for each domain: 436s == domain 1 score: 36.9 bits; conditional E-value: 4.3e-13 436s Fungal_trans 4 ffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLlll 100 436s +f++fhp fp++h+ sf+++ + +l+++a+l++G + s + + s ++ + l + +++ w+ qs ll+ 436s CUFF.45.1.p1 151 YFEWFHPVFPFIHQASFNSEN-----VAASFLRSLVVIACLCTGIESDFSMALLFWDSGFHVL---------QLYL--QGDPERVKKAWVFQSRLLF 231 436s *********************.....4444444444555555555555555555544444433.........3333..3566667779********* PP 436s 436s Fungal_trans 101 elyektssdralher.....hhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddl 192 436s ++ ++ + ++ ++ v+ +r+ g + +v+ ++ + ++ e+ rR ++ ++l+ ++al+++ pp l+ ++++pLP ++ l 436s CUFF.45.1.p1 232 CTASLFEKT--ACFSgighvLLKDLVHESRTFGWTKLNWSVEGDTDISNLID-LECIRRSVFCLYILEWFLALIFNKPPSLSVLELQMPLPISSA-L 324 436s *99988775..55555445666666676777777666666676668888899.**************************99**************.9 PP 436s 436s Fungal_trans 193 wesdd 197 436s w+s + 436s CUFF.45.1.p1 325 WSSKE 329 436s 99875 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (267 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 436s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 4 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 833.33 436s // 436s Query: GalKase_gal_bdg [M=49] 436s Accession: PF10509.8 436s Description: Galactokinase galactose-binding signature 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00013 14.2 0.0 0.00024 13.3 0.0 1.4 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 13.3 0.0 2.6e-06 0.00024 12 44 .. 5 37 .. 2 41 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 13.3 bits; conditional E-value: 2.6e-06 436s EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEE CS 436s GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieldiy 44 436s +++s+PG + L GEH g l++A+ l+ y 436s CUFF.60.2.p2 5 LIVSSPGKTILFGEHAVVYGATALAAAVSLRSY 37 436s 799************************998866 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (49 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2188.20 436s // 436s Query: GDC-P [M=430] 436s Accession: PF02347.15 436s Description: Glycine cleavage system P-protein 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.4e-215 707.3 0.0 1.6e-202 665.5 0.0 3.2 3 CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 665.5 0.0 1.7e-204 1.6e-202 2 430 .] 66 504 .. 65 504 .. 0.99 436s 2 ! 36.7 0.0 1.2e-13 1.2e-11 22 285 .. 529 810 .. 525 822 .. 0.77 436s 3 ? 0.7 0.0 0.01 0.96 332 373 .. 840 881 .. 836 926 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 665.5 bits; conditional E-value: 1.7e-204 436s HH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S-------............--HHHHHHHHHHHHTTB---EE--BTTB------HHHHHH CS 436s GDC-P 2 rhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleap............ksEeellaelekiasknkvvksfiGaGyydtilPaviqrn 86 436s rhigps++dq+++Le+lG+k++d+++++ +P+++++++++ ++ + +sE+e+++ +++a++nk++ksfiG+Gyy+++lPa+iqrn 436s CUFF.57.1.p1 66 RHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGsvnpneknppvnYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRN 162 436s 9******************************************9999************************************************** PP 436s 436s TTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEE CS 436s GDC-P 87 ilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqtlevlktrakglgieiv 183 436s +lenpewyt+YtPYqaEisqGrLe+++n+qt++adltGl+i+nasllDegtAa+EA++++++++kkk+k+++vdk+++p+tl+vl+tra+g+gi+i+ 436s CUFF.57.1.p1 163 VLENPEWYTQYTPYQAEISQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIYPNTLSVLRTRASGFGIKIE 259 436s ************************************************************************************************* PP 436s 436s EE-GGG--S-...S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGG CS 436s GDC-P 184 evdlteekvtdkekevagvlvqypnteGriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkekl 280 436s ++++t e +t+++k+v+g++vqyp+++G+i d+ +l+++a++ +++vv+a+dllaLt+lk+Pge+gaD++vGs+qrfG+P+gyGGPhagffA++e++ 436s CUFF.57.1.p1 260 LDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATARSFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEF 356 436s ************************************************************************************************* PP 436s 436s GGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSS CS 436s GDC-P 281 kRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffd 377 436s kRkiPGRl+G+skD+ +++a+rlalqtREqHirR+kAtsniCtaqaLlAn++a+ya+yhG++gl+eia+ri+++t++l+++l+++ ++ ++k++ffd 436s CUFF.57.1.p1 357 KRKIPGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGLQEIANRIYASTSFLKSALESSGYKIVNKSHFFD 453 436s ************************************************************************************************* PP 436s 436s EEEEE--TTTHHHHHHHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS 436s GDC-P 378 tllieveekaaekvlkkaekeglnlrkvelktvgialdEtvtkedieallkvl 430 436s tl+ieve +a+kvl+ka+++g+nlrkv++++vg++ldEtv+++di+al++++ 436s CUFF.57.1.p1 454 TLTIEVE--SADKVLAKALDHGYNLRKVDDSHVGLSLDETVCDKDIQALFSIF 504 436s ****999..889**************************************987 PP 436s 436s == domain 2 score: 36.7 bits; conditional E-value: 1.2e-13 436s SHHHHHHHHS-GGGB--S-------.....--HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG.G-HHHHHH CS 436s GDC-P 22 slddliekavPkeiklkkelkleap.....ksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE.isqGrLea 111 436s ++d+l ++P++ + +++l l++p +sE+el++ ++++ sk+ ++ + G ++l av + + np + ++ PY +E ++G + 436s CUFF.57.1.p1 529 TVDNLSICSLPENFR-RTTLYLQHPvfnryHSETELMRYIHHLQSKDLSlAHAMTPLGSCTMKLNAVTEMMPITNPLF-ANIHPYVPEeQAKGYRHV 623 436s 677888888899985.456667777777779****************987899999************9988999976.5678999963789***** PP 436s 436s HHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHH.HH-SSS.....--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-......... CS 436s GDC-P 112 llnfqtlvadltGldianasllDegtAaaEAvllaa.raskkk.....akkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd........ 194 436s + + q +++ +tG+d a + ++ Aa+E l++ ra ++ ++ ++ + h + a g+ ++ v++ +++ d 436s CUFF.57.1.p1 624 IEDLQLMLTTITGFDAA--CFQPNSGAAGEYTGLSViRAYQRSigqghRNICLIPVSAHGTN----PASAAMAGFTVIPVKCLNNGYLDmqdlkeka 714 436s **************975..6778888888877665412222221111134444444444333....3445566666666666666666666677777 PP 436s 436s ....S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG-- CS 436s GDC-P 195 ..kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiP 285 436s +++++a+ +v yp+t+G e+ +ke e ++++ v a++ a++ l g++gaD+ + + f +P g GGP +g + vk++l+ +P 436s CUFF.57.1.p1 715 skHADKLAAFMVTYPSTFGIFEPdVKEALEVIHEHGGQVYFdGANMNAMVGLCKAGDIGADVChLNLHKTFCIPHGGGGPGVGPICVKKHLADFLP 810 436s 768899**************99669*********99888763689999999***********84667889******************99988777 PP 436s 436s == domain 3 score: 0.7 bits; conditional E-value: 0.01 436s HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--S CS 436s GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkkleeelkkk 373 436s + y+ + G gl++ ++ + +++++ak l ++ + + ++k 436s CUFF.57.1.p1 840 SWAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNK 881 436s 567999*************************98755444443 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (430 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 1022.35 436s // 436s Query: GHMP_kinases_C [M=85] 436s Accession: PF08544.12 436s Description: GHMP kinases C terminal 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.4e-08 27.7 0.0 5e-08 25.9 0.0 1.9 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 436s 1.8e-08 27.3 0.0 6.2e-08 25.6 0.0 1.9 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 25.9 0.0 1.1e-09 5e-08 8 66 .. 233 287 .. 221 298 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 25.9 bits; conditional E-value: 1.1e-09 436s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 436s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 436s CUFF.60.1.p2 233 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 287 436s 6678999********..899********************..*************9997 PP 436s 436s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 25.6 0.0 1.3e-09 6.2e-08 8 66 .. 284 338 .. 272 349 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 25.6 bits; conditional E-value: 1.3e-09 436s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 436s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 436s CUFF.60.2.p2 284 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 338 436s 6678999********..899********************..*************9997 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (85 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 738.85 436s // 436s Query: GHMP_kinases_N [M=66] 436s Accession: PF00288.25 436s Description: GHMP kinases N terminal domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.2e-18 58.0 1.6 8.7e-18 57.0 1.6 1.6 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 436s 1.1e-17 56.7 4.8 1.1e-17 56.7 1.6 2.3 2 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 57.0 1.6 1.8e-19 8.7e-18 2 66 .] 75 152 .. 74 152 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 57.0 bits; conditional E-value: 1.8e-19 436s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 436s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 436s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 436s CUFF.60.1.p2 75 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 152 436s 799****************************877765543352257899999***********.************998 PP 436s 436s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? 0.1 0.1 0.11 5.2 19 40 .. 25 47 .. 22 57 .. 0.68 436s 2 ! 56.7 1.6 2.3e-19 1.1e-17 2 66 .] 126 203 .. 125 203 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 0.1 bits; conditional E-value: 0.11 436s HHHHHHHHHHHHHTTEHH.HHHH CS 436s GHMP_kinases_N 19 AlavalvaAlaallglsl.eeak 40 436s A a+a+++ l +++ l+ ++++ 436s CUFF.60.2.p2 25 ATALAAAVSLRSYCKLQTtNNNE 47 436s 77888888888999655323344 PP 436s 436s == domain 2 score: 56.7 bits; conditional E-value: 2.3e-19 436s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 436s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 436s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 436s CUFF.60.2.p2 126 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 203 436s 799****************************877765543352257899999***********.************998 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (66 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1995.58 436s // 436s Query: GLEYA [M=91] 436s Accession: PF10528.8 436s Description: GLEYA domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.6e-21 67.8 1.8 1.7e-20 65.9 1.8 2.0 1 CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+ 436s 2.4e-20 65.5 3.2 2.9e-20 65.2 2.1 1.8 2 CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-88 436s 4.1e-19 61.5 0.7 1.6e-18 59.6 0.7 2.1 1 CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007 436s 9.4e-19 60.3 0.7 9.4e-19 60.3 0.7 1.9 3 CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 65.9 1.8 7.1e-22 1.7e-20 2 89 .. 256 345 .. 255 347 .. 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: 65.9 bits; conditional E-value: 7.1e-22 436s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEE CS 436s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyangggagslnfsv 89 436s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang g+++f + 436s CUFF.31.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANGAYIGGFDFAF 345 436s 789***********************************************9666899999999************************987 PP 436s 436s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -3.6 0.0 3.6 85 70 84 .. 13 27 .. 3 33 .. 0.60 436s 2 ! 65.2 2.1 1.2e-21 2.9e-20 2 90 .. 157 253 .. 156 254 .. 0.92 436s 436s Alignments for each domain: 436s == domain 1 score: -3.6 bits; conditional E-value: 3.6 436s EEEEEEEEE-S-.EE CS 436s GLEYA 70 yPiRivyangggags 84 436s +P+ +a++ g+ s 436s CUFF.11.1.p1 13 LPFTTTLAQASGTVS 27 436s 577777777766555 PP 436s 436s == domain 2 score: 65.2 bits; conditional E-value: 1.2e-21 436s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.......TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEEE CS 436s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.......sgssesktvt.vtltaGtyyPiRivyangggagslnfsvt 90 436s +++++ +++ p+t tYt+ ++n+Dd+++ w+GdkA+s+w+++n d+++ + g+ + +++t + +G+++P+R+v+ang g+++f +t 436s CUFF.11.1.p1 157 VIVYQFFLRIPETDTYTLVVNNVDDVFFGWFGDKAISGWSNNNFDAYSYWhespnmgLGTVGMGNFTvGNYPEGYFLPVRFVVANGAYIGGFDFYFT 253 436s 689***********************************************9999888444677777757899**********************998 PP 436s 436s >> CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 59.6 0.7 6.9e-20 1.6e-18 2 79 .. 256 335 .] 255 335 .] 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: 59.6 bits; conditional E-value: 6.9e-20 436s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 436s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 436s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 436s CUFF.30.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 335 436s 789***********************************************9666899999999***************96 PP 436s 436s >> CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -3.0 0.0 2.3 55 59 86 .. 20 45 .. 14 50 .. 0.50 436s 2 ? -2.0 0.1 1.1 26 75 75 .. 66 66 .. 31 96 .. 0.59 436s 3 ! 60.3 0.7 4e-20 9.4e-19 2 79 .. 170 249 .] 169 249 .] 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: -3.0 bits; conditional E-value: 2.3 436s EEEEEE-TT-BEEEEEEEEE-S-.EEEE CS 436s GLEYA 59 tvtvtltaGtyyPiRivyangggagsln 86 436s + +v+++ G+ + +y g ++++ 436s CUFF.30.2.p1 20 SSSVSVETGSCVRYTTIYSSGS--SEFT 45 436s 4455666666554444444433..3444 PP 436s 436s == domain 2 score: -2.0 bits; conditional E-value: 1.1 436s E CS 436s GLEYA 75 v 75 436s 436s CUFF.30.2.p1 66 H 66 436s 1 PP 436s 436s == domain 3 score: 60.3 bits; conditional E-value: 4e-20 436s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 436s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 436s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 436s CUFF.30.2.p1 170 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 249 436s 789***********************************************9666899999999***************96 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (91 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 436s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 4 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1037.22 436s // 436s Query: Glyco_hydro_cc [M=239] 436s Accession: PF11790.7 436s Description: Glycosyl hydrolase catalytic core 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.9e-61 199.6 0.0 4.3e-61 199.1 0.0 1.3 1 CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 199.1 0.0 4.5e-63 4.3e-61 1 239 [] 298 528 .. 298 528 .. 0.92 436s 436s Alignments for each domain: 436s == domain 1 score: 199.1 bits; conditional E-value: 4.5e-63 436s Glyco_hydro_cc 1 GlaynadasddkllsaksskisWyYnwsskpsselssaalefvPmlwgaksadtdalanvksaakenskylLgFNePDlks.qsnmspeeAaklw 94 436s Gla++ +++ ++ + ++ i+WyYnw+s++s+ +ss e+v ++a+s + +++s+ ++ +++gFNePDl+ + +++++Aa+++ 436s CUFF.59.1.p1 298 GLAWIPGTDLGYSDNFVNKGINWYYNWGSYSSGLSSSF--EYVLNQHDANSLS-----SASSV-FTGGATVIGFNEPDLSAaGNPIDAATAASYY 384 436s 78999888888888999**************9988885..********99865.....44444.55579**********8889************ PP 436s 436s Glyco_hydro_cc 95 kqliqplre..kgvklvsPavaatnseegleWldeFleacskdckvdflavHwYkgdfeelkehieelheaynkpiWvTEfalqs..esgdasqe 185 436s q+++plre +l+sPa+++ g +Wl+eF++acs dck+df+a+HwY+ df++l+++i++l ++y++piW+TEfa+++ +s+ s + 436s CUFF.59.1.p1 385 LQYLTPLREsgAIGYLGSPAISN--V--GEDWLSEFMSACS-DCKIDFIACHWYGIDFSNLQDYINSL-ANYGLPIWLTEFACTNwdDSNLPSLD 473 436s ********6355669******33..3..669**********.************999***********.9***************999999**** PP 436s 436s Glyco_hydro_cc 186 etkeflnevlawldsqeyVeryawfg.frsevsnvgannaLldenGeltelgsaY 239 436s e+k++++++l +ld + +Very+wf+ +++ ++vg+nnaL++++G+l+e+g++Y 436s CUFF.59.1.p1 474 EVKTLMTSALGFLDGHGSVERYSWFApATELGAGVGNNNALISSSGGLSEVGEIY 528 436s *****************************************************99 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (239 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2860.92 436s // 436s Query: Glyco_tranf_2_3 [M=230] 436s Accession: PF13641.5 436s Description: Glycosyltransferase like family 2 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00012 14.6 0.0 0.00045 12.7 0.0 1.8 2 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 0.00012 14.6 0.0 0.00045 12.7 0.0 1.8 2 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 436s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 436s 436s Alignments for each domain: 436s == domain 1 score: -1.4 bits; conditional E-value: 0.19 436s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 436s + ++ D+ t ++P+tl++l++ 436s CUFF.60.1.p1 237 VCIISDGRTKIHPRTLAYLAA 257 436s 45688999*******999876 PP 436s 436s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 436s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 436s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 436s CUFF.60.1.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 436s 5667889999********************9999999999999888766666666668888********************8566779****** PP 436s 436s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 436s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 436s CUFF.60.1.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 436s ******999****************9984466699************9988899*****************************86 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 436s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 436s 436s Alignments for each domain: 436s == domain 1 score: -1.4 bits; conditional E-value: 0.19 436s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 436s + ++ D+ t ++P+tl++l++ 436s CUFF.60.2.p1 237 VCIISDGRTKIHPRTLAYLAA 257 436s 45688999*******999876 PP 436s 436s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 436s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 436s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 436s CUFF.60.2.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 436s 5667889999********************9999999999999888766666666668888********************8566779****** PP 436s 436s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 436s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 436s CUFF.60.2.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 436s ******999****************9984466699************9988899*****************************86 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (230 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1401.43 436s // 436s Query: Glyco_transf_34 [M=239] 436s Accession: PF05637.11 436s Description: galactosyl transferase GMA12/MNN10 family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.2e-87 284.1 0.3 6.5e-87 283.8 0.3 1.1 1 CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+ 436s 2.8e-86 281.7 0.0 3.4e-86 281.4 0.0 1.1 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 283.8 0.3 1.4e-88 6.5e-87 2 238 .. 98 334 .. 97 335 .. 0.97 436s 436s Alignments for each domain: 436s == domain 1 score: 283.8 bits; conditional E-value: 1.4e-88 436s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 436s +++ivlllvs+ ++++ ++ +++++++i+NrvdY++k++y+++y++v+ l ++vW+k+pa+ ++mkkyP+aewiW+lDqdA+i+n++ls 436s CUFF.51.1.p2 98 SQNIVLLLVSDGHTSY--NNGANTFEEAIQNRVDYSTKQNYNFEYVNVTGLPI---PAVWSKMPAVLQTMKKYPKAEWIWLLDQDAIITNTHLS 186 436s 789***********97..455559***************************99...************************************** PP 436s 436s Glyco_transf_34 96 leehvlkperLeelllkntpv........vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesd 181 436s l++++lkpe+L+++l++nt + +lr+++++++ +d+e+ +viisqd+nglnags+l+rns +++l+lD+w+dp+++e++ka ++ 436s CUFF.51.1.p2 187 LQDSFLKPENLQKTLITNTILtkrpinanGDLRYTPSNYSLKDIENLMVIISQDHNGLNAGSILFRNSPATALFLDIWTDPVVAECAKA---NN 277 436s *******************999*****9999**********************************************************...** PP 436s 436s Glyco_transf_34 182 eqsaleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankc 238 436s eq++l+yl++kh++++s vgl++q+ in+++eg++++++++gdlv+hfagC+v+n+c 436s CUFF.51.1.p2 278 EQDMLGYLISKHSQLASLVGLIPQRKINAFHEGPENMEWQKGDLVIHFAGCWVENRC 334 436s ********************************************************9 PP 436s 436s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 281.4 0.0 7.1e-88 3.4e-86 2 239 .] 84 318 .. 83 318 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 281.4 bits; conditional E-value: 7.1e-88 436s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 436s ++eiv+ll+s+ + s +++ll++++kNr++Ya++++y++++++vs+l + vW k+pai ++m+kyP+a+wiWwlDqdAlimn++ls 436s CUFF.52.1.p2 84 SHEIVMLLASDGNVG---SFESNLLDDCFKNRIEYAKLQNYNFEFVNVSSLVV---PPVWGKMPAILQTMRKYPSAKWIWWLDQDALIMNKNLS 171 436s 79**********997...58999***************************999...************************************** PP 436s 436s Glyco_transf_34 96 leehvlkperLeelllkntpv......vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesdeq 183 436s l+e +l+p +L+++ll+++p+ ++ r ++ +++e++e+++++isqd+nglnagsfl+rns+ +ll+Dl++dp+l++++++ ++eq 436s CUFF.52.1.p2 172 LQELFLSPAMLQKSLLREQPIinsfgeDNFRITPAAYSKEMIEQIQFLISQDHNGLNAGSFLVRNSRSIALLMDLLTDPSLADAGVV---RHEQ 262 436s **************************999**********************************************************...**** PP 436s 436s Glyco_transf_34 184 saleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankca 239 436s ++++y+++kh++v+s+vg+++q++in+++eg+++++++egdl++hfagC+v+nkca 436s CUFF.52.1.p2 263 DLIGYFIQKHSQVASMVGILPQRFINAFHEGPPTMQWQEGDLALHFAGCWVENKCA 318 436s ******************************************************96 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (239 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2518.63 436s // 436s Query: Glyco_transf_8 [M=256] 436s Accession: PF01501.19 436s Description: Glycosyl transferase family 8 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.7e-12 39.3 1.6 1e-11 37.5 1.6 1.8 1 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 37.5 1.6 1.1e-13 1e-11 9 221 .. 84 321 .. 77 336 .. 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 37.5 bits; conditional E-value: 1.1e-13 436s Glyco_transf_8 9 nYllgasvviksllknakepawfalnfhiltaeievenleklnklassykevlellesdkksledfesklklrspkylsllnylRlylpelfpkl 103 436s Y ++ v+i+ l + +++ +++ + ++++ ++e+++k + s++ ++++ sd+ ++++++++ ++ + ++ +l+++e ++ 436s CUFF.51.1.p1 84 YYFNATRVLIHRLKYHPTTKSKYPIHIL-ALRGVDEWKIERFRKDGASVIVIDPIASSDIVY----DTSSFSQEISARYEQMFSKLRIFEQ-IQF 172 436s 5677778888888888886556666666.7899*******************9999998843....3578899999999999*********.9** PP 436s 436s Glyco_transf_8 104 dkilylDaDvvvqgdlseLwdldlk.gkvlaaved............................krfkkylnksepliaenfkp..eacyFnaGvl 167 436s dki +D+D+++ +++++++d++ ++++ + + + + l + + +++p + yFnaG++ 436s CUFF.51.1.p1 173 DKICVIDSDILIMKNIDDIFDTPYMyQQINTLNYTrlpsytkpdddtvyhfnedfkeygasrsEFYPYLLAAVSDRGEHHSIPpeDTPYFNAGLM 267 436s **********************9997888888888*************************8863333333444444444444411567******* PP 436s 436s Glyco_transf_8 168 lfdldewrkenitetlikwlnlnekrtllklgdqdilnivfk....gkvkeldkkynv 221 436s l+ + e + + i + + ++e+ k ++q +ln++f + +ld++yn 436s CUFF.51.1.p1 268 LIRPSELHFNRILKI-GRFPYMYEN---AKMMEQSLLNLAFSldgwFPWTRLDPYYNG 321 436s *******99988764.455566666...89***********86655789999999995 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (256 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1304.08 436s // 436s Query: Glyco_trans_2_3 [M=197] 436s Accession: PF13632.5 436s Description: Glycosyl transferase family group 2 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.8e-11 36.3 7.3 1.5e-10 33.9 7.3 2.2 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 2.8e-11 36.3 7.3 1.5e-10 33.9 7.3 2.2 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 436s 436s Alignments for each domain: 436s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 436s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 436s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 436s CUFF.60.1.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 436s 799**************999*988************97765333347788888888**********************************8888 PP 436s 436s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 436s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 436s CUFF.60.1.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 436s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 436s 436s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 436s +r++ +++++s ++ +++++f+++ + ++++l 436s CUFF.60.1.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 436s 3333313445555555555555566665544333321....22222 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 436s 436s Alignments for each domain: 436s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 436s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 436s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 436s CUFF.60.2.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 436s 799**************999*988************97765333347788888888**********************************8888 PP 436s 436s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 436s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 436s CUFF.60.2.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 436s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 436s 436s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 436s +r++ +++++s ++ +++++f+++ + ++++l 436s CUFF.60.2.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 436s 3333313445555555555555566665544333321....22222 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (197 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 436s # Mc/sec: 432.04 436s // 436s Query: GNAT_acetyltr_2 [M=227] 436s Accession: PF13718.5 436s Description: GNAT acetyltransferase 2 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00031 12.8 0.0 0.00041 12.4 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 436s 0.00032 12.7 0.0 0.00043 12.3 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.4 0.0 8.6e-06 0.00041 94 131 .. 72 109 .. 67 128 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 12.4 bits; conditional E-value: 8.6e-06 436s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 436s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 436s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 436s 679******************98766666666665554 PP 436s 436s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.3 0.0 9e-06 0.00043 94 131 .. 72 109 .. 67 130 .. 0.79 436s 436s Alignments for each domain: 436s == domain 1 score: 12.3 bits; conditional E-value: 9e-06 436s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 436s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 436s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 436s 679******************98766666666665554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (227 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4047.34 436s // 436s Query: His_Phos_1 [M=194] 436s Accession: PF00300.21 436s Description: Histidine phosphatase superfamily (branch 1) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.2e-24 77.6 0.0 6.6e-24 77.3 0.0 1.1 1 CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 77.3 0.0 7e-26 6.6e-24 1 181 [. 9 203 .. 9 215 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: 77.3 bits; conditional E-value: 7e-26 436s EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT.......--EEE-GGGS----GGGT. CS 436s His_Phos_1 1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg.......lpveldegLrEidfGdwe. 86 436s +yL+RHG+ ++n+ d+ Lt eG+eq eala+ l++ +pid i++Sp++R+ qT+e+++++ +pv + + ++E+ + ++ 436s CUFF.48.1.p2 9 VYLIRHGQAQHNVGPDeDHNIRDPVLTSEGIEQCEALAKELESkqIPIDGIVCSPMRRTLQTMEIALKKYLaeggpdkVPVYISPFFQEVGHLPCDi 105 436s 69*********99877778889999****************9988999999***************99876788999************99999999 PP 436s 436s T-B.HHHHHH..HSHHHHHHHHH-GGG-B....S-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH.T--GGGGG.GB---TT-EE CS 436s His_Phos_1 87 glttaeiaeeypeeleawlrdpadvrppg....gEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll.glpleelr.rleldnaslt 177 436s gl+ +++++ yp++ + +d p++ + a R ++ale laa +++ ++v++H ++ir ll++++ ++++l+ +l ++n++ 436s CUFF.48.1.p2 106 GLELDKLNKLYPKYNFQSCQDGIY--PEKrdiyASDVTISAIRSKEALEYLAALPQQQ-IAVITHSAFIRFLLKKMVkAADIDFLPpQLSFKNCEFR 199 436s **********99987777666653..3334587888888899***********99987.*****************966777766546777999887 PP 436s 436s EEEE CS 436s His_Phos_1 178 vley 181 436s + ++ 436s CUFF.48.1.p2 200 IYDL 203 436s 7765 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (194 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4339.31 436s // 436s Query: Hpt [M=85] 436s Accession: PF01627.22 436s Description: Hpt domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00033 13.6 0.3 0.0011 11.9 0.3 1.8 1 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.9 0.3 1.1e-05 0.0011 32 64 .. 217 248 .. 205 267 .. 0.74 436s 436s Alignments for each domain: 436s == domain 1 score: 11.9 bits; conditional E-value: 1.1e-05 436s HHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTS CS 436s Hpt 32 aaHtLKGsagmlGltelaelahelEdlldrage 64 436s ++H+++Gsa+ lGl+ l ++a+ ++++d a 436s CUFF.19.1.p1 217 LVHKIAGSAAALGLD-LHQVAQVAQSVIDNAAT 248 436s 79***********64.66666666666654444 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (85 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2895.40 436s // 436s Query: HTH_29 [M=63] 436s Accession: PF13551.5 436s Description: Winged helix-turn helix 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00071 12.3 0.0 0.1 5.3 0.0 2.6 2 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 5.3 0.0 0.0011 0.1 16 35 .. 122 141 .. 111 145 .. 0.88 436s 2 ! 4.0 0.0 0.0027 0.26 10 30 .. 278 298 .. 271 301 .. 0.83 436s 436s Alignments for each domain: 436s == domain 1 score: 5.3 bits; conditional E-value: 0.0011 436s HTH_29 16 sqiAkllglsrrtvyrwlkr 35 436s ++A ++glsr+++++++++ 436s CUFF.17.1.p1 122 PELANQCGLSRKHIFDAVED 141 436s 589************99986 PP 436s 436s == domain 2 score: 4.0 bits; conditional E-value: 0.0027 436s HTH_29 10 eGvstvsqiAkllglsrrtvy 30 436s +s+v ++Ak +++s+ t 436s CUFF.17.1.p1 278 AILSRVEELAKKYNVSMATLA 298 436s 456799************986 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (63 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2710.29 436s // 436s Query: HTH_psq [M=45] 436s Accession: PF05225.15 436s Description: helix-turn-helix, Psq domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00097 11.5 0.3 0.2 4.1 0.0 3.0 3 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 3.8 0.0 0.0026 0.25 24 33 .. 81 90 .. 80 93 .. 0.91 436s 2 ? -1.9 0.0 0.16 16 7 16 .. 169 179 .. 165 180 .. 0.80 436s 3 ! 4.1 0.0 0.0021 0.2 21 33 .. 285 297 .. 281 304 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 3.8 bits; conditional E-value: 0.0026 436s HTH_psq 24 rkYgiPrsTL 33 436s rkY+iPrs++ 436s CUFF.17.1.p1 81 RKYEIPRSSI 90 436s 79******98 PP 436s 436s == domain 2 score: -1.9 bits; conditional E-value: 0.16 436s HTH_psq 7 aAleavv.nGk 16 436s +Al++vv +Gk 436s CUFF.17.1.p1 169 RALNDVVeSGK 179 436s 8******8887 PP 436s 436s == domain 3 score: 4.1 bits; conditional E-value: 0.0021 436s HTH_psq 21 kAArkYgiPrsTL 33 436s ++A+kY+++ TL 436s CUFF.17.1.p1 285 ELAKKYNVSMATL 297 436s 79********999 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (45 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1976.05 436s // 436s Query: Hydantoinase_A [M=291] 436s Accession: PF01968.17 436s Description: Hydantoinase/oxoprolinase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.5e-107 349.6 0.2 6.5e-107 349.6 0.2 1.7 2 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ 436s 7.5e-91 296.9 0.0 1.3e-90 296.2 0.0 1.4 1 CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -3.5 0.2 0.54 26 82 95 .. 5 18 .. 4 22 .. 0.87 436s 2 ! 349.6 0.2 1.4e-108 6.5e-107 1 290 [. 239 540 .. 239 541 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: -3.5 bits; conditional E-value: 0.54 436s Hydantoinase_A 82 ItfDmGGTstDvsl 95 436s I +D GGT tD+++ 436s CUFF.44.1.p1 5 IHIDRGGTFTDAIA 18 436s 889********875 PP 436s 436s == domain 2 score: 349.6 bits; conditional E-value: 1.4e-108 436s Hydantoinase_A 1 rtetavvnAylspilreylesvekslekrgak......arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaat.sklagekkvItfDmGG 88 436s r+++a+ +Aylsp++r+yl ++++ + + ++ r+ +mqsdGglv+++++++ ++ilSGPa+Gvvg+a t ++++ + +vI+fDmGG 436s CUFF.44.1.p1 239 RATSATADAYLSPVVRRYLAGFQSGFLHGLKTkdnskgVRCEFMQSDGGLVDVNKFSGL--HAILSGPAGGVVGFALTsYDEDVKIPVIGFDMGG 331 436s 7889*********************9997776999999********************9..*****************77888888********* PP 436s 436s Hydantoinase_A 89 TstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls. 182 436s TstDvs++ g++e+++et++agv++++p+ldi+tv+agGgs+l ++++g + vgpesaga+pgp+cyrkGg ltvTDanl+LGrl pe+f++ 436s CUFF.44.1.p1 332 TSTDVSRYG-GSYEHVFETTTAGVTIQSPQLDINTVAAGGGSRL-FWKNGLFVVGPESAGAHPGPVCYRKGG-YLTVTDANLLLGRLLPESFPKi 423 436s *********.**********************************.***************************.********************** PP 436s 436s Hydantoinase_A 183 .gpdgdqkldvelarrafeelakelnlk........veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkv 268 436s gp++d++ldve +r++fe+l++e+n + ++evA g++++a+e+ma+++r l++++g+d++ + l++fGGaG+qh+aa+a++lg+++v 436s CUFF.44.1.p1 424 fGPNEDESLDVESTRKEFEKLTAEINSGlekerqmtADEVAFGFIKIANETMARPIRALTEAKGHDISIHRLTSFGGAGGQHCAAIAKSLGITQV 518 436s *********************************************************************************************** PP 436s 436s Hydantoinase_A 269 ivppyagvlsalGmalAdvree 290 436s +v++y+++lsa+GmalAdv +e 436s CUFF.44.1.p1 519 LVHKYSSILSAYGMALADVVSE 540 436s ******************9876 PP 436s 436s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 296.2 0.0 2.7e-92 1.3e-90 44 290 .. 1 252 [. 1 253 [. 0.97 436s 436s Alignments for each domain: 436s == domain 1 score: 296.2 bits; conditional E-value: 2.7e-92 436s Hydantoinase_A 44 lvsadearkkpvetilSGPaaGvvgaaat..sklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvde 136 436s lv++d+++ +i+SGPaaG vg+a+t + ++++++I+fDmGGTstDvs+++ g++e+ +e +i g+ +++p+ldi+tv+agGgs+l +++ 436s CUFF.42.1.p1 1 LVDIDNFTAI--SAIMSGPAAGTVGFAKTssLHADDKTPAIGFDMGGTSTDVSRYD-GKFEHIYEANIFGLYIQSPQLDIQTVAAGGGSRL-FWR 91 436s 6789999987..*****************5445567788*****************.**********************************.999 PP 436s 436s Hydantoinase_A 137 ggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvave 223 436s ++ ++vgpesaga pgpacy +Gg +ltvTDan++LGr+ p++f++ gp+++++++++++ ++f+el + +n + +ee+A+g+++va+e 436s CUFF.42.1.p1 92 NQLFSVGPESAGAFPGPACYLNGG-PLTVTDANVLLGRIIPDFFPKifGPKENESMNKDIVIEKFSELRDIINIDiekektIEEIAMGFIQVANE 185 436s ************************.********************************************************************** PP 436s 436s Hydantoinase_A 224 nmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290 436s +m++++rkl+++rgld + ++l+vfGGaG+qha+a+a l+++k+i+++y++vlsa+G+alA+v++e 436s CUFF.42.1.p1 186 TMCRPIRKLTESRGLDLSAHHLAVFGGAGGQHACAIASLLNIEKIIIHKYSSVLSAYGLALAHVTHE 252 436s ****************************************************************998 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (291 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1496.75 436s // 436s Query: Hydantoinase_B [M=516] 436s Accession: PF02538.13 436s Description: Hydantoinase B/oxoprolinase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.6e-215 708.9 0.1 2.7e-215 708.2 0.1 1.3 1 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ 436s 2.2e-213 701.8 0.3 2.8e-213 701.5 0.3 1.1 1 CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 708.2 0.1 5.6e-217 2.7e-215 1 516 [] 749 1285 .. 749 1285 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 708.2 bits; conditional E-value: 5.6e-217 436s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyagg 93 436s Dpi l+vf +r+m++ae+mgr+lq+t++S+n+kerlD+scalfda+g+lva+aph+pvhlgsms++v+++++ +eg+lkpGDvl+tN+P +gg 436s CUFF.44.1.p1 749 DPIYLSVFGSRFMAVAEQMGRALQKTSVSTNVKERLDYSCALFDAKGNLVANAPHMPVHLGSMSTCVRTQAKIHEGKLKPGDVLVTNHPSYGG 841 436s 9**********************************************************************99999***************** PP 436s 436s Hydantoinase_B 94 tHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........Rtpednl 176 436s tHlpDit+itP f +e++f+va+raHhaDiGGi pGsmp++++e+ eEG+ i++ klv +g+ +ee++++ll +++ R+++dnl 436s CUFF.44.1.p1 842 THLPDITTITPHFEGDEIMFYVAARAHHADIGGILPGSMPSSSKELSEEGATIKSEKLVVDGVfQEERMIDLLYNEPakveggsgsRCLRDNL 934 436s *************9889*********************************************************999**************** PP 436s 436s Hydantoinase_B 177 gDlkAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgts 263 436s +DlkAq++anq+g+++++ li+eyG++ v ++m++i++nae avr++l +++ +++ aed++ddg++i++++tid+++ a++Dftgt 436s CUFF.44.1.p1 935 NDLKAQVSANQKGINLITSLIKEYGKNSVLRYMKAIQENAESAVRQLLLGVRErflgEDLYAEDHMDDGSKICLRITIDEENgdAIFDFTGTT 1027 436s ************************************************7777777778899*******************9999********* PP 436s 436s Hydantoinase_B 264 pqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtm 356 436s ++++gniNap+avt+sa+iy+lr+l++e+iplN+Gcl pi+v++p++++l+pse+aavvggnv+tsqr++d++lka++ ++Aasqg++ 436s CUFF.44.1.p1 1028 EEIYGNINAPEAVTYSAIIYCLRVLISENIPLNQGCLLPIKVIIPDNCFLKPSETAAVVGGNVLTSQRITDTILKAFQ------ACAASQGDT 1114 436s ******************************************************************************......********* PP 436s 436s Hydantoinase_B 357 nnltf..ggvderg...geffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreief 444 436s nnltf gg+d+++ + fgyyeti+gGsGA g dG+s+vh+hmtntr+td E+lErryPv++++f +r++sgGaGky+GGdGv+r+ief 436s CUFF.44.1.p1 1115 NNLTFgiGGKDPETgevKPGFGYYETICGGSGAIDGLDGTSGVHTHMTNTRITDLEVLERRYPVILRKFIIRENSGGAGKYKGGDGVIRDIEF 1207 436s ****94446677669998889************************************************************************ PP 436s 436s Hydantoinase_B 445 lepevtvsilserrvfapwGlaGGepGargrvvlnllvr..........greenlggkatvelkagdvlvietpGGGGyGdp 516 436s + p vt+silserr ++p+G++GG+++++g+ n+++r r++n+ggk+t++++agd +vi+tpGGGGyG p 436s CUFF.44.1.p1 1208 RIP-VTLSILSERRAYHPYGMKGGKDAECGK---NIWIRkdilpsgeqrVRQINVGGKNTCHMQAGDHIVIMTPGGGGYGPP 1285 436s **9.***************************...88888899999998899*****************************86 PP 436s 436s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 701.5 0.3 5.9e-215 2.8e-213 1 515 [. 459 986 .. 459 987 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 701.5 bits; conditional E-value: 5.9e-215 436s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyaggtH 95 436s Dpit+ +f+nr+msi e+mg++lq+ta+S+n+kerlD+scalf++dg+lva+aph+p +lgsm++avk+++++++g+l pGDvll+N+P+agg H 436s CUFF.42.1.p1 459 DPITMTIFANRFMSISEQMGQVLQKTAVSVNVKERLDYSCALFSPDGGLVANAPHVPAMLGSMQTAVKWQHNYWKGKLVPGDVLLSNHPIAGGVH 553 436s 9********************************************************************************************** PP 436s 436s Hydantoinase_B 96 lpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........RtpednlgDl 179 436s lpD+tv+tPvf +++ ++f++a+r+H++D+GGitpGsmp++++ i+eEG++i+++k+v++g+ +e+++++ll +++ Rt++dn++D+ 436s CUFF.42.1.p1 554 LPDLTVVTPVFDNNKdIIFYCAARGHMVDVGGITPGSMPSNSKAIYEEGAAIKTFKVVKAGTfDEKGLTQLLFDEPakypdcsgsRTLRDNISDV 648 436s ***********98879******************************************************************************* PP 436s 436s Hydantoinase_B 180 kAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgtspqvkg 268 436s kA+++a+++g++ +++l+ eyGl+ v++ m i++ ae+avr++l++++ + ++a dy+ddg+p++++v+id+++ a++Df+gt+p+v+g 436s CUFF.42.1.p1 649 KAMLSACHRGRSMVEKLVVEYGLDIVQRSMYGIQAAAEKAVRDVLKAFSVqnsqKPLKAIDYMDDGTPLQLEVKIDPETgdAVFDFEGTGPEVYG 743 436s *********************************************9877766777899********************99*************** PP 436s 436s Hydantoinase_B 269 niNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfgg 363 436s n+Nap a+t+s viy+lr+++++diplNeGcl+pie+++p+ ++lnpse+aavvggnv+tsqr++dv+lka++ ++Aasqg+mnnltfg 436s CUFF.42.1.p1 744 NWNAPIAITYSSVIYCLRSIINQDIPLNEGCLKPIEIRIPPSCFLNPSETAAVVGGNVLTSQRITDVILKAFS------ICAASQGCMNNLTFGY 832 436s *************************************************************************......***************7 PP 436s 436s Hydantoinase_B 364 vderggeffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserr 458 436s e+g+e f++yetiagG+GA+p+++G+s+vh+hmtntr+td+E++Err Pv+++rf lr++sgG+G+y+GGdGv+r++ef+++ +++silserr 436s CUFF.42.1.p1 833 DGENGEEGFAMYETIAGGAGAGPTWNGTSGVHTHMTNTRITDPEVVERRAPVILRRFCLRENSGGKGEYHGGDGVIRHFEFRRS-MHCSILSERR 926 436s 777779999**************************************************************************7.********** PP 436s 436s Hydantoinase_B 459 vfapwGlaGGepGargrvvlnllvr......greenlggkatvelkagdvlvietpGGGGyGd 515 436s + ap+G++GGe+Ga+g n+++ r +nlggk++v + +gd +vietpGGGGyG 436s CUFF.42.1.p1 927 SRAPYGMNGGEDGAMGV---NTWIDcsnpdfPRYVNLGGKNHVLMGKGDHIVIETPGGGGYGA 986 436s *****************...99999999999*******************************6 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (516 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 1046.58 436s // 436s Query: Hydant_A_N [M=178] 436s Accession: PF05378.12 436s Description: Hydantoinase/oxoprolinase N-terminal region 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.6e-66 214.0 1.6 1.1e-64 210.0 0.0 2.4 2 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 210.0 0.0 1.1e-66 1.1e-64 1 178 [] 4 220 .. 4 220 .. 0.98 436s 2 ! 2.4 0.6 0.0062 0.59 2 14 .. 325 337 .. 324 355 .. 0.82 436s 436s Alignments for each domain: 436s == domain 1 score: 210.0 bits; conditional E-value: 1.1e-66 436s Hydant_A_N 1 rigIDvGGTfTDavaldeke.eevavlKllst.....pdavaegirealeevleesipr.....tskidvvrmGTTvatNallerkgervaLittkg 86 436s +i+ID+GGTfTDa+a+ ++e + +v+Klls+ +da +e++r++le v+++sipr ts+i+++r+GTTvatNallerkger+a+ittkg 436s CUFF.44.1.p1 4 KIHIDRGGTFTDAIATFADEsRPPIVIKLLSEdpsnyKDASIEAVRRILEIVQGKSIPRtekldTSCINHLRCGTTVATNALLERKGERCAFITTKG 100 436s 699************998777999************************************************************************* PP 436s 436s Hydant_A_N 87 frdlleigrqnrpdlfelrikkplvlyeevvevdervead............................gevlkpldeeevrealkalkaagvesiav 155 436s f+d l ig+q+rp++fel i++p+vly++v+evderv+++ ++++k++d++++r++l+al+++g++siav 436s CUFF.44.1.p1 101 FKDGLLIGNQSRPNIFELGIRRPEVLYSKVIEVDERVTLEdyvedpmkvkttidgsdpslvvgrsgevVRIMKKVDCDALRKDLQALYDEGFTSIAV 197 436s ***************************************99******************************************************** PP 436s 436s Hydant_A_N 156 vllhSylnpehElrvaeiareig 178 436s +l+hS+++p+hEl v++ia+e+g 436s CUFF.44.1.p1 198 CLAHSFTFPDHELLVGKIAEEVG 220 436s ********************975 PP 436s 436s == domain 2 score: 2.4 bits; conditional E-value: 0.0062 436s Hydant_A_N 2 igIDvGGTfTDav 14 436s ig D+GGT TD+ 436s CUFF.44.1.p1 325 IGFDMGGTSTDVS 337 436s 899********96 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (178 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1962.72 436s // 436s Query: IBR [M=62] 436s Accession: PF01485.20 436s Description: IBR domain, a half RING-finger domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00056 12.8 2.4 0.0012 11.8 2.4 1.4 1 CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.8 2.4 1.2e-05 0.0012 10 51 .. 569 611 .. 561 613 .. 0.71 436s 436s Alignments for each domain: 436s == domain 1 score: 11.8 bits; conditional E-value: 1.2e-05 436s IBR 10 kslesdpnlkwCprpdCeaiiekseg...cksvtCskCgfefCfn 51 436s ++ ++++++ C C i ++ e ++ +Cs+C +e+C++ 436s CUFF.12.1.p1 569 TTQNNNESFAVCL--ACAIIQRSLERkklSTPTQCSSCFQEYCWD 611 436s 33455777999*9..9997776555544445578**********6 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (62 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1974.86 436s // 436s Query: Lung_7-TM_R [M=295] 436s Accession: PF06814.12 436s Description: Lung seven transmembrane receptor 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.2e-08 25.0 18.7 8e-08 24.4 18.7 1.4 1 CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 24.4 18.7 8.4e-10 8e-08 59 258 .. 80 270 .. 26 288 .. 0.83 436s 436s Alignments for each domain: 436s == domain 1 score: 24.4 bits; conditional E-value: 8.4e-10 436s Lung_7-TM_R 59 vllgilWlfilakykkdilkiqkliaavivlkmlelaf.vyieYatinskGssievlavlasilsalkktlsrlliliislGygivkpkLgdllkkvl 155 436s +l+ W++ ++ + k i++ qk+i + i+l +l++ + ie ++++s+ + ++ +++i+ l+ + rl ++ +lG+gi ++ + k l 436s CUFF.6.1.p1 80 LLFLSYWIWTCLHFSKIIFPAQKVICLYIFLFALNQTLqECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRT-----VPKYL 172 436s 466778*******************9999887776655167899999**************************************865.....66666 PP 436s 436s Lung_7-TM_R 156 llglllfvla.evlelvresseesessakllkvllfliplalldlffvvwifrsLqktlrdlklkrnlvklklYrkftvvlvisvvasviivlvekil 252 436s ++ ++ +v+a + + + ++ ++++ +i+ + ++ v+++ +L k + + n k++ +r+ +++ ++ + as + ++++i+ 436s CUFF.6.1.p1 173 MIKGISIVIAlCSVYWISLYKDVYVV-----SEIFDMIQYEVS-PAIWVYSICHLLKQCTSVTTYENASKARFFRRMLNAFIFIFCASPMLHYLSNII 264 436s 66555544441455555555444444.....689999999666.578888999********************************************9 PP 436s 436s Lung_7-TM_R 253 lktvds 258 436s + ++d+ 436s CUFF.6.1.p1 265 FGNFDY 270 436s 988775 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (295 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1459.56 436s // 436s Query: malic [M=182] 436s Accession: PF00390.18 436s Description: Malic enzyme, N-terminal domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.8e-20 66.1 0.0 2.4e-20 65.7 0.0 1.1 1 CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 65.7 0.0 2.5e-22 2.4e-20 3 76 .. 32 108 .. 30 110 .. 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: 65.7 bits; conditional E-value: 2.5e-22 436s TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGET..CHHHHHTTSS..SS..EEEEE-SS CS 436s malic 3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdke..kikeilknlp.eedvkvivvtdge 76 436s +n+tlfy+l++++l e++pi+YtPt g+a++++s++yr+++g+yl+i++++ ik++l+++ +++v++i++td+e 436s CUFF.1.1.p1 32 TNQTLFYALISQHLIEMIPIIYTPTEGDAIKQFSDIYRYPEGCYLDIDHSDlsYIKQQLSEFGkSDSVEYIIITDSE 108 436s 799*******************************************99988779********97899********97 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (182 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4904.31 436s // 436s Query: Mannosyl_trans3 [M=275] 436s Accession: PF11051.7 436s Description: Mannosyltransferase putative 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00023 13.1 1.3 0.00039 12.4 1.2 1.5 1 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.4 1.2 4.1e-06 0.00039 92 143 .. 171 223 .. 85 298 .. 0.70 436s 436s Alignments for each domain: 436s == domain 1 score: 12.4 bits; conditional E-value: 4.1e-06 436s Mannosyl_trans3 92 sFeevllLDaDnvplknpdklFese.eYkktglllw.kdrdlwkrstspkfyei 143 436s F+++ ++D+D +++kn+d++F+++ Y++ ++l + + ++++k +++ y++ 436s CUFF.51.1.p1 171 QFDKICVIDSDILIMKNIDDIFDTPyMYQQINTLNYtRLPSYTKPD-DDTVYHF 223 436s 69*********************97358888888882224443333.4444444 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (275 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1629.32 436s // 436s Query: MatE [M=161] 436s Accession: PF01554.17 436s Description: MatE 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 9e-64 206.6 23.8 7.4e-38 122.3 4.7 2.3 2 CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907( 436s 9e-64 206.6 23.8 7.4e-38 122.3 4.7 2.3 2 CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 436s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 436s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 436s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 436s CUFF.38.1.p3 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 436s 99****************************************************************************************.****** PP 436s 436s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 436s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 436s CUFF.38.1.p3 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 436s ***************************************************************86 PP 436s 436s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 436s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 436s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 436s CUFF.38.1.p3 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 436s 667789******************************************************************************************* PP 436s 436s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 436s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 436s CUFF.38.1.p3 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 436s *******************************************************99997 PP 436s 436s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 436s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 436s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 436s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 436s CUFF.39.1.p1 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 436s 99****************************************************************************************.****** PP 436s 436s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 436s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 436s CUFF.39.1.p1 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 436s ***************************************************************86 PP 436s 436s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 436s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 436s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 436s CUFF.39.1.p1 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 436s 667789******************************************************************************************* PP 436s 436s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 436s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 436s CUFF.39.1.p1 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 436s *******************************************************99997 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (161 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 22 (0.231579); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1877.52 436s // 436s Query: MDM31_MDM32 [M=525] 436s Accession: PF08118.10 436s Description: Yeast mitochondrial distribution and morphology (MDM) proteins 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00098 10.4 0.1 0.0016 9.7 0.1 1.2 1 CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 9.7 0.1 1.7e-05 0.0016 365 448 .. 134 218 .. 124 228 .. 0.68 436s 436s Alignments for each domain: 436s == domain 1 score: 9.7 bits; conditional E-value: 1.7e-05 436s MDM31_MDM32 365 eeevtskkaleeeekseelakeaks.aeeseeekeeeeekeeeeeekyvvvdlklklndvkAavPlftkdlsyvnnaliRpivay 448 436s e++++k+++ ++ +++++++a+s a++s + + + + + +++ k v ++klnd A++P ++ +s ++a Rp v++ 436s CUFF.20.1.p1 134 VEKISQKNQEARSRANSRVNSRANSrANSSVSLAGMDGSPNWKRKMKSAVFGSRVKLNDEEAQLPRNKSSVSIAEQAASRPKVSF 218 436s 33344443333333333444333330333444444555666678889999*********************************99 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (525 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4440.75 436s // 436s Query: MFS_1 [M=353] 436s Accession: PF07690.15 436s Description: Major Facilitator Superfamily 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.4e-41 135.1 27.5 1.4e-41 135.1 27.5 1.6 2 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ 436s 1.3e-39 128.6 21.0 1.3e-39 128.6 21.0 1.5 2 CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280( 436s 1.3e-23 76.0 37.2 3.5e-17 54.9 16.8 2.3 2 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s 1.8e-20 65.7 28.3 1.3e-16 53.0 19.0 2.1 2 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 135.1 27.5 5.9e-43 1.4e-41 2 349 .. 113 492 .. 112 497 .. 0.82 436s 2 ? -1.5 0.1 0.2 4.8 230 256 .. 500 529 .. 493 543 .. 0.53 436s 436s Alignments for each domain: 436s == domain 1 score: 135.1 bits; conditional E-value: 5.9e-43 436s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGl 97 436s +++++++++a+s++++ + +a++l++s +++l ++ + +g++v+slp+++lsd +Gr +++++ll+f ++ + + a+++w+l+++r++qG+ 436s CUFF.37.1.p1 113 SVITIVVTFASSVYSSGII-DIASELHSSIP-VSTLGSCtFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGV 207 436s 56889999**********9.9******5555.56666664888********************************6666645*************** PP 436s 436s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeee..... 188 436s ++++ +++++ i+d+f++ +r+ ++ + ++ lG+i+gp++g +++ s+l Wr++f+i+ i ++ ++v++++++pe++ + + +++ + 436s CUFF.37.1.p1 208 FGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFITqSYLEWRWTFWINMIWAAAVIVFVFIFFPETHEDTILDYKAKYLrkttg 304 436s ************************************************99999*********************************999999***** PP 436s 436s MFS_1 189 ..........kgtgpaplvp....awkallkdpvlwillialllfffgfsglltllplylqevlgls.glllaglllallalvgail....allagr 266 436s +++ + ++++ a +++++ p + +++ l++ +++++ + ++ +g++ g +++ +++++ +++++ ++ + + 436s CUFF.37.1.p1 305 ntayytiherERDPKNAMIQaatqAVSLIFTEPIVV-CFTLYLTVVYIINYINFEGYPIVFAKYGFNkG-EQGLSFIGVGVGIVCAGlctpFIYWHY 399 436s ******9999777777777789999********554.44444444444444444444446888899984.555555555555544444444888888 PP 436s 436s MFS_1 267 ls.dr.....lgrrrrlllallllllaalglallavt...ssavllll..vlvliGf.glgfvfpsllalasdlappeeagtasglfntagslgg 349 436s l ++ + ++ rl+ +++++l+ ++++++a+t ++ ++++ +++++Gf l ++f+s++++++++ ++a +a+++++++++ ++ 436s CUFF.37.1.p1 400 LKvNKkrngvICPEDRLYPLFIGCFLLPISMFWFAWTcypHHIHWIVPiiASAFFGFsLLIVFFVSYNYIIDSYQ--HMAPSALAAATLVRYSAS 492 436s 8766666666555************************98855555544558888***888888899888888888..999999999998877443 PP 436s 436s == domain 2 score: -1.5 bits; conditional E-value: 0.2 436s MFS_1 230 lplylqevlgls....glllaglllallalv 256 436s p+yl+ +++ g +++++++++++++ 436s CUFF.37.1.p1 500 RPMYLNLGDHWAtsvlG-FISVAMVPIPFIF 529 436s 57777777777744443.3333333333333 PP 436s 436s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 128.6 21.0 5.6e-41 1.3e-39 2 352 .. 66 429 .. 65 430 .. 0.87 436s 2 ? -2.4 0.0 0.39 9.4 282 296 .. 450 464 .. 440 476 .. 0.44 436s 436s Alignments for each domain: 436s == domain 1 score: 128.6 bits; conditional E-value: 5.6e-41 436s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlg 98 436s +++++++l+rs++g a+ ++e+l + + ++ +++++++++++ p +l+ r+ + r+l + ++++ ++l+ f ss+ l++ r++ Gl 436s CUFF.45.1.p2 66 GFLYLMAFLDRSNIGNAAVAGMTEALSLYGERLNVAVSIFYVLYILVETPSVVLVKRIKASRMLAFISFAWSMTVLFSGFMSSYGGLIATRLILGLL 162 436s 6899******************************************************999988888888888834444536666************ PP 436s 436s MFS_1 99 agalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg....Wravfyilaivsllafvlfllllpeepperkrkspkeee.. 188 436s +g+lfpa + +++ ++++e+ + +++l a+++l+ ++g l++ +l ++g W++++++ ++vs++++ l l+ lp++ + + + +e+e 436s CUFF.45.1.p2 163 EGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEqVHAGnkegWQWIYIVEGLVSFIGVPLCLFALPDKMENAWFLTREEREva 259 436s ********************************************999666669******************776555555555555555555555** PP 436s 436s MFS_1 189 ..........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275 436s +g +++++++ ++ +kdp +++ ++ +++ ++++g++++lp++ + lg+ g l++ ++ ++++g+i++l++++lsdr++ 436s CUFF.45.1.p2 260 iirrdinaryHGEQHFEWSE-VRKAFKDPKVYVSATSQFCADMVLYGFSSFLPVI-IKGLGFVG-LQTNYMTIPVYIAGVISFLFVAWLSDRTQL-- 351 436s ********************.888888888878*********************7.*******8.888889999999999************776.. PP 436s 436s MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntagslggalg 352 436s r + +++ +++a+g++++ +++s+++ + + ++i +g + ++ l ++++++ + +++ta+g+ +t+ + +g+++ 436s CUFF.45.1.p2 352 RAVYLISASTVVAVGYIIMLASDSNAAKYTATYIIAIGCYIGPGLNLGWLNNNVaGHYKRATAIGIQQTLANSSGIVA 429 436s 88889999999999999999998999999988887775555566666666665546689*********9999999987 PP 436s 436s == domain 2 score: -2.4 bits; conditional E-value: 0.39 436s MFS_1 282 lllllaalglallav 296 436s ++++++ l+++++ + 436s CUFF.45.1.p2 450 GCVIVGGLAYVVMFF 464 436s 222222222222222 PP 436s 436s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 54.9 16.8 1.5e-18 3.5e-17 2 263 .. 92 349 .. 85 361 .. 0.77 436s 2 ! 26.7 12.4 5.4e-10 1.3e-08 212 353 .] 370 516 .. 357 516 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 54.9 bits; conditional E-value: 1.5e-18 436s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGl 97 436s l + + sa+++s++++ + + +++ s i++l + a+ ++v ++lG +sd +r ++ l ll++++g ++ + + s++ + +++ v+ ++ 436s CUFF.25.1.p1 92 LACSWASAIQSSTTYSYQV-YATASFN-RTSMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIG-FIVVASsSTISAYVIGSVFISI 185 436s 5677778888888777777.8999999.88889999999******************96666************.55552446677*********** PP 436s 436s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyilaivsllafv.lfllllpeepperkrkspkeee.... 188 436s g+++l + ++ d+++ + rg++++lls+ + + + g ++ g++ +Wr+ + ++ai++ ++ +++l++ e+ ++k ++ k+ 436s CUFF.25.1.p1 186 GSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVwFTGFIVQGIID--SNWRWGYGMFAIIMPAVMTpAVIILMYLERQANKDENIKKIInyqt 280 436s *************************************666677777777..45*****999999999955533444444444444444333335577 PP 436s 436s MFS_1 189 ...kgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailall 263 436s ++ +++++ ++wka+l l+ +ll+ +g+s+ l + l++y g+++ +++ +++++ v++i+ 436s CUFF.25.1.p1 281 eekNKNKQSKWQKLWKAVLEVD----LFGLILLG-VGWSIllLPFSLTSY--AKNGWKNPSMIA--MMVVGGVILIA--Y 349 436s 77788999999999*****999....44444444.366665588888887..777777335555..77777776666..4 PP 436s 436s == domain 2 score: 26.7 bits; conditional E-value: 5.4e-10 436s MFS_1 212 llialllfffgfsg....lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallll.llaalglallavt.ssavl 302 436s +i+++++ f++++ ++++++y+ +++s + +++ + ++ ++++++ag++++ + r ++l +++l++ ++++ +l+ +++ + +v 436s CUFF.25.1.p1 370 TFITAVIIDFFYYLagylQSMYFTTYTWILYDWS-YRDWTYFNNTMTIALCVFGVFAGAMHRVFHRYKYLQIIGLVIkIVGYGILIRPNFAaTGKVD 465 436s 3444444444444445558889999999******.55555556666666666689999999998887766655555505555555555555999999 PP 436s 436s MFS_1 303 lllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353 436s l+++l+liG+g++f ++ +++ ++ ++p + + as+l ++ ++gga+g+ 436s CUFF.25.1.p1 466 LAWSLILIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGA 516 436s 999**********************************************96 PP 436s 436s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 53.0 19.0 5.4e-18 1.3e-16 23 293 .. 47 347 .. 6 350 .. 0.71 436s 2 ! 26.7 11.5 5.6e-10 1.3e-08 3 201 .. 267 475 .. 266 507 .. 0.74 436s 436s Alignments for each domain: 436s == domain 1 score: 53.0 bits; conditional E-value: 5.4e-18 436s MFS_1 23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpke 117 436s +++++ +s+ + ll+++ +g+++++++ +++++r+G + +++ +++++ lll + a ++w +lv+ +l+G+g gal ++ + ++++p++ 436s CUFF.24.1.p1 47 ISNSYSYSAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAeLLLVT-AVPSWiQVLVGKILAGVGIGALSVLSPGYQSEVAPPQ 142 436s 24444466666888999999*********************************666666.567787******************************* PP 436s 436s MFS_1 118 ergraigllsagfslGailgpllgg...llasslgWravfyilaivsllafvlfllllpeepperkrkspkeee....................... 188 436s rg +++ +++++ +a++++ + l ++Wr +f i+ + ++l++v ++l+lpe+p+ k ee 436s CUFF.24.1.p1 143 IRGAVVATYQIFSTGAALVAACINMgthKLRKTASWRTSFGINMLWGILLMV-GVLFLPESPRYLIYKGRDEEAlrimcnmaelspeseiiqtnfnt 238 436s ***********999999999888772323335555***************88.558888888888887777776*******9888887777666666 PP 436s 436s MFS_1 189 ........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrl 277 436s g+a w +++ + + +++l++ f + + + y+ +v++ +g + l +l++++++ + a + +d lgrr++l 436s CUFF.24.1.p1 239 iksdieieMAGGKA----RWIEIFGKDIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGMTDIFLPAVILGAINFGTTFGALYTIDNLGRRNPL 331 436s 65555444344444....4444555553322333333333333334444444455555555533444446777777777676666667********* PP 436s 436s MFS_1 278 llallllllaalglal 293 436s +++ ++ +++++++a 436s CUFF.24.1.p1 332 IFGAAFQSICFFIYAA 347 436s ************9986 PP 436s 436s == domain 2 score: 26.7 bits; conditional E-value: 5.6e-10 436s MFS_1 3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrl..sdrfGrrrvlllglllfalglllll.fa............s 83 436s +++fl++l r ++g ++ + ++ + ++ + +l + + lga+ + +G+l +d++Grr l++g+++ ++++++ + ++ + 436s CUFF.24.1.p1 267 CLGFLVMLFRELIGNNYYFyYATQVFKGTGMTDIFLPA-VILGAINFGTTFGALytIDNLGRRNPLIFGAAFQSICFFIYAaVGdrkliykngtsdH 362 436s 67889999999999999987888888855555555444.556666666666655569*******************555552314444455555664 PP 436s 436s MFS_1 84 slw.lllvlrvlqGlgagalf.pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178 436s +++v+ +l + +++++ p+g +++ + fp + r++ +++++g+ lG + + +++ ++g+ + ++ ++i ++ +f+ +++++++++ 436s CUFF.24.1.p1 363 RAGsVMIVFSCLFLFSYCCSWgPMGWVIVGETFPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIGFKLGYIYACINLFSSFM---IFFLAKETK 456 436s 45556777777777777666537777999*****************************************998888888888877...677677766 PP 436s 436s MFS_1 179 rkrkspkeeekgtgpaplvpawk 201 436s + +++ ++ ++++p w+ 436s CUFF.24.1.p1 457 GLTLEEVNDL---YMSNIKP-WE 475 436s 6666666663...4444444.44 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (353 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 27 (0.284211); expected 1.9 (0.02) 436s Passed bias filter: 9 (0.0947368); expected 1.9 (0.02) 436s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 436s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 4 [number of targets reported over threshold] 436s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 436s # Mc/sec: 308.90 436s // 436s Query: MFS_3 [M=522] 436s Accession: PF05977.12 436s Description: Transmembrane secretion effector 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.0022 9.0 5.5 0.0033 8.4 5.5 1.2 1 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 8.4 5.5 3.5e-05 0.0033 258 364 .. 60 168 .. 49 202 .. 0.73 436s 436s Alignments for each domain: 436s == domain 1 score: 8.4 bits; conditional E-value: 3.5e-05 436s MFS_3 258 illgalGvGAilgalllsrLRerlsser.lvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavql.avPrWvvgRalavYltvl 352 436s +l g++ +G ++ga+l+s er++++ + + v + + ll ++ ++s ++++ +l+G i als l q + P ++g ++a Y+ + 436s CUFF.24.1.p1 60 LLTGTINAGCLFGAMLSSPFTERIGKKYsICFFSGVYIIAELLLVTAVPSWIQVLVGKILAG-VGIGALSVLSPGYQSeVAPPQIRGAVVATYQIFS 155 436s 688999******************98861555666665555555555555555555555555.56********9999735699************** PP 436s 436s MFS_3 353 aGg.laaGsllWG 364 436s +G+ l a + G 436s CUFF.24.1.p1 156 TGAaLVAACINMG 168 436s 9972455555555 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (522 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2920.37 436s // 436s Query: MFS_4 [M=363] 436s Accession: PF06779.13 436s Description: Uncharacterised MFS-type transporter YbfB 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.8e-06 18.6 6.1 1.6e-05 16.9 0.5 2.7 3 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.2 0.2 0.053 5.1 146 206 .. 101 156 .. 98 157 .. 0.65 436s 2 ! 16.9 0.5 1.7e-07 1.6e-05 38 175 .. 152 288 .. 132 311 .. 0.84 436s 3 ! 4.3 0.1 0.0012 0.11 119 144 .. 374 399 .. 365 405 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: -1.2 bits; conditional E-value: 0.053 436s MFS_4 146 sasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfG 206 436s s s W+++ +s++ +++ ++ + + ++++s+p+ l +l+GfG 436s CUFF.37.1.p1 101 SHSYKWWIVIQVSVITIVVTFASSV---YSSGIIDIA--SELHSSIPVSTLGSCTFLVGFG 156 436s 5566699999999998888877665...333333333..3677777777777777777776 PP 436s 436s == domain 2 score: 16.9 bits; conditional E-value: 1.7e-07 436s MFS_4 38 ylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavs 133 436s ++G+ vG+l + ls R + ll ++ + ++++++++++++Rf Gv + + l ++ ++ ++ +r v+ + + lG +++ 436s CUFF.37.1.p1 152 LVGFGVGSLPF-APLSDIYGRFIiYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGVFGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIG 247 436s 57999999988.677888888884567778888899999*********************************************99999******** PP 436s 436s MFS_4 134 gllvllllqlglsasslWlalavlsavllllvalllpraalr 175 436s ++ ++ q l++ ++ ++ + +a++++ v++ p + ++ 436s CUFF.37.1.p1 248 PIIGDFITQSYLEWRWTFWINMIWAAAVIVFVFIFFP-ETHE 288 436s ****************977777889999999999999.3333 PP 436s 436s == domain 3 score: 4.3 bits; conditional E-value: 0.0012 436s MFS_4 119 gallfaGvGlGiavsgllvllllqlg 144 436s ++l f GvG+Gi+ +gl+ +++ + 436s CUFF.37.1.p1 374 QGLSFIGVGVGIVCAGLCTPFIYWHY 399 436s 6899*************999887665 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (363 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 1047.65 436s // 436s Query: MIP [M=227] 436s Accession: PF00230.19 436s Description: Major intrinsic protein 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.8e-51 167.6 6.0 2.3e-51 167.2 6.0 1.1 1 CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 167.2 6.0 2.4e-53 2.3e-51 6 227 .] 308 548 .. 303 548 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 167.2 bits; conditional E-value: 2.4e-53 436s HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS 436s MIP 6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllG 102 436s +f r+ +AEfl+tl+lv++gvgs+l+ +v++ + +++e+ ++a+g++ + +vy+a+giSG+H+NPavT++l+++rk++ ++++Yi Q+ G 436s CUFF.20.1.p1 308 HFFREGFAEFLGTLVLVVFGVGSNLQA--TVTN---GAGGSFESLSFAWGFGCMLGVYIAGGISGGHVNPAVTISLAIFRKFPWYKVPIYIFFQIWG 399 436s 6899******************99844..3433...34579******************************************************** PP 436s 436s HHHHHHHHHHHCHHH............HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHH CS 436s MIP 103 aivaaallklltkgl............esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgiplt 187 436s a+ + al ++ + + g + +kp+++ +a++ E+i t+vLv ++fa+ dd+++ + +++ +gll+a+i ++ +++t 436s CUFF.20.1.p1 400 AFFGGALAYGYHWSSitefeggkdirtPATGGCLYTNPKPYVTWRNAFFDEFIGTAVLVGCLFAILDDTNSPPTQGMTAFIVGLLIAAIGMALGYQT 496 436s *********99988889******9976556666678899*********************************99899******************** PP 436s 436s ST-SSHHHHHHHHHHHTH............STTTTHHHHHHHHHHHHHHHHH CS 436s MIP 188 GaamNpArslgpavvlnk............fedhwvylvGPliGailgalvY 227 436s +++NpAr+lgp+++++ + w + G + G+i+g+l+Y 436s CUFF.20.1.p1 497 SFTLNPARDLGPRMFAWWigygphsfhlyhWWWTWGAWGGTIGGGIAGGLIY 548 436s *************************98855555566788999999999**99 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (227 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3239.41 436s // 436s Query: MVP_shoulder [M=118] 436s Accession: PF11978.7 436s Description: Shoulder domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00057 12.5 0.0 0.0018 11.0 0.0 1.8 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 436s 0.00057 12.5 0.0 0.0018 11.0 0.0 1.8 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 436s 436s Alignments for each domain: 436s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 436s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 436s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 436s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 436s CUFF.60.1.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 436s 57799999**************************************9.5555555554444 PP 436s 436s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 436s 436s Alignments for each domain: 436s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 436s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 436s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 436s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 436s CUFF.60.2.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 436s 57799999**************************************9.5555555554444 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (118 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1869.66 436s // 436s Query: Na_H_Exchanger [M=381] 436s Accession: PF00999.20 436s Description: Sodium/hydrogen exchanger family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.1e-42 138.8 8.5 1.3e-42 138.5 8.5 1.1 1 CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 436s 3.7e-27 87.6 2.1 4.1e-27 87.5 2.1 1.0 1 CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414 436s 8.2e-16 50.3 1.9 1.1e-15 49.8 1.9 1.1 1 CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-58 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 138.5 8.5 4.2e-44 1.3e-42 1 198 [. 83 291 .] 83 291 .] 0.97 436s 436s Alignments for each domain: 436s == domain 1 score: 138.5 bits; conditional E-value: 4.2e-44 436s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 436s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 436s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 436s CUFF.13.2.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 436s 6889999******997799999********************99999************************************************ PP 436s 436s HHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSX CS 436s Na_H_Exchanger 87 vlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeaggetslll 178 436s ++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++++ ++ 436s CUFF.13.2.p1 178 MAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRNAGRDW 271 436s **********9**8.69***************************988889**********************************99********* PP 436s 436s HHHHHHHHHHHHHHHHHHHH CS 436s Na_H_Exchanger 179 llliflvvavgglllglvig 198 436s +ll++l+++++g+++g+vig 436s CUFF.13.2.p1 272 VLLVVLYECAFGIFFGCVIG 291 436s ******************97 PP 436s 436s >> CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414-1770(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 87.5 2.1 1.3e-28 4.1e-27 82 198 .. 1 119 [] 1 119 [] 0.97 436s 436s Alignments for each domain: 436s == domain 1 score: 87.5 bits; conditional E-value: 1.3e-28 436s HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTS CS 436s Na_H_Exchanger 82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeagge 173 436s ++l++++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++ 436s CUFF.13.1.p2 1 MLLPVMAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRN 94 436s 67999*******9999998.79***************************988889**********************************99**** PP 436s 436s SSTSXHHHHHHHHHHHHHHHHHHHH CS 436s Na_H_Exchanger 174 tslllllliflvvavgglllglvig 198 436s ++ +++ll++l+++++g+++g+vig 436s CUFF.13.1.p2 95 AGRDWVLLVVLYECAFGIFFGCVIG 119 436s ***********************97 PP 436s 436s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 49.8 1.9 3.6e-17 1.1e-15 1 93 [. 83 184 .. 83 185 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 49.8 bits; conditional E-value: 3.6e-17 436s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 436s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 436s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 436s CUFF.13.3.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 436s 6889999******997799999********************99999************************************************ PP 436s 436s HHHHHHH CS 436s Na_H_Exchanger 87 vlitvvl 93 436s ++ +++ 436s CUFF.13.3.p1 178 MAYGWIF 184 436s ****987 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (381 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 3 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2771.74 436s // 436s Query: NEMO [M=68] 436s Accession: PF11577.7 436s Description: NF-kappa-B essential modulator NEMO 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00049 12.8 0.0 0.0014 11.3 0.0 1.7 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.3 0.0 1.5e-05 0.0014 22 55 .. 54 87 .. 50 98 .. 0.93 436s 436s Alignments for each domain: 436s == domain 1 score: 11.3 bits; conditional E-value: 1.5e-05 436s NEMO 22 lkqsNqalkeRlEeLsawqekqkeerefleeklr 55 436s lk N++lk+R+ e s ++ ee f + klr 436s CUFF.54.1.p1 54 LKNANDSLKGRILEVSLADLQKDEEHSFRKVKLR 87 436s 89**************************999998 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (68 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2557.48 436s // 436s Query: Nucleotid_trans [M=212] 436s Accession: PF03407.15 436s Description: Nucleotide-diphospho-sugar transferase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.4e-05 15.8 0.0 9.9e-05 15.0 0.0 1.4 1 CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 15.0 0.0 1e-06 9.9e-05 106 189 .. 238 318 .. 210 333 .. 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 15.0 bits; conditional E-value: 1e-06 436s Nucleotid_trans 106 desknliNsGfffvrateatkallkkwaeelase.sglw.DqdvfnlllregaakesglkvrvLdtalfvngkgyfvq.vrdeeevk 189 436s ++++n +N G + +r+++at +l+ w + + +e +++ +qd++ +l + + + v++++++++ + f + ++ e+ k 436s CUFF.51.1.p2 238 SQDHNGLNAGSILFRNSPATALFLDIWTDPVVAEcAKANnEQDMLGYLISKHSQ--LASLVGLIPQRKI----NAFHEgPENMEWQK 318 436s 4567888************************999855556*********99664..8888999999999....77777655555554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (212 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4330.32 436s // 436s Query: Oleosin [M=113] 436s Accession: PF01277.16 436s Description: Oleosin 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s ------ inclusion threshold ------ 436s 0.037 6.4 6.6 0.007 8.8 1.0 2.3 3 CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -2.3 0.0 0.21 20 87 107 .. 57 77 .. 47 82 .. 0.60 436s 2 ? -0.2 0.1 0.045 4.3 35 46 .. 107 118 .. 104 127 .. 0.85 436s 3 ? 8.8 1.0 7.4e-05 0.007 41 63 .. 141 163 .. 140 167 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: -2.3 bits; conditional E-value: 0.21 436s Oleosin 87 gadqldqakrrlaekasevke 107 436s +++++ k++++ k++++ke 436s CUFF.5.1.p1 57 FTNTIKPQKDKMNIKTNKIKE 77 436s 455555666666666666655 PP 436s 436s == domain 2 score: -0.2 bits; conditional E-value: 0.045 436s Oleosin 35 tPllvlfSPvlv 46 436s Pll++ S ++v 436s CUFF.5.1.p1 107 WPLLIIWSIIIV 118 436s 69*****99998 PP 436s 436s == domain 3 score: 8.8 bits; conditional E-value: 7.4e-05 436s Oleosin 41 fSPvlvPaaivialavagflasg 63 436s +S ++vP+ai + l+v ++l+ 436s CUFF.5.1.p1 141 YSEIWVPIAIYVCLLVLMLLSLI 163 436s 688*************9999864 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (113 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3257.19 436s // 436s Query: Orthopox_A5L [M=271] 436s Accession: PF06193.10 436s Description: Orthopoxvirus A5L protein-like 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.0058 8.6 4.9 0.008 8.2 4.9 1.2 1 CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-88 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 8.2 4.9 8.4e-05 0.008 146 192 .. 3 49 .. 1 92 [. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 8.2 bits; conditional E-value: 8.4e-05 436s Orthopox_A5L 146 ttpstqpsqtlPtttcvrqsdasistttdivtppqppivatvctptP 192 436s t t s tlP tt q+ +++s t +iv+p + p t + 436s CUFF.11.1.p1 3 TVTETITSGTLPFTTTLAQASGTVSGTVEIVSPKNNPTTVYSGTVAT 49 436s 56678899*************************98886543322222 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (271 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4879.25 436s // 436s Query: Oxidored_FMN [M=341] 436s Accession: PF00724.19 436s Description: NADH:flavin oxidoreductase / NADH oxidase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.2e-138 453.2 0.0 3.6e-138 453.0 0.0 1.0 1 CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080( 436s 1e-136 448.2 0.0 1.1e-136 448.0 0.0 1.0 1 CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843( 436s 1e-136 448.2 0.0 1.1e-136 448.0 0.0 1.0 1 CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 453.0 0.0 1.1e-139 3.6e-138 1 341 [] 12 360 .. 12 360 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 453.0 bits; conditional E-value: 1.1e-139 436s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 436s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 436s kLF+Pik+gn++L++R+v+ap+trlr+ ++g v++dl++eYy+qrs+ipgtl+ite++f+++ksggf+n p++++de++e+wk++++a+h+n++f++ 436s CUFF.52.1.p1 12 KLFQPIKVGNMQLQHRMVHAPATRLRCLDNGLVMTDLVKEYYKQRSSIPGTLLITESLFSGAKSGGFSNIPCLYNDEHVEAWKPIVQAIHDNDCFVF 108 436s 7************************************************************************************************ PP 436s 436s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 436s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 436s +q+w+l++e+k++yl+d+e ++p+dp++l+a+ ++g+el k++tk++i+e+i++y+eAAkra+ +G+DgVe+h++nG+Lld+ 436s CUFF.52.1.p1 109 IQFWNLPGELKVDYLEDQErlekvtqGECPMDPTGLPAALGsaysICGEELyvdKFMTKQDIQEHITTYTEAAKRAVFgCGADGVEVHQVNGFLLDK 205 436s *************************99************99999999999999******************************************** PP 436s 436s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 436s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 436s F+ +++++++D+++ Gs+enRarF+le++++v++a+g+ervgyR+Sp+++++k++d++e+ +++++k++++r++ +la++h++epr++++g+v+ 436s CUFF.52.1.p1 206 FVLNGYGDKCDPEYcGSLENRARFCLELLESVVNAIGQERVGYRISPFSDIWKDKDSFEA--HVFMIKKIKERFP---NLAYLHAIEPRQYWNGHVH 297 436s ************************************************************..*************...******************* PP 436s 436s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 436s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 436s ++q+ kn+ ++k++w +p+it+G++d+++ a+++a++e+tlvafgR+fl++pdl+++lk+++pln 436s CUFF.52.1.p1 298 ITQE-KNTLIYKNLWGDPFITAGGHDRDS--AIQMAEQENTLVAFGRYFLSNPDLPFRLKYNLPLN 360 436s **66.************************..********************************997 PP 436s 436s >> CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 436s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 436s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 436s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 436s CUFF.48.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 436s 69*****************************.9999************************************************************* PP 436s 436s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 436s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 436s +q+w l++++k+ey++d e +d+p+dp +l+a ++ ++g e+ k+++k++i+e+iq++v+AA++a++ A++DgVeih++nG+Lld+ 436s CUFF.48.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 436s *************************9***************9999888888999******************************************* PP 436s 436s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 436s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 436s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 436s CUFF.48.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 436s ************************************************************..*************...******************* PP 436s 436s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 436s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 436s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 436s CUFF.48.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 436s **66.9**********************9..********************************987 PP 436s 436s >> CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 436s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 436s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 436s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 436s CUFF.49.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 436s 69*****************************.9999************************************************************* PP 436s 436s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 436s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 436s +q+w l++++k+ey++d e +d+p+dp +l+a ++ ++g e+ k+++k++i+e+iq++v+AA++a++ A++DgVeih++nG+Lld+ 436s CUFF.49.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 436s *************************9***************9999888888999******************************************* PP 436s 436s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 436s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 436s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 436s CUFF.49.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 436s ************************************************************..*************...******************* PP 436s 436s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 436s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 436s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 436s CUFF.49.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 436s **66.9**********************9..********************************987 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (341 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 3 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1478.30 436s // 436s Query: Pantoate_ligase [M=266] 436s Accession: PF02569.14 436s Description: Pantoate-beta-alanine ligase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.3e-104 341.7 0.0 1.4e-104 341.6 0.0 1.0 1 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 341.6 0.0 1.5e-106 1.4e-104 4 265 .. 5 278 .. 2 279 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 341.6 bits; conditional E-value: 1.5e-106 436s -SHHHHHHHHHHHHHTT-EEEEEEE-SS--HHHHHHHHHHHHHSSEEEEEE---GGGSSTTSCTTTS---HHHHHHHHHHTT-SEEE---HHHH CS 436s Pantoate_ligase 4 ktvaelrellkelrkegkkvglVpTmGaLHeGHlsLvkaakeendvvvvSiFvNplqFgpkedlekYPrtleaDlelleeagvdlvFaPsveem 97 436s k+ ++++++++rk+g+++++VpTmG+LHeGH sLv++ak+++++vvvSiFvNp+qF++ +dl YPrt+++D+++l+++gvdlv+aP+vee+ 436s CUFF.50.1.p2 5 KEKLLIHQQVDNWRKDGNRIAFVPTMGNLHEGHFSLVREAKRHAEKVVVSIFVNPMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYAPTVEEL 98 436s 55566788999***9999**************************************************************************** PP 436s 436s ST......EEEEECSGGCSTHHHHSTTHHHHHHHHHHHHHHHH--SEEEEEGGGHHHHHHHHHHHHHTT-SSEEEEE-XXBXTTSXBXXGGGGG CS 436s Pantoate_ligase 98 yp......tevevkelsevlegasrpghFrGVatvvtkLfnivqpdrayfGqKDaqqlavirrlvkdlnlpveivavpivReedgLAlSSRNky 185 436s yp t v+v++ls++legasrpghFrGV+tvv+kLf+iv+pd+a+fG+KD+qq+a+i+++v+dln+ +ei++vpivR++dgLAlSSRN y 436s CUFF.50.1.p2 99 YPegsqdiTFVDVPKLSTMLEGASRPGHFRGVTTVVSKLFHIVNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQVPIVRADDGLALSSRNGY 192 436s ********99************************************************************************************ PP 436s 436s SXHHHHHHTTHHHHHHHHHH........BHHHHHHHHHHHHHTHTTEEEEEEEEEETTTSSX.BSSBXSEEEEEEEEEETTEEEEEEE CS 436s Pantoate_ligase 186 LseeerkaAlvlykaLkaak........eaealkeaakeeleeeelekadyveivdaetleeleleeekkavllvaakvgkvrLiDni 265 436s L++eerk A++lyk+Lk+++ + e+l +++++el++ ++ d +ei+d++tle+++ + +k++v+l+aa++gk+rLiDni 436s CUFF.50.1.p2 193 LTSEERKIAPNLYKILKKLAqelsngngDLEKLIAETNTELSRCRFI-PDQLEICDSTTLEPFT-AGTKNVVILAAAWLGKARLIDNI 278 436s *******************9555555444444445555555544433.5***********9964.55588*****************8 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (266 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3482.13 436s // 436s Query: Pantoate_transf [M=259] 436s Accession: PF02548.14 436s Description: Ketopantoate hydroxymethyltransferase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.2e-104 341.9 0.0 1.3e-104 341.7 0.0 1.0 1 CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 436s 7.2e-98 319.6 0.0 8.1e-98 319.5 0.0 1.0 1 CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 341.7 0.0 2.8e-106 1.3e-104 2 258 .. 6 261 .. 5 262 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 341.7 bits; conditional E-value: 2.8e-106 436s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 436s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 436s CUFF.50.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 436s 79*************************************************************************************.99**** PP 436s 436s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 436s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 436s CUFF.50.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 436s *********9.********99866********************************************************************** PP 436s 436s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPa 258 436s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ a +i++a+++Y+ ev++g +Pa 436s CUFF.50.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLSGAGDIRTAIQRYIYEVEQGLYPA 261 436s *********************************************************************8 PP 436s 436s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 319.5 0.0 1.7e-99 8.1e-98 2 235 .. 6 238 .. 5 240 .] 0.98 436s 436s Alignments for each domain: 436s == domain 1 score: 319.5 bits; conditional E-value: 1.7e-99 436s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 436s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 436s CUFF.52.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 436s 79*************************************************************************************.99**** PP 436s 436s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 436s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 436s CUFF.52.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 436s *********9.********99866********************************************************************** PP 436s 436s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyae 235 436s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ 436s CUFF.52.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLS 238 436s ********************************************986 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (259 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2928.99 436s // 436s Query: Phosphodiest [M=357] 436s Accession: PF01663.21 436s Description: Type I phosphodiesterase / nucleotide pyrophosphatase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.1e-16 53.9 2.6 1.5e-12 40.3 0.1 2.1 2 CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 13.6 0.3 2e-06 0.00019 1 59 [. 48 108 .. 48 116 .. 0.87 436s 2 ! 40.3 0.1 1.6e-14 1.5e-12 143 237 .. 166 261 .. 117 275 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 13.6 bits; conditional E-value: 2e-06 436s EEEEEETT-BCCHHHHCGGTSHHHHHHHHHSEEESE..EE-SSS-SHHHHHHHHHHSS-HH CS 436s Phosphodiest 1 vlvislDGlradlldrlaellpnlaaLakegvsapn..lrpvfPtlTfpnhaslvTGlyPg 59 436s v+++ +D lrad ++ ++ +p+ ++L+ +++++ + Pt+T+p + +l TG+ Pg 436s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGfsAFARSPTVTMPRLKALTTGTIPG 108 436s 7999***********9448*********977666643488889***************997 PP 436s 436s == domain 2 score: 40.3 bits; conditional E-value: 1.6e-14 436s THHHHHHHHHHCHHHHCHTHCHHHHHTT.TSECEEEEEEEHHHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEE....EEEEES--- CS 436s Phosphodiest 143 pledkvdkavlqtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetn....iilvSDHGm 234 436s ++ ++v + ++++f +++l+ +l +d l++++ ++D++gH +Gp sp ++ +l ++D i +++++l+e +++tn i+l +DHGm 436s CUFF.53.1.p1 166 SFFVSDYTEVD-NNVTRNF-DHALPSSLsHSWDALILHYLGVDHIGHLYGPSSPLLNIKLLEIDTIISRIYKYLQEY--DEKTNthslIVLCGDHGM 258 436s 33332223344.4478888.568888889**********************************************98..444444466********* PP 436s 436s EE- CS 436s Phosphodiest 235 adv 237 436s ++v 436s CUFF.53.1.p1 259 NEV 261 436s 998 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (357 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 1402.46 436s // 436s Query: PLA2_B [M=491] 436s Accession: PF01735.17 436s Description: Lysophospholipase catalytic domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.4e-206 677.9 1.8 4.2e-206 677.6 1.8 1.1 1 CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 677.6 1.8 4.4e-208 4.2e-206 1 490 [. 132 614 .. 132 615 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 677.6 bits; conditional E-value: 4.4e-208 436s PLA2_B 1 iaiavSGGGyramltgaGvlkAldsRtdnatglgGlLqsatYlaGlsGgsWlvgslavNnftsvqellkkkeedsvwdlensivnpeglnlvknikr 97 436s ++ia+SGGG+ram++g+G+ +A+dsR + + l+GlLqsa+Y++GlsGgsWlvgs+a+Nnft+++ l++ +vw+le+s+++p+g n+++n+++ 436s CUFF.12.1.p1 132 LGIAFSGGGLRAMVNGGGAFNAFDSRFESDSPLSGLLQSAMYISGLSGGSWLVGSVAINNFTNITYLRD-----NVWNLEHSVFAPHGDNVIENLNY 223 436s 69*******************************************************************.....8********************** PP 436s 436s PLA2_B 98 yeeivdevekKksagfnvsltDiwGralseklveleegganltlsslkdaekfqnaemplPiivadgrkpgesvinlNatvfEfsPyelgswdakln 194 436s y+++ +e+++Kk+agf+ sltD+wGrals+klv++e+gg+ +t+ss++++++fqna++p+Piivad+r ++e++i +N+++fEf+ ye+g+wd++++ 436s CUFF.12.1.p1 224 YNDLRKEIDQKKHAGFDCSLTDLWGRALSRKLVDAERGGPGITYSSMRNQSWFQNADYPYPIIVADSRLEEETAIPANTSIFEFTAYEFGTWDNGIK 320 436s ************************************************************************************************* PP 436s 436s PLA2_B 195 sFvdvkylGtklsnGtvvkkgkcvagfdnaGflmgtsstlFnevlleinstsmlesllkellkkllkdlsedsediaqyapnpfkdaeeenqnatqs 291 436s +F++++y+Gt+l +G+++ +++c++++dnaGf+mgts+tlFn++ll++n++ +++ +++l+ +l+dls+ ++dia y+ np++++++ n+ + ++ 436s CUFF.12.1.p1 321 AFIPMEYVGTHLLDGVPP-DKSCIHNYDNAGFVMGTSATLFNSFLLDWNENVKKNDTYYDILHAILEDLSKHQDDIAPYP-NPYQNYTTSNTSVVNA 415 436s ******************.*********************************9**************************9.**************** PP 436s 436s PLA2_B 292 ivesktLdlvdggedgqniplvpllqkerkvdvifaldssadteeswpdgsslvktyeRvle...ssqvkgkkfpyvpdqntfvnlgLnkrptffGc 385 436s ++ +t+dlvdgged +nipl+pll+++r vdv+fa+ds+++ + wp gss+v+tyeRv++ +++v++++fpy+pd+nt+++lgLn+rptffGc 436s CUFF.12.1.p1 416 FEPYDTIDLVDGGEDRENIPLWPLLHPQRFVDVVFAIDSTYNDPYGWPLGSSIVATYERVVTfnaNKSVDVRGFPYIPDENTIISLGLNTRPTFFGC 512 436s ************************************************************999889999**************************** PP 436s 436s PLA2_B 386 DarnltdlsatvdestpPlvvylpnekytylsnlstfklsykdseregliengfeaatqdnekdddefaacvacaiirRklerknittpseckkcFe 482 436s D++n+t++++ vd++tpPl+vy+pn+++ty+sn+stf++s++d++ +g++en+f ++tq+n +++fa+c+acaii+R+lerk ++tp +c++cF+ 436s CUFF.12.1.p1 513 DGKNTTAGNHDVDNNTPPLLVYFPNYPWTYYSNISTFTMSMDDKMANGILENAFMSTTQNN---NESFAVCLACAIIQRSLERKKLSTPTQCSSCFQ 606 436s ************************************************************9...9******************************** PP 436s 436s PLA2_B 483 nycwngtv 490 436s +ycw+gt+ 436s CUFF.12.1.p1 607 EYCWDGTL 614 436s ******97 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (491 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2187.19 436s // 436s Query: Polysacc_synt_C [M=142] 436s Accession: PF14667.5 436s Description: Polysaccharide biosynthesis C-terminal domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.7e-09 30.5 3.6 1.7e-09 30.5 3.6 4.0 4 CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907( 436s 1.7e-09 30.5 3.6 1.7e-09 30.5 3.6 4.0 4 CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 436s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 436s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 436s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: -1.8 bits; conditional E-value: 0.34 436s Polysacc_synt_C 13 slstvlssiLqglg 26 436s +++ ++++ L++lg 436s CUFF.38.1.p3 51 YMFAMSTGWLIALG 64 436s 33333333333332 PP 436s 436s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 436s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 436s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 436s CUFF.38.1.p3 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 436s 7899999999999999*********************************8883357******************99999999999889955555 PP 436s 436s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 436s l p++ ++giv++ ++ +++ 436s CUFF.38.1.p3 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 436s 4444666666666666555555555543 PP 436s 436s == domain 3 score: -0.6 bits; conditional E-value: 0.14 436s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 436s +l gl+ +a +a +++v+vg ++ + + 436s CUFF.38.1.p3 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 436s 33333333331111335555555555555544 PP 436s 436s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 436s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 436s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 436s CUFF.38.1.p3 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 436s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 436s 436s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 436s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 436s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 436s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: -1.8 bits; conditional E-value: 0.34 436s Polysacc_synt_C 13 slstvlssiLqglg 26 436s +++ ++++ L++lg 436s CUFF.39.1.p1 51 YMFAMSTGWLIALG 64 436s 33333333333332 PP 436s 436s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 436s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 436s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 436s CUFF.39.1.p1 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 436s 7899999999999999*********************************8883357******************99999999999889955555 PP 436s 436s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 436s l p++ ++giv++ ++ +++ 436s CUFF.39.1.p1 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 436s 4444666666666666555555555543 PP 436s 436s == domain 3 score: -0.6 bits; conditional E-value: 0.14 436s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 436s +l gl+ +a +a +++v+vg ++ + + 436s CUFF.39.1.p1 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 436s 33333333331111335555555555555544 PP 436s 436s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 436s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 436s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 436s CUFF.39.1.p1 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 436s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (142 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 18 (0.189474); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 365.16 436s // 436s Query: Pombe_5TM [M=256] 436s Accession: PF09437.9 436s Description: Pombe specific 5TM protein 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.6e-158 516.6 19.2 9.1e-158 516.1 19.2 1.2 1 CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 516.1 19.2 9.6e-160 9.1e-158 15 256 .] 1 242 [. 1 242 [. 1.00 436s 436s Alignments for each domain: 436s == domain 1 score: 516.1 bits; conditional E-value: 9.6e-160 436s Pombe_5TM 15 sfaysgnsesvlvgenitsirktllinetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 112 436s sfaysgnsesv++genitsi+kt+linetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 436s CUFF.6.1.p1 1 SFAYSGNSESVWTGENITSIWKTILINETGSYCVAARPMTMDGAEFNLDLMGYSVSEDQINNDEIGIWNYISVAEMGGVLLFLSYWIWTCLHFSKIIF 98 436s 8************************************************************************************************* PP 436s 436s Pombe_5TM 113 paqkviclyiflfalnqtlqekieeyvfssevikyrkfysvyeiidflrtnfyrlfviycalgigiirtvskylvikgisivialesvyrislkkdvy 210 436s paqkviclyiflfalnqtlqe+ieeyvfsse+ikyr+fysvyeiidflrtnfyrlfviycalg+gi+rtv+kyl+ikgisivial+svy+isl+kdvy 436s CUFF.6.1.p1 99 PAQKVICLYIFLFALNQTLQECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRTVPKYLMIKGISIVIALCSVYWISLYKDVY 196 436s ************************************************************************************************** PP 436s 436s Pombe_5TM 211 vvseifdliqyevfpaiwvysichllkqctsvttyenaskarfirr 256 436s vvseifd+iqyev paiwvysichllkqctsvttyenaskarf+rr 436s CUFF.6.1.p1 197 VVSEIFDMIQYEVSPAIWVYSICHLLKQCTSVTTYENASKARFFRR 242 436s *********************************************8 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (256 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2873.70 436s // 436s Query: PsbN [M=43] 436s Accession: PF02468.14 436s Description: Photosystem II reaction centre N protein (psbN) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00014 14.3 0.0 0.00043 12.8 0.0 1.9 1 CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-58 436s 0.00021 13.8 0.0 0.00075 12.0 0.0 2.0 1 CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.8 0.0 9e-06 0.00043 27 43 .] 118 136 .. 106 136 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: 12.8 bits; conditional E-value: 9e-06 436s PsbN 27 FGPPskeLaDPF..edHED 43 436s FGP +++L DPF dH D 436s CUFF.13.3.p1 118 FGPHAAKLVDPFswGDHGD 136 436s ***********84469988 PP 436s 436s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.0 0.0 1.6e-05 0.00075 27 43 .] 118 136 .. 107 136 .. 0.84 436s 436s Alignments for each domain: 436s == domain 1 score: 12.0 bits; conditional E-value: 1.6e-05 436s PsbN 27 FGPPskeLaDPF..edHED 43 436s FGP +++L DPF dH D 436s CUFF.13.2.p1 118 FGPHAAKLVDPFswGDHGD 136 436s ***********84469988 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (43 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1662.83 436s // 436s Query: REPA_OB_2 [M=98] 436s Accession: PF16900.4 436s Description: Replication protein A OB domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00048 12.7 0.0 0.00085 11.9 0.0 1.4 1 CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899( 436s 0.00048 12.7 0.0 0.00085 11.9 0.0 1.4 1 CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 436s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 436s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 436s CUFF.40.1.p3 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 436s 689999****555554444444367789**********************9875 PP 436s 436s >> CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 436s 436s Alignments for each domain: 436s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 436s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 436s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 436s CUFF.41.1.p2 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 436s 689999****555554444444367789**********************9875 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (98 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2725.14 436s // 436s Query: Ribosomal_S3Ae [M=205] 436s Accession: PF01015.17 436s Description: Ribosomal S3Ae family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4e-93 303.3 3.9 4.7e-93 303.1 3.9 1.0 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 303.1 3.9 5e-95 4.7e-93 2 205 .] 16 221 .. 15 221 .. 0.99 436s 436s Alignments for each domain: 436s == domain 1 score: 303.1 bits; conditional E-value: 5e-95 436s S----S-TTSSEEEEEEE--TTSSSSEECEEEEE--BTTC-SCCCHCC-EEEEESHCCCTTCCCSS-EEEEEEEEEETT.EEEEEEEEE--HHHH CS 436s Ribosomal_S3Ae 2 kkkkvvDkfkkKeWydvkaPalfgkreiGktlvtrtqgtkiaseglkgrvvevslaDLtndeeqafrklklkiedvqgk.altnFhgmeltrDkl 95 436s kk+vvD+f++K+Wyd+kaPa+f+ +++Gktlv+rt+g k+a+++lkgr++evslaDL++dee++frk+kl++ed+qgk +lt+F+g ++t+Dkl 436s CUFF.54.1.p1 16 IKKRVVDPFSRKDWYDIKAPAFFEVKNVGKTLVNRTAGLKNANDSLKGRILEVSLADLQKDEEHSFRKVKLRVEDIQGKsCLTSFNGFDMTSDKL 110 436s 599***********************************************************99******************************* PP 436s 436s HHC--CTB-EEEEEEEEEETTTEEEEEEEEEEE--TGCGS.S-B---HHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHCTTHHHHHHHHHHTTTS CS 436s Ribosomal_S3Ae 96 rslvrkwsslIeaivdvkttDgyllrvfvvafTkkrenqk.ktsyakssqvkaIrkkmveilteeaseldlkelvkklipesigkeiekeakkIy 189 436s rslvrkw+s+Iea+ ++kttDgyl r+fv++fT +r nq+ kt+ya+ssq++aI++km+++++++a+ +++kelv+klipe ig+ iek++++Iy 436s CUFF.54.1.p1 111 RSLVRKWQSTIEANQTIKTTDGYLCRIFVIGFTSRRVNQVkKTTYAQSSQIRAIHQKMFQVIQNQANGCSMKELVQKLIPEVIGRAIEKATNNIY 205 436s *********************************************************************************************** PP 436s 436s -EEEEEEEEEEEEE-- CS 436s Ribosomal_S3Ae 190 plrnveirKvkvlkkP 205 436s pl+nv++rKvk+lk+P 436s CUFF.54.1.p1 206 PLQNVFVRKVKILKAP 221 436s **************98 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (205 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3539.87 436s // 436s Query: Ribosomal_S6e [M=126] 436s Accession: PF01092.18 436s Description: Ribosomal protein S6e 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.6e-62 200.2 0.0 6.2e-62 199.8 0.0 1.2 1 CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 199.8 0.0 6.5e-64 6.2e-62 1 126 [] 11 136 .. 11 136 .. 1.00 436s 436s Alignments for each domain: 436s == domain 1 score: 199.8 bits; conditional E-value: 6.5e-64 436s -EEEEEETTTTEEEEEE---HHHHTTCTT-BSSEEEESTTT-SSS-S-EEEEEEEEESCC-BB-TT--SSSEEEEEE-TTSSS---SSSS--EEEE CS 436s Ribosomal_S6e 1 mklnisdpatgkqklievddekklrtfiekrigeevdgdalgeelkgyvlkitggsdkqGfpmkqgvlthgrvrlLlskggsgyrprrkGerkrks 96 436s mklnis+pa+g+qklie+dd+++lr f+ekr+g+ev gd++g+e++gyv+kitgg+dkqGfpm qgvl ++rvrlLl+ g+++yrprr+Gerkrks 436s CUFF.58.1.p1 11 MKLNISYPANGTQKLIEIDDDRRLRVFMEKRMGQEVPGDSVGPEFAGYVFKITGGNDKQGFPMFQGVLLPHRVRLLLRAGHPCYRPRRDGERKRKS 106 436s 9*********************************************************************************************** PP 436s 436s EE-SB--SSEEEEEEEEEE--SS--TTSSS CS 436s Ribosomal_S6e 97 vrgcivsadlsvlnlvivkkgekdiegLtd 126 436s vrgciv +dl+vl l i+k+ge+di+gLtd 436s CUFF.58.1.p1 107 VRGCIVGQDLAVLALAIIKQGEQDIPGLTD 136 436s *****************************8 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (126 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4338.71 436s // 436s Query: RNA_POL_M_15KD [M=36] 436s Accession: PF02150.15 436s Description: RNA polymerases M/15 Kd subunit 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.2e-05 16.1 0.0 0.0043 9.6 0.0 2.4 2 CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 9.6 0.0 4.5e-05 0.0043 19 33 .. 56 70 .. 53 72 .. 0.78 436s 2 ! 4.0 0.0 0.0026 0.24 8 24 .. 112 128 .. 109 130 .. 0.87 436s 436s Alignments for each domain: 436s == domain 1 score: 9.6 bits; conditional E-value: 4.5e-05 436s STEEEETTSS-EEES CS 436s RNA_POL_M_15KD 19 gknfeCrqCgYeepa 33 436s +k++ C+qC+ +epa 436s CUFF.7.1.p1 56 NKVLRCSQCDWHEPA 70 436s 33466*********8 PP 436s 436s == domain 2 score: 4.0 bits; conditional E-value: 0.0026 436s TSBEEEEECSSSTEEEE CS 436s RNA_POL_M_15KD 8 gNlLlpkedkegknfeC 24 436s Nl l+k+++eg++f C 436s CUFF.7.1.p1 112 QNLFLSKSKEEGVIFLC 128 436s 59**********99988 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (36 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1471.71 436s // 436s Query: SAUGI [M=111] 436s Accession: PF06106.10 436s Description: S. aureus uracil DNA glycosylase inhibitor 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00064 12.5 0.8 0.062 6.1 0.1 2.1 2 CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) 436s 0.00064 12.5 0.8 0.062 6.1 0.1 2.1 2 CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 436s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 436s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 436s y ++ n ++i g +nhf ++++ 436s CUFF.26.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 436s 4666788999***********998754 PP 436s 436s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 436s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 436s +n + + i+ lm+an l s+ +l h+ + + 436s CUFF.26.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 436s 555566667764269**************997654 PP 436s 436s >> CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 436s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 436s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 436s y ++ n ++i g +nhf ++++ 436s CUFF.27.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 436s 4666788999***********998754 PP 436s 436s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 436s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 436s +n + + i+ lm+an l s+ +l h+ + + 436s CUFF.27.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 436s 555566667764269**************997654 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (111 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 788.24 436s // 436s Query: Smim3 [M=60] 436s Accession: PF17307.1 436s Description: Small integral membrane protein 3 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00099 11.3 0.5 0.068 5.4 0.1 2.5 2 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 3.5 0.0 0.0027 0.26 12 33 .. 11 32 .. 2 35 .. 0.70 436s 2 ! 5.4 0.1 0.00072 0.068 42 56 .. 88 102 .. 85 106 .. 0.89 436s 436s Alignments for each domain: 436s == domain 1 score: 3.5 bits; conditional E-value: 0.0027 436s Smim3 12 vLPkhiLDiWvivLiiLativi 33 436s LP++ ++ +vLii+ t ++ 436s CUFF.51.1.p1 11 SLPRYKFLLFSVVLIIVMTTLV 32 436s 5677777777788877766555 PP 436s 436s == domain 2 score: 5.4 bits; conditional E-value: 0.00072 436s Smim3 42 ataviiYRvrthPvl 56 436s at v+i+R++ hP+ 436s CUFF.51.1.p1 88 ATRVLIHRLKYHPTT 102 436s 9************85 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (60 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2253.68 436s // 436s Query: SnoaL [M=126] 436s Accession: PF07366.11 436s Description: SnoaL-like polyketide cyclase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.7e-08 25.3 0.2 4.1e-07 22.5 0.1 2.1 2 CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 5.8 0.0 0.00065 0.062 45 64 .. 7 26 .. 3 28 .. 0.89 436s 2 ! 22.5 0.1 4.3e-09 4.1e-07 5 110 .. 14 107 .. 9 114 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 5.8 bits; conditional E-value: 0.00065 436s HHHHHHHHHCTTCEEEEEEE CS 436s SnoaL 45 afveelfkafPDlkvevedl 64 436s f+++lfkaf D++++ve+l 436s CUFF.36.1.p1 7 SFIRQLFKAFTDFSTDVESL 26 436s 5889*************986 PP 436s 436s == domain 2 score: 22.5 bits; conditional E-value: 4.3e-09 436s HHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE-TT-EEEEEEEE CS 436s SnoaL 5 rfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGipptGkkvkfeeit 101 436s ++++++ s d++ l+ ++++d+ + ++++ l++f ++++l++ + l ++v+++v++g k+a+ + + i +G + +++ i 436s CUFF.36.1.p1 14 KAFTDF--STDVESLRGFLTPDYRQL--VDGRELTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIA--------HAIRSSGESSRIKVIA 98 436s 556666..779***********9988..559**********************************99998885........56999*********** PP 436s 436s EEEEETTEE CS 436s SnoaL 102 llrvedGkI 110 436s ++ ++dG+I 436s CUFF.36.1.p1 99 FYSFKDGRI 107 436s ********9 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (126 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1322.61 436s // 436s Query: SnoaL_2 [M=102] 436s Accession: PF12680.6 436s Description: SnoaL-like domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.7e-12 38.7 0.0 8.1e-12 38.4 0.0 1.1 1 CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 38.4 0.0 8.5e-14 8.1e-12 2 100 .. 10 108 .. 9 110 .. 0.92 436s 436s Alignments for each domain: 436s == domain 1 score: 38.4 bits; conditional E-value: 8.5e-14 436s HHHHHHHH..TTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEET CS 436s SnoaL_2 2 rrflaaln..agdldalaalfapdvvwedpggelrGreairaffraafaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrved 96 436s r+++ a++ + d++ l+ +++pd+++ g e ++++ + +a++ ++ l++ ++++v++g+++a+ +++ i+ +g+ ++++++++ ++d 436s CUFF.36.1.p1 10 RQLFKAFTdfSTDVESLRGFLTPDYRQLVDGRE-LTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIAHA-IRSSGESSRIKVIAFYSFKD 104 436s 789999998899***************999865.5889999999999999*******************9888877.9******************* PP 436s 436s TEEE CS 436s SnoaL_2 97 GkIv 100 436s G+I 436s CUFF.36.1.p1 105 GRIS 108 436s ***6 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (102 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3793.70 436s // 436s Query: Sugar_tr [M=452] 436s Accession: PF00083.23 436s Description: Sugar (and other) transporter 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.4e-113 370.7 24.1 6.7e-113 370.4 24.1 1.1 1 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ 436s 6.2e-10 31.0 30.1 1.3e-09 30.0 30.1 1.5 1 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 370.4 24.1 1.4e-114 6.7e-113 2 451 .. 10 466 .. 9 467 .. 0.95 436s 436s Alignments for each domain: 436s == domain 1 score: 370.4 bits; conditional E-value: 1.4e-114 436s HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTST.T--SHHHHHH....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-T CS 436s Sugar_tr 2 alvaalggllfgYdtgvigafltllkfaknfg.lsksksskee.ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaa 96 436s +++++++g l+g dtg i+++l + +f+++f ++ s+ ++ s+ ++ l+++ ++G+++G+++++++++r+G+k+s+ +++ +++i+ +l ++a 436s CUFF.24.1.p1 10 VVFISMSGWLQGADTGSISGILGMRDFQSRFAdRYNPISNSYSySAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAELLLVTA 106 436s 67899**********************99987534433333334899************************************************** PP 436s 436s TTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS 436s Sugar_tr 97 kgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193 436s s+ +++vg++l+G+g+G+ svl+P y+sE+Ap+++Rga+v yq + t lvaa++++g+ k +++ wr +g+++++ +ll++++lflPE 436s CUFF.24.1.p1 107 V--PSWIQVLVGKILAGVGIGALSVLSPGYQSEVAPPQIRGAVVATYQIFSTGAALVAACINMGTHKLRKTASWRTSFGINMLWGILLMVGVLFLPE 201 436s *..89******************************************************************************************** PP 436s 436s -HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS- CS 436s Sugar_tr 194 SPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeee....kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgl 286 436s SPryl+ kg++eea +++ ++ + +++++ ++ +++++ e e ka w e++++ ++r+r+ +g+++++f l G+n+ +yy++++f+ +g+ 436s CUFF.24.1.p1 202 SPRYLIYKGRDEEALRIMCNMAELSPESEIIQTNFNTIKSDIEIEmaggKARWIEIFGK-DIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGM 297 436s ********************99999999988888888888888888888*********9.99*********************************** PP 436s 436s THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH.....HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH CS 436s Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg...ivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsEl 378 436s ++ +l +i+g++nf +tf a++++d +GRR+ l++Gaa+++icf+i++ l++++++ a+ v+ivf +lf++ + ++wgp+ wv+v E+ 436s CUFF.24.1.p1 298 TDIFLPAVILGAINFGTTFGALYTIDNLGRRNPLIFGAAFQSICFFIYAavgDRKLIYKNGTsdHRAGSVMIVFSCLFLFSYCCSWGPMGWVIVGET 394 436s *************************************************87655667777768899******************************* PP 436s 436s SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS 436s Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieel 451 436s fp + Rsk++++a+ nwl nf is+++p+i +aig ++ ++++a++++++ +++ff etkg+tlee++ l 436s CUFF.24.1.p1 395 FPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIG-FKLGYIYACINLFSSFMIFFLAKETKGLTLEEVNDL 466 436s ************************************.********************************9976 PP 436s 436s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 30.0 30.1 2.7e-11 1.3e-09 25 437 .. 121 530 .. 105 534 .. 0.75 436s 436s Alignments for each domain: 436s == domain 1 score: 30.0 bits; conditional E-value: 2.7e-11 436s HHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS 436s Sugar_tr 25 llkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121 436s + + ++ g s+ +s s+l + flvG +Gsl + +l+d++GR ++ ++ ++f i +v ++a+ +v+ l++ R++ G++ + + 436s CUFF.37.1.p1 121 FASSVYSSGIIDIASELHSSIPVSTLGSCTFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAH---NVWTLAIVRFFQGVFGSTPLA 214 436s 5555555555555555555677899999*********************************************...********************* PP 436s 436s HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS---HHHHHHTT-HHHHHHHHHHHHH CS 436s Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill.lflPESPrylvekgkeeeakevlaklrg 216 436s + +is + ++ R ++ + ++ +G +++ i+g ++ + + + wr+++++++++a ++++++ +f+PE+ e + + + l+k g 436s CUFF.37.1.p1 215 NAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFItQSYLE---WRWTFWINMIWAAAVIVFVfIFFPET----HEDTILDYKAKYLRKTTG 304 436s *********999999999999999999********99888455555...**************99998689****....333333333334444333 PP 436s 436s C....HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHT.TTHHHHSS-THH.....HHHHHHHHHH.HHH CS 436s Sugar_tr 217 e....edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyys.ptifenlglsks.....llvtiivgvv.nfv 302 436s + + +re + + ++++a+ ++ ++ ++++ ++++ + ++ + in+i + + p +f + g++k + + ++vg+v + 436s CUFF.37.1.p1 305 NtayyTIHERERDPKNAMIQAA----TQAVSLIFTE------PIVVCFTLYLTVVYIINYINFEGyPIVFAKYGFNKGeqglsF-IGVGVGIVcAGL 390 436s 3123333333333333333333....3344444444......455555666666777787777654889********9988844.444444440445 PP 436s 436s HHHHHHHHHHHS-SHHHHHHH........HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH..SHTTTHHHHHH CS 436s Sugar_tr 303 atfvaiflvdrfGRRtllllG........aagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsEl..fpqsvRskala 389 436s t + + ++ +++ +++ ++g++++ + + ++++ i iv ++ a+f++++ v++v + + q++ ++ala 436s CUFF.37.1.p1 391 CTPFIYWHYLKVNKKRNGVICpedrlyplFIGCFLLPISMF--WFAWTCYP--HHIHWIVP-IIASAFFGFSLLIVFFVSYNYIidSYQHMAPSALA 482 436s 56666688999999999****9***7765555555555554..44444443..23444444.455699999******999999844469******** PP 436s 436s HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS CS 436s Sugar_tr 390 iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffv 437 436s a+ v a+ is++ + ++g + v +++ v+++ + f+f+ 436s CUFF.37.1.p1 483 AATLVRYSASGGISMVARPMYLNLGDHWATSVLGFISVAMVPIPFIFY 530 436s *************************99999999999999999998886 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (452 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 2 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 436s # Mc/sec: 725.67 436s // 436s Query: SUI1 [M=76] 436s Accession: PF01253.21 436s Description: Translation initiation factor SUI1 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.5e-05 18.2 0.3 4.8e-05 16.5 0.2 2.0 2 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 16.5 0.2 5e-07 4.8e-05 3 52 .. 82 132 .. 80 177 .. 0.88 436s 2 ? -1.8 0.0 0.26 25 16 38 .. 167 188 .. 158 189 .. 0.69 436s 436s Alignments for each domain: 436s == domain 1 score: 16.5 bits; conditional E-value: 5e-07 436s SUI1 3 pkihirveqrggrKkvTtvsglepfgidlkklakelkkkfacsgsvvk.dg 52 436s +k+++rve +g+ ++T +g+++ +l +l+++++++ ++ ++ dg 436s CUFF.54.1.p1 82 RKVKLRVEDIQGKSCLTSFNGFDMTSDKLRSLVRKWQSTIEANQTIKTtDG 132 436s 69*******************************************944444 PP 436s 436s == domain 2 score: -1.8 bits; conditional E-value: 0.26 436s SUI1 16 KkvTtvsglepfgidlkklakel 38 436s K ++++ ++g +k+l+++l 436s CUFF.54.1.p1 167 KMFQVIQNQ-ANGCSMKELVQKL 188 436s 444455555.8888888888876 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (76 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1028.02 436s // 436s Query: Sulfatase [M=309] 436s Accession: PF00884.22 436s Description: Sulfatase 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.4e-08 25.4 0.1 0.00069 11.6 0.1 2.3 2 CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.6 0.1 7.3e-06 0.00069 3 61 .. 48 106 .. 46 125 .. 0.91 436s 2 ! 11.6 0.0 7.7e-06 0.00073 218 309 .] 223 321 .. 221 321 .. 0.71 436s 436s Alignments for each domain: 436s == domain 1 score: 11.6 bits; conditional E-value: 7.3e-06 436s EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS- CS 436s Sulfatase 3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgry 61 436s vv++++d l+a+ + + ++ ++ t+ l + ++g+ f+ f + +++ p + al tg 436s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGFSAFARSPTVTMPRLKALTTGTI 106 436s 9***********9999999999999999999**********999************975 PP 436s 436s == domain 2 score: 11.6 bits; conditional E-value: 7.7e-06 436s HHHHHHHHHHHHHHHHHTTTGGGE..EEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC......EEECSEEE......GGGHH CS 436s Sulfatase 218 veyvDdligrvlaaLeenglldnt..lvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap......rvseelvs......hiDlf 300 436s + ++D i+r++++L+e ++ nt l+v +Dhg + +gg + + + t l+ ++e+++ ++++++s ++D++ 436s CUFF.53.1.p1 223 LLEIDTIISRIYKYLQEYDEKTNThsLIVLCGDHGMNEVG----NHGGSS---SGETTAALSLLFPSNELSHinkpilNMDDNPYSilerveQVDVV 312 436s 6799************999999987789999****94322....222222...33444444455555555556666776888888888888899999 PP 436s 436s HHHHHHTTE CS 436s Sulfatase 301 ptildlagi 309 436s pti l+gi 436s CUFF.53.1.p1 313 PTICLLLGI 321 436s 999888875 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (309 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3425.46 436s // 436s Query: ThiJ_like [M=196] 436s Accession: PF17124.4 436s Description: ThiJ/PfpI family-like 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.4e-10 33.8 0.3 3.3e-09 29.3 0.3 2.2 1 CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 436s 1.7e-10 33.5 0.2 3.9e-09 29.1 0.2 2.2 1 CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028( 436s 0.00078 11.8 0.2 0.0014 10.9 0.2 1.7 1 CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 29.3 0.3 1.1e-10 3.3e-09 3 155 .. 47 185 .. 46 198 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 29.3 bits; conditional E-value: 1.1e-10 436s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 436s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 436s CUFF.47.1.p1 47 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 134 436s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 436s 436s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlw 155 436s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + 436s CUFF.47.1.p1 135 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYH 185 436s 99.9999999999988888.......4568*****************999998887655 PP 436s 436s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 29.1 0.2 1.2e-10 3.9e-09 3 160 .. 26 169 .. 25 185 .. 0.78 436s 436s Alignments for each domain: 436s == domain 1 score: 29.1 bits; conditional E-value: 1.2e-10 436s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 436s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 436s CUFF.46.1.p1 26 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 113 436s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 436s 436s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmerts 160 436s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + t+ 436s CUFF.46.1.p1 114 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYHKHVTA 169 436s 99.9999999999988888.......4568*****************99999998866655555 PP 436s 436s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.9 0.2 4.5e-05 0.0014 77 169 .. 77 164 .. 16 190 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 10.9 bits; conditional E-value: 4.5e-05 436s ThiJ_like 77 sesFsleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpe...ldlktttlPlwmertsillgstaek 169 436s ++ ++ +y++ + GG++ ++ lh+ ++ + v++a+c+g + l + k+ +k t+ ++ e + ++ +++ 436s CUFF.42.1.p2 77 ASDINFSDYSIFFAAGGHGTLF-DFPSATNLHKGAAKIY-------SMGGVIAAVCHGPVILPCIKDStgfSIVKGKTVTAFNEIAEQQMNLMPTF 164 436s 3345889************999.9999999999988877.......5568********99998887775554456666666666555555555555 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (196 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 3 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 436s # Mc/sec: 517.19 436s // 436s Query: TPP_enzyme_C [M=153] 436s Accession: PF02775.20 436s Description: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 8.1e-27 86.5 0.6 2.2e-25 81.8 0.0 2.6 3 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 2.2 0.0 0.0076 0.72 115 153 .] 132 172 .. 107 172 .. 0.80 436s 2 ? -3.6 0.1 0.47 45 112 124 .. 234 246 .. 227 252 .. 0.76 436s 3 ! 81.8 0.0 2.3e-27 2.2e-25 24 153 .] 415 539 .. 395 539 .. 0.85 436s 436s Alignments for each domain: 436s == domain 1 score: 2.2 bits; conditional E-value: 0.0076 436s HHHHHTTSE.EE..EESSH.HHHHHHHHHHHHCSSSEEEEEE CS 436s TPP_enzyme_C 115 klaealGak.ga..rvekadveeleealkealekkgpaliev 153 436s ++a+ l + +a r e+a + ++ a+++a+ +++p++ie+ 436s CUFF.32.1.p1 132 EIAKKLTCAaVAikRAEDA-PVMIDHAIRQAILQHKPVYIEI 172 436s 6788887775667665555.78899*******999****996 PP 436s 436s == domain 2 score: -3.6 bits; conditional E-value: 0.47 436s -HHHHHHHTTSEE CS 436s TPP_enzyme_C 112 dfaklaealGakg 124 436s f+klaeal + + 436s CUFF.32.1.p1 234 AFVKLAEALNCAA 246 436s 6999999998874 PP 436s 436s == domain 3 score: 81.8 bits; conditional E-value: 2.3e-27 436s ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHT CS 436s TPP_enzyme_C 24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaeal 120 436s + +g++G+++p A+G ++a+p+r+ +++vGDG+f+ ++qe+++++r++lp+++++lnN+gy + ++ ++ r ++ dfa+++e+l 436s CUFF.32.1.p1 415 EMQWGHIGWSVPSAMGYAVAAPERRTIVMVGDGSFQLTGQEISQMIRHKLPVLIFLLNNRGYTIEIQIHDGPYN-R--------IQNWDFAAFCESL 502 436s 56789*********************************************************766666666664.2........6799********* PP 436s 436s TSE.EE....EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS 436s TPP_enzyme_C 121 Gak.ga....rvekadveeleealkeal.ekkgpaliev 153 436s + g ++ eel a+k al +k+gp+lie+ 436s CUFF.32.1.p1 503 NGEtGKakglHAKTG--EELTSAIKVALqNKEGPTLIEC 539 436s 666555674455555..***********99*******97 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (153 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 3080.11 436s // 436s Query: TPP_enzyme_M [M=137] 436s Accession: PF00205.21 436s Description: Thiamine pyrophosphate enzyme, central domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 3.6e-24 77.7 0.0 6.9e-24 76.8 0.0 1.4 1 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 76.8 0.0 7.2e-26 6.9e-24 3 113 .. 207 316 .. 205 325 .. 0.90 436s 436s Alignments for each domain: 436s == domain 1 score: 76.8 bits; conditional E-value: 7.2e-26 436s HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHH.HH-SEEEEES-SSSTCCCTTTT CS 436s TPP_enzyme_M 3 raaellkkakrpvilvGggvsrsgaskelrelaeklgiPvvttlmgkgaipedhplylG.mlgllgspaaneal.eeaDlvlllGarlsdirttgss 97 436s aael++k+++p++l+G + + +ga+ ++++lae+l++ + ++++kg+++e+h++y+G ++g ++s++ +a+ e++Dlv+ G+ ++d++t g 436s CUFF.32.1.p1 207 IAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMPAAKGFYSEEHKNYAGvYWGEVSSSETTKAVyESSDLVIGAGVLFNDYSTVGWR 303 436s 599***************************************************************99999999899****************9966 PP 436s 436s TTTTTT-EEEEEESSC CS 436s TPP_enzyme_M 98 pefapeakiihididp 113 436s + +p+ i +++d 436s CUFF.32.1.p1 304 AAPNPN---ILLNSDY 316 436s 666666...5555554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (137 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3271.42 436s // 436s Query: TPP_enzyme_N [M=172] 436s Accession: PF02776.17 436s Description: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.1e-39 126.5 0.0 1.3e-37 121.7 0.1 2.3 2 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 121.7 0.1 1.3e-39 1.3e-37 1 170 [. 9 183 .. 9 185 .. 0.94 436s 2 ! 2.6 0.0 0.005 0.48 136 161 .. 516 541 .. 428 545 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 121.7 bits; conditional E-value: 1.3e-39 436s EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEE CS 436s TPP_enzyme_N 1 ltvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvls 97 436s +tv+++l+++L + g++ f vpG+ +l lld l+ +g++ + + +E ++afaA+gyar+ g +++++vt+ +Ga+ a+ ++ +A+ +++P++++s 436s CUFF.32.1.p1 9 MTVGTYLAQRLVEIGIKNHFVVPGDYNLRLLDFLEYYPGLSEIGCCNELNCAFAAEGYARSNG-IACAVVTYSVGALTAFDGIGGAYAENLPVILVS 104 436s 89**********************************************************976.********************************* PP 436s 436s EE--CCCHH.....S--TC.-T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EEEH CS 436s TPP_enzyme_N 98 gdrptslrg.....qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleevde 170 436s g+++t + + +++l q+++++++t +a+ ++++e++p++++ Air+a ++ Pvy+e+p ++ +++++ 436s CUFF.32.1.p1 105 GSPNTNDLSsghllHHTLGTHDfeYQMEIAKKLTCAAVAIKRAEDAPVMIDHAIRQA-ILQHKPVYIEIPTNMANQPCPV 183 436s *********9888755555333657********************************.99****************9986 PP 436s 436s == domain 2 score: 2.6 bits; conditional E-value: 0.005 436s HHHHHHHHHHHHHSSS--EEEEEEEH CS 436s TPP_enzyme_N 136 lpealrrAirtalsgrpgPvylelpk 161 436s + e+l Ai++al+++ gP ++e + 436s CUFF.32.1.p1 516 TGEELTSAIKVALQNKEGPTLIECAI 541 436s 568999***************99665 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (172 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 2977.27 436s // 436s Query: Transferase [M=434] 436s Accession: PF02458.14 436s Description: Transferase family 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00025 12.3 0.0 0.0003 12.1 0.0 1.0 1 CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.1 0.0 3.1e-06 0.0003 348 403 .. 49 107 .. 37 111 .. 0.76 436s 436s Alignments for each domain: 436s == domain 1 score: 12.1 bits; conditional E-value: 3.1e-06 436s Transferase 348 nstlkaelv..skgkkdgeevtvsswlklplyevdFGwgkP..vyvvpvvsskkdnkill 403 436s n tl+a+++ ++g ++ + +v +wlk++l v FG g P v++ +++s+ + ++i++ 436s CUFF.2.1.p1 49 N-TLMAHCFetYNGVEKSGTQCVADWLKVGLLAVTFGAGGPrlVNTLGGSSPTTKRVIYI 107 436s 4.5666664226777777*********************995566777888888877554 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (434 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 7844.18 436s // 436s Query: TRAPP [M=146] 436s Accession: PF04051.15 436s Description: Transport protein particle (TRAPP) component 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 6.2e-26 83.5 0.2 8e-26 83.1 0.2 1.1 1 CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-50 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-505(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 83.1 0.2 8.5e-28 8e-26 1 99 [. 34 142 .. 34 163 .. 0.88 436s 436s Alignments for each domain: 436s == domain 1 score: 83.1 bits; conditional E-value: 8.5e-28 436s TRAPP 1 fefllgelvsylirdskdveeve..........krLekmGyrvGlrllelllarerpretdilevlkfickdlWkalfgkqidnlktnhrgeyvltd 87 436s ++fll+elv+++ r ++d ++ + + Le++G++vG +++e +l+ +r+r t++ +v+ f+c++lW ++f+k+ dnlktn+rg +vltd 436s CUFF.55.1.p1 34 LDFLLIELVHTAKRLAEDRKKKSsseksiesdfQMLESIGFQVGRKITE-RLLLNRNRITETTDVMRFLCRELWPIVFRKPLDNLKTNRRGIFVLTD 129 436s 58************9999888889999**********************.888888***************************************** PP 436s 436s TRAPP 88 nef.pltrfvelp 99 436s + f ++t+++ + 436s CUFF.55.1.p1 130 TYFyWFTKMTAMT 142 436s *********6433 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (146 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 3791.63 436s // 436s Query: TRI12 [M=599] 436s Accession: PF06609.12 436s Description: Fungal trichothecene efflux pump (TRI12) 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 5.4e-10 30.8 27.0 1.2e-09 29.7 27.0 1.4 1 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 29.7 27.0 1.3e-11 1.2e-09 31 494 .. 69 553 .. 49 575 .. 0.69 436s 436s Alignments for each domain: 436s == domain 1 score: 29.7 bits; conditional E-value: 1.3e-11 436s TRI12 31 elpegyyrsprvvasfaafslnvvatyfvlqasasa.lpnilqdvgqsensslfstlwttgqavsil...vmgrltdrfgrrpfvilthilglvgai 123 436s + + y+ r + af + ++a + +s+ + + +s++stl +s + ++g+++d r l ++ ++g i 436s CUFF.25.1.p1 69 AVRDSIYQNKRGMYLAYAFGIAILACSWASAIQSSTtYSYQVYATASFNRTSMISTLEIATAIISSVckpILGKFSDITSRPMTYTLVLLFYVIGFI 165 436s 4567777777777666778877777766543333330333334445556679999998776665544233899999987765555666677788889 PP 436s 436s TRI12 124 vgctatkfntllaamtllgv.aagpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiy.iitsaiav.llivvwy 217 436s v ++++ + + + ++ + ++g l+vg+l s k + + ++s p ++t + ++ q + i+ +wrw + ++ ii+ a+ +i++ y 436s CUFF.25.1.p1 166 VVASSSTISAYVIGSVFISIgSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVWFTGFIVQGI-IDSNWRWGYGMFaIIMPAVMTpAVIILMY 261 436s 888888888877777776662457777899*********9987777889********9999999986.9******9987646777765514555555 PP 436s 436s TRI12 218 ypps......fa.....qlhgk...kvrkreelak....ldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkp 296 436s ++ q k k +k ++l k +d g+il+ vg s++ll s ++ w+ +i ++ g l+ ++ ye++ p 436s CUFF.25.1.p1 262 LERQankdenIKkiinyQTEEKnknKQSKWQKLWKavleVDLFGLILLGVGWSILLLPFSLTSYAKNGWKNPSMIAMMVVGGVILIAYSGYEMFIAP 358 436s 4332111111221111122223111444555554444448*******************************************************99 PP 436s 436s TRI12 297 vrpivppalfkdtrgfvcillissimgamnlslviiypqq.vvnifgsslknwee..tawmsatasfgtgagvvvlgslfhlvrhirwqilvgalwl 390 436s p p +++ r f+ ++i + l +y ++ s ++w + a + fg +ag + +fh ++++ lv + 436s CUFF.25.1.p1 359 Y-PSCPRRVMN--RTFITAVIIDFFYY-LAGYLQSMYFTTyTWILYDWSYRDWTYfnNTMTIALCVFGVFAGAM--HRVFHRYKYLQIIGLVIKI-- 447 436s 6.888998875..77999888876554.44455556655504556889*****8521334457789******87..6899977776544444333.. PP 436s 436s TRI12 391 taflgamssvnrd.nknaaialsv.lsgfvvawaqditmllvqfittdedlgvafavvaaarpfagsiftaafislysnrypkelashlssalrgtd 485 436s g + n + +a s+ l g+ +++ + + q +dl +a +++ + g+i +a ++sn+ pk l +l s++ t+ 436s CUFF.25.1.p1 448 -VGYGILIRPNFAaTGKVDLAWSLiLIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGAAIASPIFSNKVPKYLREYLPSSINDTQ 543 436s .33344433332202233344443144555555555566778999999***************999999999999*******************999 PP 436s 436s TRI12 486 ipq.asfssl 494 436s + + s ssl 436s CUFF.25.1.p1 544 VYNfYSDSSL 553 436s 7651455555 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (599 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 436s # Mc/sec: 999.38 436s // 436s Query: UPF0489 [M=178] 436s Accession: PF12640.6 436s Description: UPF0489 domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00064 12.6 0.0 0.00099 12.0 0.0 1.2 1 CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 12.0 0.0 1e-05 0.00099 7 43 .. 186 229 .. 183 270 .. 0.67 436s 436s Alignments for each domain: 436s == domain 1 score: 12.0 bits; conditional E-value: 1e-05 436s UPF0489 7 HheaLeaiyraigskklpsdlslvHlDaHpDllipk..........k 43 436s H+ +L+ i r +++ + ++s++H+D+H D pk 436s CUFF.38.1.p4 186 HTIVLP-ILRSVSRAY--GPVSIIHFDSHLDSWKPKvfgggkssvgS 229 436s 444444.555566666..99***********8777666555554440 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (178 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 4338.31 436s // 436s Query: Usher [M=551] 436s Accession: PF00577.19 436s Description: Outer membrane usher protein 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00057 11.4 0.0 0.00069 11.1 0.0 1.1 1 CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612- 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 11.1 0.0 7.2e-06 0.00069 35 132 .. 17 114 .. 2 116 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 11.1 bits; conditional E-value: 7.2e-06 436s EEEEEEEEEETTTTEEEEEEEEE--SSSS---EEEEEEEEE-GGGS-CCCCCEEEEEEEEESSSEEEEEECTTEEEEEEEE-SEEEEE-S---TTTT CS 436s Usher 35 ssrtylqraipqlkskLtlGesytssdiFdsvsfrGvsLasddnmlPdslrgyaPevrGiArtnAkVtirqnGyviYqtlVppGpFeiqdlnptsss 131 436s +s + r + +l+++ G s+++++i + + + +L+ + + + ++ +P G Ar+n +t+ + +viY+t+ +pG + + s++ 436s CUFF.20.1.p2 17 WSARRVCRIFANLRTHRARGSSNVKNEIKKQEGNVSFQLKMSVKQFVSDGHIVRPYLLGLARSNPGLTVIEHDRVIYRTASAPGSGDLPKVTLVSGG 113 436s 5555566667777777777777777777777777777777776666667777889999**************************9888888777766 PP 436s 436s C CS 436s Usher 132 g 132 436s g 436s CUFF.20.1.p2 114 G 114 436s 5 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (551 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 436s # Mc/sec: 3588.67 436s // 436s Query: zf-C2H2 [M=23] 436s Accession: PF00096.25 436s Description: Zinc finger, C2H2 type 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 4.9e-10 32.1 9.4 4.4e-06 19.7 1.9 2.7 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 16.2 1.0 5.9e-07 5.6e-05 1 20 [. 31 50 .. 31 51 .. 0.95 436s 2 ! 19.7 1.9 4.7e-08 4.4e-06 2 23 .] 60 82 .. 59 82 .. 0.96 436s 436s Alignments for each domain: 436s == domain 1 score: 16.2 bits; conditional E-value: 5.9e-07 436s EEETTTTEEESSHHHHHHHH CS 436s zf-C2H2 1 ykCpdCgksFkrksnLkrHi 20 436s ++C+ C k+F+r +nL+rH 436s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 436s 89*****************5 PP 436s 436s == domain 2 score: 19.7 bits; conditional E-value: 4.7e-08 436s EETTTTEEESSHHHHHHHHHC.C CS 436s zf-C2H2 2 kCpdCgksFkrksnLkrHirt.H 23 436s +Cp+C ++krk++LkrHi++ H 436s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRfH 82 436s 6********************99 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (23 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 983.57 436s // 436s Query: zf-C2H2_4 [M=24] 436s Accession: PF13894.5 436s Description: C2H2-type zinc finger 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 1.2e-05 18.6 12.9 0.00084 12.9 1.6 2.9 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 10.0 4.0 7.8e-05 0.0074 1 20 [. 31 50 .. 31 53 .. 0.89 436s 2 ! 12.9 1.6 8.8e-06 0.00084 2 24 .] 60 82 .. 59 82 .. 0.93 436s 436s Alignments for each domain: 436s == domain 1 score: 10.0 bits; conditional E-value: 7.8e-05 436s zf-C2H2_4 1 fkCpiCgksFsskkaLlrHl 20 436s f+C++C k+F+++++L rH 436s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 436s 89********99999****4 PP 436s 436s == domain 2 score: 12.9 bits; conditional E-value: 8.8e-06 436s zf-C2H2_4 2 kCpiCgksFsskkaLlrHlkthH 24 436s +Cp+C +++k+ L+rH+++ H 436s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRFH 82 436s 7********99999*****9988 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (24 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1156.47 436s // 436s Query: zf-C2H2_6 [M=27] 436s Accession: PF13912.5 436s Description: C2H2-type zinc finger 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 2.6e-06 20.0 3.1 2.6e-06 20.0 3.1 2.0 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 20.0 3.1 2.7e-08 2.6e-06 1 26 [. 30 55 .. 30 56 .. 0.96 436s 2 ? -3.5 0.6 0.62 59 4 7 .. 61 64 .. 60 65 .. 0.86 436s 436s Alignments for each domain: 436s == domain 1 score: 20.0 bits; conditional E-value: 2.7e-08 436s zf-C2H2_6 1 vfeCdeCsksFpslqaLggHkksHrk 26 436s vf Cd+C k+F + +L+ Hk++H k 436s CUFF.45.1.p1 30 VFPCDQCAKRFTRHENLTRHKACHSK 55 436s 79**********************97 PP 436s 436s == domain 2 score: -3.5 bits; conditional E-value: 0.62 436s zf-C2H2_6 4 CdeC 7 436s C++C 436s CUFF.45.1.p1 61 CPYC 64 436s **** PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (27 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1192.46 436s // 436s Query: zf-C2H2_jaz [M=27] 436s Accession: PF12171.7 436s Description: Zinc-finger double-stranded RNA-binding 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.002 11.1 5.8 0.017 8.2 0.2 2.8 3 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 8.2 0.2 0.00018 0.017 2 21 .. 31 50 .. 30 51 .. 0.92 436s 2 ! 5.3 0.1 0.0014 0.13 4 21 .. 61 78 .. 58 79 .. 0.93 436s 3 ? -3.8 0.1 1 95 10 16 .. 166 172 .. 165 172 .. 0.83 436s 436s Alignments for each domain: 436s == domain 1 score: 8.2 bits; conditional E-value: 0.00018 436s CBBTTTTBBBSSHHHHHCCT CS 436s zf-C2H2_jaz 2 fYCvlCdKyFksenaldnHl 21 436s f C C+K F +++l H+ 436s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 436s 77*****************6 PP 436s 436s == domain 2 score: 5.3 bits; conditional E-value: 0.0014 436s BTTTTBBBSSHHHHHCCT CS 436s zf-C2H2_jaz 4 CvlCdKyFksenaldnHl 21 436s C++C+ +k l+ H+ 436s CUFF.45.1.p1 61 CPYCEIKCKRKDLLKRHI 78 436s *****************8 PP 436s 436s == domain 3 score: -3.8 bits; conditional E-value: 1 436s BBSSHHH CS 436s zf-C2H2_jaz 10 yFksena 16 436s F+sen+ 436s CUFF.45.1.p1 166 SFNSENV 172 436s 59***96 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (27 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1414.37 436s // 436s Query: zf-Di19 [M=54] 436s Accession: PF05605.11 436s Description: Drought induced 19 protein (Di19), zinc-binding 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s ------ inclusion threshold ------ 436s 0.027 7.5 8.1 0.0019 11.2 1.0 2.2 1 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? 11.2 1.0 2e-05 0.0019 3 28 .. 59 85 .. 57 88 .. 0.79 436s 436s Alignments for each domain: 436s == domain 1 score: 11.2 bits; conditional E-value: 2e-05 436s zf-Di19 3 ftCPyCgkeltvkeLv.eHvedeHrve 28 436s ++CPyC+ + + k L+ +H++ H ++ 436s CUFF.45.1.p1 59 IPCPYCEIKCKRKDLLkRHIQRFHNDK 85 436s 68*****99877776527***999876 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (54 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 436s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 436s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 884.82 436s // 436s Query: zf-H2C2_2 [M=26] 436s Accession: PF13465.5 436s Description: Zinc-finger double domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 0.00054 13.1 15.4 0.0047 10.1 4.9 3.4 3 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 7.6 0.4 0.0003 0.028 12 26 .] 28 42 .. 26 42 .. 0.83 436s 2 ! 10.1 4.9 4.9e-05 0.0047 1 21 [. 45 65 .. 45 70 .. 0.90 436s 3 ? 0.9 0.1 0.042 4 2 10 .. 74 83 .. 74 89 .. 0.70 436s 436s Alignments for each domain: 436s == domain 1 score: 7.6 bits; conditional E-value: 0.0003 436s zf-H2C2_2 12 ekpyeCplCdkaFkt 26 436s ++ + C+ C+k+F++ 436s CUFF.45.1.p1 28 KRVFPCDQCAKRFTR 42 436s 4559*********85 PP 436s 436s == domain 2 score: 10.1 bits; conditional E-value: 4.9e-05 436s zf-H2C2_2 1 nLrrHlrkHtgekpyeCplCd 21 436s nL+rH + H + p Cp+C 436s CUFF.45.1.p1 45 NLTRHKACHSKAEPIPCPYCE 65 436s 8*******************7 PP 436s 436s == domain 3 score: 0.9 bits; conditional E-value: 0.042 436s zf-H2C2_2 2 LrrHlr.kHt 10 436s L+rH+ +H 436s CUFF.45.1.p1 74 LKRHIQrFHN 83 436s 89**962586 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (26 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1287.93 436s // 436s Query: zf-TRAF [M=60] 436s Accession: PF02176.17 436s Description: TRAF-type zinc finger 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s ------ inclusion threshold ------ 436s 0.029 7.8 9.9 0.04 7.3 8.4 1.9 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ? 7.3 8.4 0.00042 0.04 9 56 .. 30 72 .. 27 80 .. 0.77 436s 2 ? -2.0 0.0 0.33 31 26 43 .. 276 293 .. 274 294 .. 0.77 436s 436s Alignments for each domain: 436s == domain 1 score: 7.3 bits; conditional E-value: 0.00042 436s EEE-TT--S-BEEETTTCCCCCCTTSTTS--XXSSXXXXSXXXXXHHH CS 436s zf-TRAF 9 pvpCpnecckkkilRkdlkdHlekdCkkaevkCkfkevGCkekvkrea 56 436s pC ++c+k ++l H + k +++C++ C+ k+kr++ 436s CUFF.45.1.p1 30 VFPC-DQCAKRFTRHENLTRHKACHSKAEPIPCPY----CEIKCKRKD 72 436s 5689.88**9999999*****997777889*****....555555554 PP 436s 436s == domain 2 score: -2.0 bits; conditional E-value: 0.33 436s CCCCCCTTSTTS--XXSS CS 436s zf-TRAF 26 lkdHlekdCkkaevkCkf 43 436s + + ++ +C + v C + 436s CUFF.45.1.p1 276 ISNLIDLECIRRSVFCLY 293 436s 666678889999999988 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (60 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 436s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 436s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1959.54 436s // 436s Query: Zn_clus [M=40] 436s Accession: PF00172.17 436s Description: Fungal Zn(2)-Cys(6) binuclear cluster domain 436s Scores for complete sequences (score includes all domains): 436s --- full sequence --- --- best 1 domain --- -#dom- 436s E-value score bias E-value score bias exp N Sequence Description 436s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 436s 7.4e-10 31.5 13.0 1.2e-09 30.8 13.0 1.4 1 CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772( 436s 436s 436s Domain annotation for each sequence (and alignments): 436s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 436s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 436s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 436s 1 ! 30.8 13.0 1.3e-11 1.2e-09 1 39 [. 5 42 .. 5 44 .. 0.91 436s 436s Alignments for each domain: 436s == domain 1 score: 30.8 bits; conditional E-value: 1.3e-11 436s -S-HHHHHCT---STSSSS-HHHHHCT---ECCCTCCCE CS 436s Zn_clus 1 haCdnCrkkKvKCdakkPaCsnCkklnleCtfysesskr 39 436s +aCd Cr kK+KC++++P C+ C +++C ys++ +r 436s CUFF.38.1.p1 5 KACDLCRLKKIKCSRGQPRCQTCTLFQADCH-YSNRARR 42 436s 59*****************************.7777665 PP 436s 436s 436s 436s Internal pipeline statistics summary: 436s ------------------------------------- 436s Query model(s): 1 (40 nodes) 436s Target sequences: 95 (31269 residues searched) 436s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 436s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 436s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 436s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 436s Initial search space (Z): 95 [actual number of targets] 436s Domain search space (domZ): 1 [number of targets reported over threshold] 436s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 436s # Mc/sec: 1702.55 436s // 436s [ok] 436s 436s eval $cmd 436s ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v 436s * [Mon Mar 18 02:16:45 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 436s * [Mon Mar 18 02:16:45 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 436s -skipping training candidate: CUFF.60.1.p1, not unique enough 436s -skipping training candidate: CUFF.26.1.p1, not unique enough 436s -skipping training candidate: CUFF.38.1.p3, not unique enough 436s -skipping training candidate: CUFF.48.1.p1, not unique enough 436s -skipping training candidate: CUFF.60.1.p2, not unique enough 436s -skipping training candidate: CUFF.30.1.p1, not unique enough 436s -skipping training candidate: CUFF.41.1.p1, not unique enough 436s -skipping training candidate: CUFF.41.1.p2, not unique enough 436s -skipping training candidate: CUFF.30.2.p1, not unique enough 436s -skipping training candidate: CUFF.52.1.p3, not unique enough 436s -skipping training candidate: CUFF.20.1.p2, not unique enough 436s -skipping training candidate: CUFF.47.1.p1, not unique enough 436s -skipping training candidate: CUFF.48.1.p3, not unique enough 436s -skipping training candidate: CUFF.13.3.p1, not unique enough 436s -skipping training candidate: CUFF.28.1.p1, not unique enough 436s -skipping training candidate: CUFF.34.1.p2, not unique enough 436s -skipping training candidate: CUFF.13.1.p1, not unique enough 436s -skipping training candidate: CUFF.38.1.p5, not unique enough 436s -skipping training candidate: CUFF.27.1.p2, not unique enough 436s -skipping training candidate: CUFF.41.1.p3, not unique enough 436s -skipping training candidate: CUFF.13.1.p2, not unique enough 436s -skipping training candidate: CUFF.27.1.p3, not unique enough 436s -skipping training candidate: CUFF.41.1.p4, not unique enough 436s 436s -redundancy-minimized set includes 72 / 95 = 75.79% 436s 436s * [Mon Mar 18 02:16:45 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 436s PCT_GC: 37 436s * [Mon Mar 18 02:16:45 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores 437s * [Mon Mar 18 02:16:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 437s * [Mon Mar 18 02:16:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 438s Selecting best orfsblastp output found (blastp.outfmt6) and processing... 438s PFAM output found (pfam.domtblout) and processing... 438s 438s * [Mon Mar 18 02:16:47 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement 438s Training start codon pattern recognition* [Mon Mar 18 02:16:47 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 438s * [Mon Mar 18 02:16:47 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 438s -round: 1 441s -round: 2 444s -round: 3 448s -round: 4 451s -round: 5 454s * [Mon Mar 18 02:17:03 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 454s -parsing scores 458s * [Mon Mar 18 02:17:07 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 458s Error in library(ggplot2) : there is no package called ‘ggplot2’ 458s Execution halted 458s * [Mon Mar 18 02:17:07 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 459s Error in library(ggplot2) : there is no package called ‘ggplot2’ 459s Execution halted 459s * [Mon Mar 18 02:17:08 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 459s Error in library(seqLogo) : there is no package called ‘seqLogo’ 459s Execution halted 459s * [Mon Mar 18 02:17:08 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 459s Error in library(seqLogo) : there is no package called ‘seqLogo’ 459s Execution halted 459s * [Mon Mar 18 02:17:08 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 459s num features: 62 num_incorporate: 18 459s -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 459s -feature swap of score: 1.94858034627835 instead of -0.884029553505083 459s -feature swap of score: 2.12188175995298 instead of -0.685343860113718 459s -feature swap of score: 2.31823471239686 instead of 1.3320086516586 459s -feature swap of score: 3.37895288616016 instead of 1.93080159572592 459s -feature swap of score: 3.63482432490867 instead of 3.22946119764082 459s -feature swap of score: 5.41689919345157 instead of 3.20580366781557 459s -num feature swaps: 7 459s * [Mon Mar 18 02:17:08 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 459s -round: 1 463s -round: 2 466s -round: 3 470s -round: 4 473s -round: 5 476s * [Mon Mar 18 02:17:25 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 476s -parsing scores 480s * [Mon Mar 18 02:17:29 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 481s Error in library(ggplot2) : there is no package called ‘ggplot2’ 481s Execution halted 481s * [Mon Mar 18 02:17:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 481s Error in library(ggplot2) : there is no package called ‘ggplot2’ 481s Execution halted 481s * [Mon Mar 18 02:17:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 481s Error in library(seqLogo) : there is no package called ‘seqLogo’ 481s Execution halted 481s * [Mon Mar 18 02:17:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 481s Refining start codon selections. 481s -number of revised start positions: 1 481s * [Mon Mar 18 02:17:30 2024] Running CMD: cp /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 481s copying output to final output file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Mon Mar 18 02:17:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 482s Making bed file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 482s * [Mon Mar 18 02:17:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 482s Making pep file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 482s * [Mon Mar 18 02:17:31 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 482s Making cds file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 482s transdecoder is finished. See output files /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* 482s 482s 482s 482s 482s ## convert to genome coordinates 482s ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3 482s 482s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1, 612 482s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [3], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1471, 2862 482s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CUFF.30.2.p1. 482s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1164, 2072 482s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 3, 440 482s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1899, 2783 482s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 2759, 3736 482s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1142, 4111 482s -Warning [16], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 3280, 4776 482s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 1, 534 482s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 4115, 4705 482s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 482s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 482s CDS coords: 3, 722 482s 482s 482s Done. 81 / 82 transcript orfs could be propagated to the genome 482s 482s 482s 482s ## make bed files for viewing with GenomeView 482s 482s # covert cufflinks gtf to bed 482s ../../util/gtf_to_bed.pl transcripts.gtf > transcripts.bed 482s 482s # convert the genome-based gene-gff3 file to bed 482s ../../util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.genome.gff3 > transcripts.fasta.transdecoder.genome.bed 482s 482s 482s 482s # ensure no fatal problems w/ pep file 482s ../../util/fasta_prot_checker.pl transcripts.fasta.transdecoder.pep 482s 482s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 482s 482s 482s exit 0 482s make[1]: Leaving directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 482s Running example in $... 482s make[1]: Entering directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 482s ./runMe.sh 482s #!/bin/bash -ve 482s 482s if [ ! -e genome.fasta ]; then 482s gunzip -c genome.fasta.gz > genome.fasta 482s fi 482s 482s if [ ! -e pasa_assemblies.fasta ]; then 482s gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta 482s fi 482s 482s if [ ! -e pasa_assemblies.gff3 ]; then 482s gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3 482s fi 482s 482s if [ ! -e pasa_assemblies_described.txt ]; then 482s gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt 482s fi 482s 482s 482s # get the gene-to-transcript relationships 482s cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt 482s 482s ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir 482s CMD: mkdir -p /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir 482s * [Mon Mar 18 02:17:31 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat 482s 482s 482s -first extracting base frequencies, we'll need them later. 483s 483s 483s - extracting ORFs from transcripts. 483s -total transcripts to examine: 858 484s [100/858] = 11.66% done [200/858] = 23.31% done [300/858] = 34.97% done [400/858] = 46.62% done [500/858] = 58.28% done [600/858] = 69.93% done [700/858] = 81.59% done [800/858] = 93.24% done CMD: touch /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 484s 484s 484s ################################# 484s ### Done preparing long ORFs. ### 484s ################################## 484s 484s Use file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. 484s 484s Then, run TransDecoder.Predict for your final coding region predictions. 484s 484s 484s 484s 484s 484s ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir 484s * [Mon Mar 18 02:17:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 485s * [Mon Mar 18 02:17:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 485s -skipping training candidate: asmbl_804.p1, not unique enough 485s -skipping training candidate: asmbl_395.p1, not unique enough 485s -skipping training candidate: asmbl_805.p1, not unique enough 485s -skipping training candidate: asmbl_446.p1, not unique enough 485s -skipping training candidate: asmbl_745.p1, not unique enough 485s -skipping training candidate: asmbl_692.p1, not unique enough 485s -skipping training candidate: asmbl_570.p1, not unique enough 485s -skipping training candidate: asmbl_558.p1, not unique enough 485s -skipping training candidate: asmbl_694.p1, not unique enough 485s -skipping training candidate: asmbl_434.p1, not unique enough 485s -skipping training candidate: asmbl_688.p1, not unique enough 485s -skipping training candidate: asmbl_725.p1, not unique enough 485s -skipping training candidate: asmbl_507.p1, not unique enough 485s -skipping training candidate: asmbl_814.p1, not unique enough 485s -skipping training candidate: asmbl_632.p1, not unique enough 485s -skipping training candidate: asmbl_654.p1, not unique enough 485s -skipping training candidate: asmbl_777.p1, not unique enough 485s -skipping training candidate: asmbl_290.p1, not unique enough 485s -skipping training candidate: asmbl_745.p2, not unique enough 485s -skipping training candidate: asmbl_746.p1, not unique enough 485s -skipping training candidate: asmbl_290.p2, not unique enough 485s -skipping training candidate: asmbl_746.p2, not unique enough 485s -skipping training candidate: asmbl_115.p1, not unique enough 485s -skipping training candidate: asmbl_560.p1, not unique enough 485s -skipping training candidate: asmbl_561.p1, not unique enough 485s -skipping training candidate: asmbl_784.p1, not unique enough 485s -skipping training candidate: asmbl_778.p1, not unique enough 485s -skipping training candidate: asmbl_508.p1, not unique enough 485s -skipping training candidate: asmbl_21.p1, not unique enough 485s -skipping training candidate: asmbl_22.p1, not unique enough 485s -skipping training candidate: asmbl_450.p1, not unique enough 485s -skipping training candidate: asmbl_448.p1, not unique enough 485s -skipping training candidate: asmbl_449.p1, not unique enough 485s -skipping training candidate: asmbl_772.p1, not unique enough 485s -skipping training candidate: asmbl_556.p1, not unique enough 485s -skipping training candidate: asmbl_68.p1, not unique enough 485s -skipping training candidate: asmbl_363.p1, not unique enough 485s -skipping training candidate: asmbl_470.p1, not unique enough 485s -skipping training candidate: asmbl_471.p1, not unique enough 485s -skipping training candidate: asmbl_773.p1, not unique enough 485s -skipping training candidate: asmbl_667.p1, not unique enough 485s -skipping training candidate: asmbl_576.p1, not unique enough 485s -skipping training candidate: asmbl_774.p1, not unique enough 485s -skipping training candidate: asmbl_234.p1, not unique enough 485s -skipping training candidate: asmbl_639.p1, not unique enough 485s -skipping training candidate: asmbl_640.p1, not unique enough 485s -skipping training candidate: asmbl_727.p1, not unique enough 485s -skipping training candidate: asmbl_672.p1, not unique enough 485s -skipping training candidate: asmbl_852.p1, not unique enough 485s -skipping training candidate: asmbl_565.p1, not unique enough 485s -skipping training candidate: asmbl_813.p1, not unique enough 485s -skipping training candidate: asmbl_786.p1, not unique enough 485s -skipping training candidate: asmbl_726.p1, not unique enough 485s -skipping training candidate: asmbl_635.p1, not unique enough 485s -skipping training candidate: asmbl_501.p1, not unique enough 485s -skipping training candidate: asmbl_559.p1, not unique enough 485s -skipping training candidate: asmbl_624.p1, not unique enough 485s -skipping training candidate: asmbl_599.p1, not unique enough 485s -skipping training candidate: asmbl_768.p1, not unique enough 485s -skipping training candidate: asmbl_537.p1, not unique enough 485s -skipping training candidate: asmbl_787.p1, not unique enough 485s -skipping training candidate: asmbl_585.p1, not unique enough 485s -skipping training candidate: asmbl_519.p1, not unique enough 485s -skipping training candidate: asmbl_734.p1, not unique enough 485s -skipping training candidate: asmbl_844.p1, not unique enough 485s -skipping training candidate: asmbl_789.p1, not unique enough 485s -skipping training candidate: asmbl_847.p1, not unique enough 485s -skipping training candidate: asmbl_554.p1, not unique enough 485s -skipping training candidate: asmbl_462.p1, not unique enough 485s -skipping training candidate: asmbl_514.p1, not unique enough 485s -skipping training candidate: asmbl_711.p1, not unique enough 485s -skipping training candidate: asmbl_790.p1, not unique enough 485s -skipping training candidate: asmbl_744.p1, not unique enough 485s -skipping training candidate: asmbl_50.p1, not unique enough 485s -skipping training candidate: asmbl_491.p1, not unique enough 485s -skipping training candidate: asmbl_489.p1, not unique enough 485s -skipping training candidate: asmbl_49.p1, not unique enough 485s -skipping training candidate: asmbl_51.p1, not unique enough 485s -skipping training candidate: asmbl_492.p1, not unique enough 485s -skipping training candidate: asmbl_490.p1, not unique enough 485s -skipping training candidate: asmbl_621.p1, not unique enough 485s -skipping training candidate: asmbl_728.p1, not unique enough 485s -skipping training candidate: asmbl_167.p1, not unique enough 485s -skipping training candidate: asmbl_625.p1, not unique enough 485s -skipping training candidate: asmbl_8.p1, not unique enough 485s -skipping training candidate: asmbl_460.p1, not unique enough 485s -skipping training candidate: asmbl_815.p1, not unique enough 485s -skipping training candidate: asmbl_9.p1, not unique enough 485s -skipping training candidate: asmbl_459.p1, not unique enough 485s -skipping training candidate: asmbl_662.p1, not unique enough 485s -skipping training candidate: asmbl_854.p1, not unique enough 485s -skipping training candidate: asmbl_636.p1, not unique enough 485s -skipping training candidate: asmbl_851.p1, not unique enough 485s -skipping training candidate: asmbl_291.p1, not unique enough 485s -skipping training candidate: asmbl_743.p1, not unique enough 485s -skipping training candidate: asmbl_467.p1, not unique enough 485s -skipping training candidate: asmbl_569.p1, not unique enough 485s -skipping training candidate: asmbl_592.p1, not unique enough 485s -skipping training candidate: asmbl_710.p1, not unique enough 485s -skipping training candidate: asmbl_686.p1, not unique enough 485s -skipping training candidate: asmbl_649.p1, not unique enough 485s -skipping training candidate: asmbl_431.p1, not unique enough 485s -skipping training candidate: asmbl_32.p1, not unique enough 485s -skipping training candidate: asmbl_441.p1, not unique enough 485s -skipping training candidate: asmbl_438.p1, not unique enough 485s -skipping training candidate: asmbl_740.p1, not unique enough 485s -skipping training candidate: asmbl_30.p1, not unique enough 485s -skipping training candidate: asmbl_439.p1, not unique enough 485s -skipping training candidate: asmbl_779.p1, not unique enough 485s -skipping training candidate: asmbl_447.p1, not unique enough 485s -skipping training candidate: asmbl_780.p1, not unique enough 485s -skipping training candidate: asmbl_803.p1, not unique enough 485s -skipping training candidate: asmbl_442.p1, not unique enough 485s -skipping training candidate: asmbl_503.p1, not unique enough 485s -skipping training candidate: asmbl_443.p1, not unique enough 485s -skipping training candidate: asmbl_531.p1, not unique enough 485s -skipping training candidate: asmbl_687.p1, not unique enough 485s -skipping training candidate: asmbl_719.p1, not unique enough 485s -skipping training candidate: asmbl_822.p1, not unique enough 485s -skipping training candidate: asmbl_287.p1, not unique enough 485s -skipping training candidate: asmbl_685.p1, not unique enough 485s -skipping training candidate: asmbl_260.p1, not unique enough 485s -skipping training candidate: asmbl_715.p1, not unique enough 485s -skipping training candidate: asmbl_775.p1, not unique enough 485s -skipping training candidate: asmbl_31.p1, not unique enough 485s -skipping training candidate: asmbl_440.p1, not unique enough 485s -skipping training candidate: asmbl_377.p1, not unique enough 485s -skipping training candidate: asmbl_378.p1, not unique enough 485s -skipping training candidate: asmbl_821.p1, not unique enough 485s -skipping training candidate: asmbl_818.p1, not unique enough 485s -skipping training candidate: asmbl_493.p1, not unique enough 485s -skipping training candidate: asmbl_553.p1, not unique enough 485s -skipping training candidate: asmbl_659.p1, not unique enough 485s -skipping training candidate: asmbl_258.p1, not unique enough 485s -skipping training candidate: asmbl_713.p1, not unique enough 485s -skipping training candidate: asmbl_653.p1, not unique enough 485s -skipping training candidate: asmbl_628.p1, not unique enough 485s -skipping training candidate: asmbl_824.p1, not unique enough 485s -skipping training candidate: asmbl_597.p1, not unique enough 485s -skipping training candidate: asmbl_753.p1, not unique enough 485s -skipping training candidate: asmbl_614.p1, not unique enough 485s -skipping training candidate: asmbl_310.p1, not unique enough 485s -skipping training candidate: asmbl_724.p1, not unique enough 485s -skipping training candidate: asmbl_382.p1, not unique enough 485s -skipping training candidate: asmbl_819.p1, not unique enough 485s -skipping training candidate: asmbl_699.p1, not unique enough 485s -skipping training candidate: asmbl_700.p1, not unique enough 485s -skipping training candidate: asmbl_643.p1, not unique enough 485s -skipping training candidate: asmbl_571.p1, not unique enough 485s -skipping training candidate: asmbl_259.p1, not unique enough 485s -skipping training candidate: asmbl_521.p1, not unique enough 485s -skipping training candidate: asmbl_761.p1, not unique enough 485s -skipping training candidate: asmbl_735.p1, not unique enough 485s -skipping training candidate: asmbl_856.p1, not unique enough 485s -skipping training candidate: asmbl_648.p1, not unique enough 485s -skipping training candidate: asmbl_607.p1, not unique enough 485s -skipping training candidate: asmbl_163.p1, not unique enough 485s -skipping training candidate: asmbl_629.p1, not unique enough 485s -skipping training candidate: asmbl_517.p1, not unique enough 485s -skipping training candidate: asmbl_178.p1, not unique enough 485s -skipping training candidate: asmbl_482.p1, not unique enough 485s -skipping training candidate: asmbl_770.p1, not unique enough 485s -skipping training candidate: asmbl_858.p1, not unique enough 485s -skipping training candidate: asmbl_481.p1, not unique enough 485s -skipping training candidate: asmbl_776.p1, not unique enough 485s -skipping training candidate: asmbl_609.p1, not unique enough 485s 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enough 485s -skipping training candidate: asmbl_854.p2, not unique enough 485s -skipping training candidate: asmbl_598.p1, not unique enough 485s -skipping training candidate: asmbl_788.p1, not unique enough 485s -skipping training candidate: asmbl_69.p1, not unique enough 485s -skipping training candidate: asmbl_472.p1, not unique enough 485s -skipping training candidate: asmbl_717.p1, not unique enough 485s -skipping training candidate: asmbl_365.p1, not unique enough 485s -skipping training candidate: asmbl_771.p1, not unique enough 485s -skipping training candidate: asmbl_619.p1, not unique enough 485s -skipping training candidate: asmbl_616.p1, not unique enough 485s -skipping training candidate: asmbl_85.p1, not unique enough 485s -skipping training candidate: asmbl_518.p1, not unique enough 485s -skipping training candidate: asmbl_668.p1, not unique enough 485s -skipping training candidate: asmbl_828.p1, not unique enough 485s -skipping training candidate: asmbl_608.p1, not 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not unique enough 485s -skipping training candidate: asmbl_513.p1, not unique enough 485s -skipping training candidate: asmbl_615.p1, not unique enough 485s -skipping training candidate: asmbl_551.p1, not unique enough 485s -skipping training candidate: asmbl_816.p1, not unique enough 485s -skipping training candidate: asmbl_837.p1, not unique enough 485s -skipping training candidate: asmbl_853.p1, not unique enough 485s -skipping training candidate: asmbl_693.p1, not unique enough 485s -skipping training candidate: asmbl_546.p1, not unique enough 485s -skipping training candidate: asmbl_538.p1, not unique enough 485s -skipping training candidate: asmbl_539.p1, not unique enough 485s -skipping training candidate: asmbl_631.p1, not unique enough 485s -skipping training candidate: asmbl_463.p1, not unique enough 485s -skipping training candidate: asmbl_452.p1, not unique enough 485s -skipping training candidate: asmbl_146.p1, not unique enough 485s -skipping training candidate: 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candidate: asmbl_754.p1, not unique enough 485s -skipping training candidate: asmbl_515.p1, not unique enough 485s -skipping training candidate: asmbl_105.p1, not unique enough 485s -skipping training candidate: asmbl_572.p1, not unique enough 485s -skipping training candidate: asmbl_611.p1, not unique enough 485s -skipping training candidate: asmbl_172.p1, not unique enough 485s -skipping training candidate: asmbl_617.p1, not unique enough 485s -skipping training candidate: asmbl_823.p1, not unique enough 485s -skipping training candidate: asmbl_1.p1, not unique enough 485s -skipping training candidate: asmbl_146.p2, not unique enough 485s -skipping training candidate: asmbl_528.p1, not unique enough 485s -skipping training candidate: asmbl_586.p2, not unique enough 485s -skipping training candidate: asmbl_606.p1, not unique enough 485s -skipping training candidate: asmbl_454.p1, not unique enough 485s -skipping training candidate: asmbl_110.p1, not unique enough 485s -skipping training candidate: asmbl_525.p1, not unique enough 485s -skipping training candidate: asmbl_566.p1, not unique enough 485s -skipping training candidate: asmbl_626.p1, not unique enough 485s -skipping training candidate: asmbl_681.p1, not unique enough 485s -skipping training candidate: asmbl_792.p1, not unique enough 485s -skipping training candidate: asmbl_310.p2, not unique enough 485s -skipping training candidate: asmbl_724.p2, not unique enough 485s -skipping training candidate: asmbl_304.p1, not unique enough 485s -skipping training candidate: asmbl_732.p1, not unique enough 485s -skipping training candidate: asmbl_451.p1, not unique enough 485s -skipping training candidate: asmbl_57.p1, not unique enough 485s -skipping training candidate: asmbl_246.p2, not unique enough 485s -skipping training candidate: asmbl_484.p1, not unique enough 485s -skipping training candidate: asmbl_678.p2, not unique enough 485s -skipping training candidate: asmbl_682.p2, not unique enough 485s 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485s -skipping training candidate: asmbl_420.p2, not unique enough 485s -skipping training candidate: asmbl_855.p2, not unique enough 485s -skipping training candidate: asmbl_809.p1, not unique enough 485s -skipping training candidate: asmbl_303.p1, not unique enough 485s -skipping training candidate: asmbl_390.p1, not unique enough 485s -skipping training candidate: asmbl_731.p1, not unique enough 485s -skipping training candidate: asmbl_810.p1, not unique enough 485s -skipping training candidate: asmbl_494.p1, not unique enough 485s -skipping training candidate: asmbl_693.p2, not unique enough 485s -skipping training candidate: asmbl_199.p1, not unique enough 485s -skipping training candidate: asmbl_605.p1, not unique enough 485s -skipping training candidate: asmbl_593.p1, not unique enough 485s -skipping training candidate: asmbl_504.p1, not unique enough 485s -skipping training candidate: asmbl_575.p1, not unique enough 485s -skipping training candidate: asmbl_745.p3, not unique enough 485s -skipping training candidate: asmbl_574.p1, not unique enough 485s -skipping training candidate: asmbl_817.p1, not unique enough 485s -skipping training candidate: asmbl_455.p1, not unique enough 485s -skipping training candidate: asmbl_480.p1, not unique enough 485s -skipping training candidate: asmbl_77.p1, not unique enough 485s -skipping training candidate: asmbl_453.p1, not unique enough 485s -skipping training candidate: asmbl_526.p1, not unique enough 485s -skipping training candidate: asmbl_584.p1, not unique enough 485s -skipping training candidate: asmbl_778.p2, not unique enough 485s -skipping training candidate: asmbl_101.p1, not unique enough 485s -skipping training candidate: asmbl_165.p1, not unique enough 485s -skipping training candidate: asmbl_366.p1, not unique enough 485s -skipping training candidate: asmbl_502.p1, not unique enough 485s -skipping training candidate: asmbl_627.p1, not unique enough 485s -skipping training candidate: asmbl_769.p1, not unique enough 485s -skipping training candidate: asmbl_765.p2, not unique enough 485s -skipping training candidate: asmbl_207.p1, not unique enough 485s -skipping training candidate: asmbl_242.p1, not unique enough 485s -skipping training candidate: asmbl_331.p1, not unique enough 485s -skipping training candidate: asmbl_669.p1, not unique enough 485s -skipping training candidate: asmbl_684.p1, not unique enough 485s -skipping training candidate: asmbl_757.p1, not unique enough 485s -skipping training candidate: asmbl_199.p2, not unique enough 485s -skipping training candidate: asmbl_200.p1, not unique enough 485s -skipping training candidate: asmbl_593.p2, not unique enough 485s -skipping training candidate: asmbl_594.p1, not unique enough 485s -skipping training candidate: asmbl_536.p1, not unique enough 485s -skipping training candidate: asmbl_660.p1, not unique enough 485s -skipping training candidate: asmbl_794.p1, not unique enough 485s -skipping training candidate: asmbl_435.p1, not unique enough 485s -skipping training candidate: asmbl_554.p2, not unique enough 485s -skipping training candidate: asmbl_614.p2, not unique enough 485s -skipping training candidate: asmbl_588.p1, not unique enough 485s -skipping training candidate: asmbl_676.p1, not unique enough 485s -skipping training candidate: asmbl_706.p1, not unique enough 485s -skipping training candidate: asmbl_590.p1, not unique enough 485s -skipping training candidate: asmbl_68.p2, not unique enough 485s -skipping training candidate: asmbl_197.p1, not unique enough 485s -skipping training candidate: asmbl_246.p4, not unique enough 485s -skipping training candidate: asmbl_470.p2, not unique enough 485s -skipping training candidate: asmbl_471.p2, not unique enough 485s -skipping training candidate: asmbl_591.p1, not unique enough 485s -skipping training candidate: asmbl_678.p4, not unique enough 485s -skipping training candidate: asmbl_564.p1, not unique enough 485s -skipping training candidate: asmbl_200.p2, not unique enough 485s -skipping training candidate: asmbl_612.p1, not unique enough 485s -skipping training candidate: asmbl_594.p2, not unique enough 485s -skipping training candidate: asmbl_436.p2, not unique enough 485s -skipping training candidate: asmbl_532.p1, not unique enough 485s -skipping training candidate: asmbl_688.p2, not unique enough 485s -skipping training candidate: asmbl_122.p1, not unique enough 485s -skipping training candidate: asmbl_555.p1, not unique enough 485s -skipping training candidate: asmbl_646.p1, not unique enough 485s -skipping training candidate: asmbl_807.p1, not unique enough 485s -skipping training candidate: asmbl_498.p1, not unique enough 485s -skipping training candidate: asmbl_724.p3, not unique enough 485s -skipping training candidate: asmbl_122.p2, not unique enough 485s -skipping training candidate: asmbl_555.p2, not unique enough 485s -skipping training candidate: asmbl_718.p1, not unique enough 485s -skipping training candidate: asmbl_35.p2, not unique enough 485s -skipping training candidate: asmbl_437.p2, not unique enough 485s -skipping training candidate: asmbl_588.p2, not unique enough 485s -skipping training candidate: asmbl_791.p1, not unique enough 485s -skipping training candidate: asmbl_856.p2, not unique enough 485s -skipping training candidate: asmbl_548.p1, not unique enough 485s -skipping training candidate: asmbl_602.p1, not unique enough 485s -skipping training candidate: asmbl_497.p1, not unique enough 485s -skipping training candidate: asmbl_311.p2, not unique enough 485s -skipping training candidate: asmbl_601.p1, not unique enough 485s -skipping training candidate: asmbl_725.p2, not unique enough 485s -skipping training candidate: asmbl_73.p1, not unique enough 485s -skipping training candidate: asmbl_529.p1, not unique enough 485s -skipping training candidate: asmbl_2.p1, not unique enough 485s -skipping training candidate: asmbl_241.p1, not unique enough 485s -skipping training candidate: asmbl_683.p1, not unique enough 485s -skipping training candidate: asmbl_816.p2, not unique enough 485s -skipping training candidate: asmbl_231.p1, not unique enough 485s -skipping training candidate: asmbl_644.p1, not unique enough 485s -skipping training candidate: asmbl_133.p1, not unique enough 485s -skipping training candidate: asmbl_544.p1, not unique enough 485s -skipping training candidate: asmbl_577.p1, not unique enough 485s -skipping training candidate: asmbl_623.p1, not unique enough 485s -skipping training candidate: asmbl_134.p1, not unique enough 485s -skipping training candidate: asmbl_545.p1, not unique enough 485s -skipping training candidate: asmbl_649.p2, not unique enough 485s -skipping training candidate: asmbl_69.p2, not unique enough 485s -skipping training candidate: asmbl_132.p1, not unique enough 485s -skipping training candidate: asmbl_472.p2, not unique enough 485s -skipping training candidate: asmbl_533.p1, not unique enough 485s -skipping training candidate: asmbl_543.p1, not unique enough 485s -skipping training candidate: asmbl_664.p1, not unique enough 485s -skipping training candidate: asmbl_677.p1, not unique enough 485s -skipping training candidate: asmbl_748.p1, not unique enough 485s -skipping training candidate: asmbl_802.p1, not unique enough 485s -skipping training candidate: asmbl_117.p2, not unique enough 485s -skipping training candidate: asmbl_559.p2, not unique enough 485s -skipping training candidate: asmbl_825.p1, not unique enough 485s -skipping training candidate: asmbl_596.p1, not unique enough 485s -skipping training candidate: asmbl_703.p1, not unique enough 485s -skipping training candidate: asmbl_838.p1, not unique enough 485s -skipping training candidate: asmbl_469.p1, not unique enough 485s -skipping training candidate: asmbl_698.p1, not unique enough 485s -skipping training candidate: asmbl_798.p1, not unique enough 485s -skipping training candidate: asmbl_290.p3, not unique enough 485s -skipping training candidate: asmbl_409.p2, not unique enough 485s -skipping training candidate: asmbl_746.p3, not unique enough 485s -skipping training candidate: asmbl_780.p2, not unique enough 485s -skipping training candidate: asmbl_838.p2, not unique enough 485s -skipping training candidate: asmbl_295.p1, not unique enough 485s -skipping training candidate: asmbl_741.p1, not unique enough 485s -skipping training candidate: asmbl_232.p1, not unique enough 485s -skipping training candidate: asmbl_645.p1, not unique enough 485s -skipping training candidate: asmbl_589.p1, not unique enough 485s -skipping training candidate: asmbl_657.p1, not unique enough 485s -skipping training candidate: asmbl_218.p1, not unique enough 485s -skipping training candidate: asmbl_658.p1, not unique enough 485s -skipping training candidate: asmbl_656.p1, not unique enough 485s -skipping training candidate: asmbl_675.p1, not unique enough 485s -skipping training candidate: asmbl_697.p1, not unique enough 485s -skipping training candidate: asmbl_808.p1, not unique enough 485s -skipping training candidate: asmbl_674.p1, not unique enough 485s -skipping training candidate: asmbl_465.p1, not unique enough 485s -skipping training candidate: asmbl_443.p2, not unique enough 485s -skipping training candidate: asmbl_673.p1, not unique enough 485s -skipping training candidate: asmbl_788.p2, not unique enough 485s -skipping training candidate: asmbl_4.p1, not unique enough 485s -skipping training candidate: asmbl_278.p3, not unique enough 485s -skipping training candidate: asmbl_408.p2, not unique enough 485s -skipping training candidate: asmbl_464.p1, not unique enough 485s -skipping training candidate: asmbl_693.p3, not unique enough 485s -skipping training candidate: asmbl_837.p2, not unique enough 485s -skipping training candidate: asmbl_463.p2, not unique enough 485s -skipping training candidate: asmbl_13.p2, not unique enough 485s -skipping training candidate: asmbl_457.p2, not unique enough 485s -skipping training candidate: asmbl_458.p2, not unique enough 485s -skipping training candidate: asmbl_637.p1, not unique enough 485s -skipping training candidate: asmbl_750.p1, not unique enough 485s -skipping training candidate: asmbl_485.p1, not unique enough 485s -skipping training candidate: asmbl_562.p1, not unique enough 485s -skipping training candidate: asmbl_636.p2, not unique enough 485s -skipping training candidate: asmbl_748.p2, not unique enough 485s -skipping training candidate: asmbl_310.p4, not unique enough 485s -skipping training candidate: asmbl_724.p4, not unique enough 485s -skipping training candidate: asmbl_723.p1, not unique enough 485s -skipping training candidate: asmbl_305.p1, not unique enough 485s -skipping training candidate: asmbl_733.p1, not unique enough 485s -skipping training candidate: asmbl_644.p2, not unique enough 485s -skipping training candidate: asmbl_498.p2, not unique enough 485s -skipping training candidate: asmbl_704.p1, not unique enough 485s -skipping training candidate: asmbl_725.p3, not unique enough 485s -skipping training candidate: asmbl_230.p2, not unique enough 485s -skipping training candidate: asmbl_221.p1, not unique enough 485s -skipping training candidate: asmbl_622.p1, not unique enough 485s -skipping training candidate: asmbl_655.p1, not unique enough 485s -skipping training candidate: asmbl_643.p2, not unique enough 485s -skipping training candidate: asmbl_716.p1, not unique enough 485s -skipping training candidate: asmbl_726.p2, not unique enough 485s -skipping training candidate: asmbl_516.p1, not unique enough 485s -skipping training candidate: asmbl_587.p1, not unique enough 485s -skipping training candidate: asmbl_813.p2, not unique enough 485s -skipping training candidate: asmbl_310.p5, not unique enough 485s -skipping training candidate: asmbl_537.p2, not unique enough 485s -skipping training candidate: asmbl_578.p1, not unique enough 485s -skipping training candidate: asmbl_724.p5, not unique enough 485s -skipping training candidate: asmbl_751.p1, not unique enough 485s -skipping training candidate: asmbl_815.p2, not unique enough 485s -skipping training candidate: asmbl_151.p1, not unique enough 485s -skipping training candidate: asmbl_410.p1, not unique enough 485s -skipping training candidate: asmbl_582.p1, not unique enough 485s -skipping training candidate: asmbl_580.p1, not unique enough 485s -skipping training candidate: asmbl_839.p1, not unique enough 485s -skipping training candidate: asmbl_290.p4, not unique enough 485s -skipping training candidate: asmbl_557.p1, not unique enough 485s -skipping training candidate: asmbl_660.p2, not unique enough 485s -skipping training candidate: asmbl_700.p2, not unique enough 485s -skipping training candidate: asmbl_745.p4, not unique enough 485s -skipping training candidate: asmbl_746.p4, not unique enough 485s -skipping training candidate: asmbl_779.p2, not unique enough 485s -skipping training candidate: asmbl_696.p1, not unique enough 485s -skipping training candidate: asmbl_452.p2, not unique enough 485s -skipping training candidate: asmbl_763.p1, not unique enough 485s -skipping training candidate: asmbl_814.p2, not unique enough 485s -skipping training candidate: asmbl_523.p1, not unique enough 485s -skipping training candidate: asmbl_752.p1, not unique enough 485s -skipping training candidate: asmbl_797.p1, not unique enough 485s -skipping training candidate: asmbl_607.p2, not unique enough 485s -skipping training candidate: asmbl_780.p3, not unique enough 485s -skipping training candidate: asmbl_127.p1, not unique enough 485s -skipping training candidate: asmbl_550.p1, not unique enough 485s -skipping training candidate: asmbl_646.p2, not unique enough 485s -skipping training candidate: asmbl_782.p1, not unique enough 485s -skipping training candidate: asmbl_362.p2, not unique enough 485s -skipping training candidate: asmbl_507.p2, not unique enough 485s -skipping training candidate: asmbl_530.p1, not unique enough 485s -skipping training candidate: asmbl_784.p2, not unique enough 485s -skipping training candidate: asmbl_772.p2, not unique enough 485s -skipping training candidate: asmbl_786.p2, not unique enough 485s -skipping training candidate: asmbl_773.p2, not unique enough 485s -skipping training candidate: asmbl_826.p1, not unique enough 485s -skipping training candidate: asmbl_15.p1, not unique enough 485s -skipping training candidate: asmbl_456.p1, not unique enough 485s -skipping training candidate: asmbl_530.p2, not unique enough 485s -skipping training candidate: asmbl_601.p2, not unique enough 485s -skipping training candidate: asmbl_641.p1, not unique enough 485s -skipping training candidate: asmbl_290.p5, not unique enough 485s -skipping training candidate: asmbl_519.p2, not unique enough 485s -skipping training candidate: asmbl_691.p1, not unique enough 485s -skipping training candidate: asmbl_745.p5, not unique enough 485s -skipping training candidate: asmbl_746.p5, not unique enough 485s -skipping training candidate: asmbl_288.p2, not unique enough 485s -skipping training candidate: asmbl_431.p2, not unique enough 485s -skipping training candidate: asmbl_687.p2, not unique enough 485s -skipping training candidate: asmbl_689.p1, not unique enough 485s -skipping training candidate: asmbl_685.p2, not unique enough 485s -skipping training candidate: asmbl_742.p1, not unique enough 485s -skipping training candidate: asmbl_765.p3, not unique enough 485s -skipping training candidate: asmbl_21.p2, not unique enough 485s -skipping training candidate: asmbl_22.p2, not unique enough 485s -skipping training candidate: asmbl_228.p2, not unique enough 485s -skipping training candidate: asmbl_378.p2, not unique enough 485s -skipping training candidate: asmbl_379.p2, not unique enough 485s -skipping training candidate: asmbl_450.p2, not unique enough 485s -skipping training candidate: asmbl_448.p2, not unique enough 485s -skipping training candidate: asmbl_449.p2, not unique enough 485s -skipping training candidate: asmbl_642.p1, not unique enough 485s -skipping training candidate: asmbl_647.p2, not unique enough 485s -skipping training candidate: asmbl_648.p2, not unique enough 485s -skipping training candidate: asmbl_821.p2, not unique enough 485s -skipping training candidate: asmbl_822.p2, not unique enough 485s -skipping training candidate: asmbl_335.p2, not unique enough 485s -skipping training candidate: asmbl_331.p2, not unique enough 485s -skipping training candidate: asmbl_328.p2, not unique enough 485s -skipping training candidate: asmbl_330.p1, not unique enough 485s -skipping training candidate: asmbl_528.p2, not unique enough 485s -skipping training candidate: asmbl_628.p2, not unique enough 485s -skipping training candidate: asmbl_736.p1, not unique enough 485s -skipping training candidate: asmbl_751.p2, not unique enough 485s -skipping training candidate: asmbl_756.p1, not unique enough 485s -skipping training candidate: asmbl_757.p2, not unique enough 485s -skipping training candidate: asmbl_754.p2, not unique enough 485s -skipping training candidate: asmbl_592.p2, not unique enough 485s -skipping training candidate: asmbl_670.p1, not unique enough 485s -skipping training candidate: asmbl_834.p1, not unique enough 485s -skipping training candidate: asmbl_90.p2, not unique enough 485s -skipping training candidate: asmbl_512.p2, not unique enough 485s -skipping training candidate: asmbl_513.p2, not unique enough 485s -skipping training candidate: asmbl_635.p2, not unique enough 485s -skipping training candidate: asmbl_764.p1, not unique enough 485s -skipping training candidate: asmbl_835.p1, not unique enough 485s -skipping training candidate: asmbl_303.p2, not unique enough 485s -skipping training candidate: asmbl_414.p1, not unique enough 485s -skipping training candidate: asmbl_479.p2, not unique enough 485s -skipping training candidate: asmbl_693.p4, not unique enough 485s -skipping training candidate: asmbl_716.p2, not unique enough 485s -skipping training candidate: asmbl_742.p2, not unique enough 485s -skipping training candidate: asmbl_731.p2, not unique enough 485s -skipping training candidate: asmbl_794.p2, not unique enough 485s -skipping training candidate: asmbl_799.p1, not unique enough 485s -skipping training candidate: asmbl_833.p1, not unique enough 485s -skipping training candidate: asmbl_433.p1, not unique enough 485s -skipping training candidate: asmbl_677.p2, not unique enough 485s -skipping training candidate: asmbl_847.p2, not unique enough 485s -skipping training candidate: asmbl_570.p2, not unique enough 485s -skipping training candidate: asmbl_535.p1, not unique enough 485s -skipping training candidate: asmbl_627.p2, not unique enough 485s -skipping training candidate: asmbl_719.p2, not unique enough 485s -skipping training candidate: asmbl_722.p1, not unique enough 485s -skipping training candidate: asmbl_150.p1, not unique enough 485s -skipping training candidate: asmbl_579.p1, not unique enough 485s -skipping training candidate: asmbl_584.p2, not unique enough 485s -skipping training candidate: asmbl_682.p3, not unique enough 485s -skipping training candidate: asmbl_712.p2, not unique enough 485s -skipping training candidate: asmbl_815.p3, not unique enough 485s -skipping training candidate: asmbl_49.p2, not unique enough 485s -skipping training candidate: asmbl_50.p2, not unique enough 485s -skipping training candidate: asmbl_51.p2, not unique enough 485s -skipping training candidate: asmbl_343.p1, not unique enough 485s -skipping training candidate: asmbl_491.p2, not unique enough 485s -skipping training candidate: asmbl_492.p2, not unique enough 485s -skipping training candidate: asmbl_489.p2, not unique enough 485s -skipping training candidate: asmbl_490.p2, not unique enough 485s -skipping training candidate: asmbl_793.p1, not unique enough 485s -skipping training candidate: asmbl_198.p3, not unique enough 485s -skipping training candidate: asmbl_199.p3, not unique enough 485s -skipping training candidate: asmbl_200.p3, not unique enough 485s -skipping training candidate: asmbl_507.p3, not unique enough 485s -skipping training candidate: asmbl_592.p3, not unique enough 485s -skipping training candidate: asmbl_606.p2, not unique enough 485s -skipping training candidate: asmbl_593.p3, not unique enough 485s -skipping training candidate: asmbl_594.p3, not unique enough 485s -skipping training candidate: asmbl_839.p2, not unique enough 485s -skipping training candidate: asmbl_6.p1, not unique enough 485s -skipping training candidate: asmbl_146.p3, not unique enough 485s -skipping training candidate: asmbl_446.p2, not unique enough 485s -skipping training candidate: asmbl_466.p1, not unique enough 485s -skipping training candidate: asmbl_531.p2, not unique enough 485s -skipping training candidate: asmbl_585.p2, not unique enough 485s -skipping training candidate: asmbl_586.p3, not unique enough 485s -skipping training candidate: asmbl_606.p3, not unique enough 485s -skipping training candidate: asmbl_635.p3, not unique enough 485s -skipping training candidate: asmbl_726.p3, not unique enough 485s -skipping training candidate: asmbl_8.p2, not unique enough 485s -skipping training candidate: asmbl_9.p2, not unique enough 485s -skipping training candidate: asmbl_57.p2, not unique enough 485s -skipping training candidate: asmbl_365.p2, not unique enough 485s -skipping training candidate: asmbl_459.p2, not unique enough 485s -skipping training candidate: asmbl_460.p2, not unique enough 485s -skipping training candidate: asmbl_461.p2, not unique enough 485s -skipping training candidate: asmbl_462.p2, not unique enough 485s -skipping training candidate: asmbl_484.p2, not unique enough 485s -skipping training candidate: asmbl_770.p2, not unique enough 485s -skipping training candidate: asmbl_771.p2, not unique enough 485s -skipping training candidate: asmbl_820.p1, not unique enough 485s -skipping training candidate: asmbl_259.p2, not unique enough 485s -skipping training candidate: asmbl_349.p2, not unique enough 485s -skipping training candidate: asmbl_692.p2, not unique enough 485s -skipping training candidate: asmbl_713.p2, not unique enough 485s -skipping training candidate: asmbl_765.p4, not unique enough 485s -skipping training candidate: asmbl_787.p2, not unique enough 485s -skipping training candidate: asmbl_85.p2, not unique enough 485s -skipping training candidate: asmbl_518.p2, not unique enough 485s -skipping training candidate: asmbl_517.p2, not unique enough 485s -skipping training candidate: asmbl_709.p2, not unique enough 485s -skipping training candidate: asmbl_778.p3, not unique enough 485s -skipping training candidate: asmbl_830.p1, not unique enough 485s -skipping training candidate: asmbl_847.p3, not unique enough 485s -skipping training candidate: asmbl_530.p3, not unique enough 485s -skipping training candidate: asmbl_722.p2, not unique enough 485s -skipping training candidate: asmbl_817.p2, not unique enough 485s -skipping training candidate: asmbl_799.p2, not unique enough 485s -skipping training candidate: asmbl_813.p3, not unique enough 485s -skipping training candidate: asmbl_290.p6, not unique enough 485s -skipping training candidate: asmbl_746.p6, not unique enough 485s -skipping training candidate: asmbl_536.p2, not unique enough 485s -skipping training candidate: asmbl_534.p1, not unique enough 485s -skipping training candidate: asmbl_692.p3, not unique enough 485s -skipping training candidate: asmbl_115.p2, not unique enough 485s -skipping training candidate: asmbl_278.p5, not unique enough 485s -skipping training candidate: asmbl_320.p1, not unique enough 485s -skipping training candidate: asmbl_452.p3, not unique enough 485s -skipping training candidate: asmbl_569.p2, not unique enough 485s -skipping training candidate: asmbl_560.p2, not unique enough 485s -skipping training candidate: asmbl_561.p2, not unique enough 485s -skipping training candidate: asmbl_693.p5, not unique enough 485s -skipping training candidate: asmbl_695.p1, not unique enough 485s -skipping training candidate: asmbl_734.p2, not unique enough 485s -skipping training candidate: asmbl_721.p1, not unique enough 485s -skipping training candidate: asmbl_765.p5, not unique enough 485s -skipping training candidate: asmbl_766.p1, not unique enough 485s -skipping training candidate: asmbl_807.p2, not unique enough 485s -skipping training candidate: asmbl_800.p1, not unique enough 485s -skipping training candidate: asmbl_164.p2, not unique enough 485s -skipping training candidate: asmbl_531.p3, not unique enough 485s -skipping training candidate: asmbl_558.p2, not unique enough 485s -skipping training candidate: asmbl_626.p2, not unique enough 485s -skipping training candidate: asmbl_831.p1, not unique enough 485s 485s -redundancy-minimized set includes 396 / 1067 = 37.11% 485s 485s * [Mon Mar 18 02:17:34 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 485s PCT_GC: 42 485s * [Mon Mar 18 02:17:34 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores 486s * [Mon Mar 18 02:17:35 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores 493s * [Mon Mar 18 02:17:42 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 493s Selecting best orfs 493s * [Mon Mar 18 02:17:42 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement 493s Training start codon pattern recognition* [Mon Mar 18 02:17:42 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 493s * [Mon Mar 18 02:17:42 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores 493s -round: 1 498s -round: 2 504s -round: 3 509s -round: 4 514s -round: 5 519s * [Mon Mar 18 02:18:08 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 519s -parsing scores 525s * [Mon Mar 18 02:18:14 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 525s Error in library(ggplot2) : there is no package called ‘ggplot2’ 525s Execution halted 525s * [Mon Mar 18 02:18:14 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 526s Error in library(ggplot2) : there is no package called ‘ggplot2’ 526s Execution halted 526s * [Mon Mar 18 02:18:15 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : 526s Error in library(seqLogo) : there is no package called ‘seqLogo’ 526s Execution halted 526s * [Mon Mar 18 02:18:15 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : 526s Error in library(seqLogo) : there is no package called ‘seqLogo’ 526s Execution halted 526s * [Mon Mar 18 02:18:15 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced 526s num features: 238 num_incorporate: 71 526s -feature swap of score: 0.52233068358735 instead of -2.4838353992418 526s -feature swap of score: 3.4925122435335 instead of -2.69571560364119 526s -feature swap of score: -0.479799656028566 instead of -2.28706103601398 526s -feature swap of score: -0.0881342990948846 instead of -2.01923571762916 526s -feature swap of score: 3.70320425069563 instead of -2.540266312821 526s -feature swap of score: -1.18001089627022 instead of -2.19874275195072 526s -feature swap of score: 0.890711131288117 instead of -1.48110814799594 526s -feature swap of score: -1.05010135127967 instead of -1.29405271062499 526s -feature swap of score: -0.0660971314530546 instead of -1.10945144224631 526s -feature swap of score: 4.44453897240347 instead of -0.978468124148539 526s -feature swap of score: -0.464399759591707 instead of -0.841794961146521 526s -feature swap of score: 0.255068847557726 instead of -0.83142113951215 526s -feature swap of score: 1.95582633064074 instead of -0.76896518568472 526s -feature swap of score: -0.0332453222172366 instead of -0.682979129272786 526s -feature swap of score: 1.8228745697833 instead of -0.653744437026382 526s -feature swap of score: 1.00115669145456 instead of -0.336891026477184 526s -feature swap of score: 0.672803798904712 instead of -0.578246064931 526s -feature swap of score: 1.8162642359003 instead of -0.452564095078051 526s -feature swap of score: 0.280846761877589 instead of -0.647264557316993 526s -feature swap of score: 0.366355095526699 instead of -0.615212412314209 526s -feature swap of score: 2.52986097726451 instead of -0.758989032460075 526s -feature swap of score: -0.0952627696553691 instead of -0.817191160815284 526s -feature swap of score: 0.996754631653053 instead of -0.80551837636419 526s -feature swap of score: 0.354999699462731 instead of -0.274911636492182 526s -feature swap of score: 1.28605443964402 instead of 0.0980797372313064 526s -feature swap of score: 0.32578718956916 instead of -0.042861330285221 526s -feature swap of score: 2.48770150611293 instead of -0.0868957590364158 526s -feature swap of score: 2.64754362015744 instead of 0.2916904256282 526s -feature swap of score: 1.01988302433125 instead of 0.036666467034015 526s -feature swap of score: 0.702376236311601 instead of -0.128287580103504 526s -feature swap of score: 2.99676647453095 instead of 0.320673377955444 526s -feature swap of score: 4.3305495710187 instead of 0.295875888654129 526s -feature swap of score: 1.17421891679809 instead of 0.254710288367653 526s -feature swap of score: 0.401521517315352 instead of 0.370606147577384 526s -feature swap of score: 3.89634731515857 instead of 0.389772413567672 526s -feature swap of score: 2.74749373854816 instead of 0.451140083480975 526s -feature swap of score: 4.14790539102617 instead of 0.173512045799991 526s -feature swap of score: 2.68928352460324 instead of 0.0987413441847772 526s -feature swap of score: 0.570947526770153 instead of -0.152678189275884 526s -feature swap of score: 2.87693452246047 instead of 0.175971771120871 526s -feature swap of score: 0.345761582949679 instead of 0.189210540579853 526s -feature swap of score: 1.75381703871986 instead of -0.176138170873724 526s -feature swap of score: 6.3225755214291 instead of 0.182318752228176 526s -feature swap of score: -0.00356336589610784 instead of -0.074332288426649 526s -feature swap of score: 1.25652300984573 instead of 0.440440454930295 526s -feature swap of score: 4.35627103288236 instead of 0.601792868596411 526s -feature swap of score: 3.34305077634812 instead of 0.646355594435306 526s -feature swap of score: 0.89148415481126 instead of 0.847522010634187 526s -feature swap of score: 3.6953445371134 instead of 0.751030612474935 526s -feature swap of score: 5.78699079524925 instead of 0.699840066363169 526s -feature swap of score: 2.15409587173251 instead of 0.715035855107118 526s -feature swap of score: 1.47994164306661 instead of 0.417255934795064 526s -feature swap of score: 4.91570803685393 instead of 0.612782191206777 526s -feature swap of score: 0.527551455366298 instead of 0.495108302468003 526s -feature swap of score: 3.40423853426828 instead of 0.883665117310717 526s -feature swap of score: 0.802539851871931 instead of 0.787642557429234 526s -num feature swaps: 56 526s * [Mon Mar 18 02:18:15 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 526s -round: 1 531s -round: 2 536s -round: 3 541s -round: 4 546s -round: 5 551s * [Mon Mar 18 02:18:39 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 551s -parsing scores 556s * [Mon Mar 18 02:18:45 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 557s Error in library(ggplot2) : there is no package called ‘ggplot2’ 557s Execution halted 557s * [Mon Mar 18 02:18:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 557s Error in library(ggplot2) : there is no package called ‘ggplot2’ 557s Execution halted 557s * [Mon Mar 18 02:18:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 557s Error in library(seqLogo) : there is no package called ‘seqLogo’ 557s Execution halted 557s * [Mon Mar 18 02:18:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 557s Refining start codon selections. 557s -number of revised start positions: 83 557s * [Mon Mar 18 02:18:46 2024] Running CMD: cp /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 557s copying output to final output file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Mon Mar 18 02:18:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 557s Making bed file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 557s * [Mon Mar 18 02:18:46 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 558s Making pep file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 558s * [Mon Mar 18 02:18:47 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 558s Making cds file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 558s transdecoder is finished. See output files /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* 558s 558s 558s 558s ../../util/cdna_alignment_orf_to_genome_orf.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 pasa_assemblies.gff3 pasa_assemblies.fasta > pasa_assemblies.fasta.transdecoder.genome.gff3 558s 558s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 205, 828 558s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_117.p2. 558s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_127.p1. 558s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 142, 1281 558s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_177.p1. 558s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_198.p3. 558s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_199.p3. 558s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_200.p3. 558s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. 558s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. 558s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. 558s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. 558s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. 558s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 107, 466 558s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_289.p2. 558s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_290.p1. 558s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [21], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [22], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [23], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_420.p1. 558s -Warning [25], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 140, 700 558s -Warning [26], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 340, 816 558s -Warning [27], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 93, 1106 558s -Warning [28], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [29], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [30], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 312, 1253 558s -Warning [31], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_550.p1. 558s -Warning [32], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_559.p2. 558s -Warning [33], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [34], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_592.p3. 558s -Warning [35], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_593.p3. 558s -Warning [36], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_594.p3. 558s -Warning [37], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [38], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_615.p1. 558s -Warning [39], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 80, 427 558s -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. 558s -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. 558s -Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. 558s -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. 558s -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 112, 447 558s -Warning [46], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_745.p2. 558s -Warning [47], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_746.p1. 558s -Warning [48], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 108, 452 558s -Warning [49], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 2, 562 558s -Warning [50], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 558s -Warning [51], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 141, 545 558s -Warning [52], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 558s CDS coords: 178, 1623 558s -Warning [53], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_855.p1. 558s 558s 558s Done. 765 / 792 transcript orfs could be propagated to the genome 558s 559s 559s 559s ../../util/fasta_prot_checker.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 559s 559s Done. See pasa_assemblies.fasta.transdecoder.\* 559s 559s echo "Done. See pasa_assemblies.fasta.transdecoder.\*" 559s 559s 559s exit 0 559s make[1]: Leaving directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 559s Running example in $... 559s make[1]: Entering directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 559s ./runMe.sh 559s CMD: mkdir -p /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir 559s * [Mon Mar 18 02:18:48 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl Trinity.fasta 0 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat 559s 559s 559s -first extracting base frequencies, we'll need them later. 559s 559s 559s - extracting ORFs from transcripts. 559s -total transcripts to examine: 921 561s [100/921] = 10.86% done [200/921] = 21.72% done [300/921] = 32.57% done [400/921] = 43.43% done [500/921] = 54.29% done [600/921] = 65.15% done [700/921] = 76.00% done [800/921] = 86.86% done [900/921] = 97.72% done CMD: touch /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 561s 561s 561s ################################# 561s ### Done preparing long ORFs. ### 561s ################################## 561s 561s Use file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. 561s 561s Then, run TransDecoder.Predict for your final coding region predictions. 561s 561s 561s * [Mon Mar 18 02:18:50 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 561s * [Mon Mar 18 02:18:50 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 561s -skipping training candidate: comp847_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp992_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp718_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1177_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp999_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp989_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp836_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp621_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp844_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp594_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp956_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1044_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp835_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp1029_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1016_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1207_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp862_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp703_c0_seq1.p2, not unique enough 561s -skipping training candidate: comp1191_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp867_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp1207_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp905_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp784_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp674_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp924_c0_seq1.p2, not unique enough 561s -skipping training candidate: comp1174_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1046_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp1191_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp1044_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp873_c0_seq1.p1, not unique enough 561s -skipping training candidate: comp1177_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp1196_c0_seq2.p1, not unique enough 561s -skipping training candidate: comp999_c0_seq2.p2, not unique enough 561s -skipping training candidate: comp985_c0_seq2.p1, not unique enough 561s 561s -redundancy-minimized set includes 810 / 844 = 95.97% 561s 562s * [Mon Mar 18 02:18:51 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 562s PCT_GC: 38 562s * [Mon Mar 18 02:18:51 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores 564s * [Mon Mar 18 02:18:53 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores 570s * [Mon Mar 18 02:18:59 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 570s Selecting best orfs 570s * [Mon Mar 18 02:18:59 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement 570s Training start codon pattern recognition* [Mon Mar 18 02:18:59 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 571s * [Mon Mar 18 02:19:00 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores 571s -round: 1 576s -round: 2 581s -round: 3 587s -round: 4 592s -round: 5 597s * [Mon Mar 18 02:19:26 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 597s -parsing scores 603s * [Mon Mar 18 02:19:32 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 604s Error in library(ggplot2) : there is no package called ‘ggplot2’ 604s Execution halted 604s * [Mon Mar 18 02:19:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 604s Error in library(ggplot2) : there is no package called ‘ggplot2’ 604s Execution halted 604s * [Mon Mar 18 02:19:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : 604s Error in library(seqLogo) : there is no package called ‘seqLogo’ 604s Execution halted 604s * [Mon Mar 18 02:19:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : 604s Error in library(seqLogo) : there is no package called ‘seqLogo’ 604s Execution halted 604s * [Mon Mar 18 02:19:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced 604s num features: 358 num_incorporate: 107 604s -feature swap of score: 2.01860755745774 instead of -2.43253294753209 604s -feature swap of score: 2.34732451463516 instead of -2.03515280104856 605s -feature swap of score: 2.42600756963178 instead of -1.88586714183678 605s -feature swap of score: 4.04692570560011 instead of -2.07838396233827 605s -feature swap of score: -2.10349049055208 instead of -2.14357898216183 605s -feature swap of score: 3.34270681682176 instead of -1.68919591401722 605s -feature swap of score: 0.785638027271692 instead of -1.75537844488172 605s -feature swap of score: 0.124937617546208 instead of -1.42423447927029 605s -feature swap of score: 3.80360939610757 instead of -1.25581956645478 605s -feature swap of score: 2.22972790847055 instead of -1.43724022198391 605s -feature swap of score: 1.87223224767761 instead of -1.39134963935408 605s -feature swap of score: -0.869196741065359 instead of -1.45437592553593 605s -feature swap of score: 2.61126122082178 instead of -1.4644389491732 605s -feature swap of score: 0.041614898233897 instead of -1.38236698907653 605s -feature swap of score: 5.23702512832804 instead of -1.06647647854364 605s -feature swap of score: 0.489018424262898 instead of -0.95713076184448 605s -feature swap of score: 1.06810458576389 instead of -0.894284983683669 605s -feature swap of score: -0.226298629660561 instead of -0.948994050642804 605s -feature swap of score: 0.450699974271914 instead of -0.959497695240219 605s -feature swap of score: 4.28695919068754 instead of -0.978907600609435 605s -feature swap of score: 2.14133448495559 instead of -0.753180766675387 605s -feature swap of score: 4.12202729113471 instead of -0.76828282708309 605s -feature swap of score: -0.104946382094106 instead of -0.628776084467911 605s -feature swap of score: 0.000572807808514326 instead of -0.53263942949094 605s -feature swap of score: 0.198006134044188 instead of -0.34106805075173 605s -feature swap of score: 3.6047163749624 instead of -0.51212082035361 605s -feature swap of score: 0.814286538900709 instead of -0.339061555243772 605s -feature swap of score: 4.97523538835402 instead of -0.219644205392414 605s -feature swap of score: 1.97045125499639 instead of -0.113036838336636 605s -feature swap of score: 4.13053733045551 instead of -0.170052581383971 605s -feature swap of score: 0.00206436128981199 instead of -0.181062974960661 605s -feature swap of score: 1.604245252388 instead of 0.0517161275151237 605s -feature swap of score: 4.3932806981529 instead of 0.0860431565952234 605s -feature swap of score: 1.72957229182765 instead of 0.221968210457067 605s -feature swap of score: 1.57263236697426 instead of 0.288968311790631 605s -feature swap of score: 0.203166281459456 instead of 0.10534662338876 605s -feature swap of score: 4.38190400149154 instead of 0.196370432457334 605s -feature swap of score: 5.04613038233112 instead of 0.150614918926321 605s -feature swap of score: 2.26071953474249 instead of 0.230526386115092 605s -feature swap of score: 5.13639850152629 instead of 0.252892697647447 605s -feature swap of score: 1.17098382473728 instead of 0.282995900530861 605s -feature swap of score: 4.34776268138483 instead of 0.41430990147474 605s -feature swap of score: 2.15329616437699 instead of 0.429451771590664 605s -feature swap of score: 5.09229418476461 instead of 0.297828956020416 605s -feature swap of score: 1.13675328930652 instead of 0.171694593520241 605s -feature swap of score: 2.02231900226323 instead of 0.206703978994726 605s -feature swap of score: 2.66734827613583 instead of 0.443525927859022 605s -feature swap of score: 3.77684820014943 instead of 0.599510264128007 605s -feature swap of score: 1.29789971226826 instead of 0.51658385615187 605s -feature swap of score: 3.74256664801257 instead of 0.445260647950643 605s -feature swap of score: 4.32680419305246 instead of 0.596611075477652 605s -feature swap of score: 1.77920876164079 instead of 0.52605377488021 605s -feature swap of score: 1.61583261588263 instead of 0.65317830698915 605s -feature swap of score: 4.10400531839299 instead of 0.789843632233928 605s -feature swap of score: 1.83659343125585 instead of 0.716731928502843 605s -feature swap of score: 1.6438027810344 instead of 0.767790779444299 605s -feature swap of score: 2.51637019194037 instead of 0.699527206449989 605s -feature swap of score: 1.60560873858958 instead of 1.07464412670026 605s -feature swap of score: 2.89883210321421 instead of 1.07157389032513 605s -feature swap of score: 2.93101514977772 instead of 0.988616846801185 605s -feature swap of score: 3.72069918320373 instead of 0.868454192870146 605s -feature swap of score: 1.03519107357972 instead of 0.753010048444791 605s -feature swap of score: 4.01020820806659 instead of 0.886358064075704 605s -feature swap of score: 0.879618323769624 instead of 0.61109819149034 605s -feature swap of score: 7.15234940921215 instead of 1.03360771341683 605s -feature swap of score: 1.83921458905268 instead of 1.02334035960285 605s -feature swap of score: 2.23998772164463 instead of 0.834483027752134 605s -feature swap of score: 2.16522830829353 instead of 1.1968190751818 605s -feature swap of score: 3.565902255058 instead of 1.04816444694555 605s -feature swap of score: 1.1156878707122 instead of 0.972785593550388 605s -feature swap of score: 1.63015648897591 instead of 1.12916093095551 605s -feature swap of score: 3.15623525707792 instead of 1.19443129843577 605s -feature swap of score: 1.75064193312005 instead of 1.22439213990375 605s -feature swap of score: 2.22558017270471 instead of 1.41095670579146 605s -feature swap of score: 1.69472767650654 instead of 1.47090708539632 605s -feature swap of score: 5.71675848798316 instead of 1.54417528485585 605s -feature swap of score: 2.36834513989863 instead of 1.56065511814006 605s -feature swap of score: 4.72132107671951 instead of 1.39108914413569 605s -feature swap of score: 2.98996061269645 instead of 1.4726797291019 605s -feature swap of score: 2.30202014931778 instead of 1.35942459345001 605s -feature swap of score: 6.94448025054924 instead of 1.53071141968655 605s -feature swap of score: 2.02147832129674 instead of 1.39293685217156 605s -feature swap of score: 3.0540382236436 instead of 1.47682791921283 605s -feature swap of score: 8.35170655675059 instead of 1.54271367706925 605s -feature swap of score: 2.3591087448739 instead of 1.62983627612991 605s -feature swap of score: 3.33896220987853 instead of 1.74551832680512 605s -feature swap of score: 4.47931807129169 instead of 1.65656837994906 605s -feature swap of score: 6.43889512650897 instead of 1.63523856658065 605s -feature swap of score: 4.44139726355316 instead of 1.62413947257281 605s -feature swap of score: 4.3934217091148 instead of 1.5563895897064 605s -feature swap of score: 2.4178749161712 instead of 1.53540854291086 605s -feature swap of score: 4.50084537762944 instead of 1.99813615680005 605s -feature swap of score: 4.36085158331683 instead of 1.81509165074822 605s -feature swap of score: 3.50540200807125 instead of 1.84763588301182 605s -feature swap of score: 2.14307301177581 instead of 1.58943578807425 605s -feature swap of score: 2.80249705432441 instead of 2.03323063135445 605s -feature swap of score: 2.51995823874979 instead of 1.80649830131556 605s -feature swap of score: 2.18546699630314 instead of 2.01678734343503 605s -feature swap of score: 6.02870360838808 instead of 2.11230538713769 605s -feature swap of score: 4.79559537621424 instead of 1.93041915648434 605s -feature swap of score: 8.43445355562363 instead of 2.187388349484 605s -feature swap of score: 3.43057432858564 instead of 2.04524276099259 605s -feature swap of score: 2.64567534439595 instead of 1.91708045098195 605s -num feature swaps: 103 605s * [Mon Mar 18 02:19:34 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 605s -round: 1 610s -round: 2 615s -round: 3 620s -round: 4 624s -round: 5 629s * [Mon Mar 18 02:19:58 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 629s -parsing scores 635s * [Mon Mar 18 02:20:04 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 636s Error in library(ggplot2) : there is no package called ‘ggplot2’ 636s Execution halted 636s * [Mon Mar 18 02:20:05 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 636s Error in library(ggplot2) : there is no package called ‘ggplot2’ 636s Execution halted 636s * [Mon Mar 18 02:20:05 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 636s Error in library(seqLogo) : there is no package called ‘seqLogo’ 636s Execution halted 636s * [Mon Mar 18 02:20:05 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 636s Refining start codon selections. 636s -number of revised start positions: 43 636s * [Mon Mar 18 02:20:05 2024] Running CMD: cp /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 636s copying output to final output file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Mon Mar 18 02:20:05 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 636s Making bed file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 636s * [Mon Mar 18 02:20:05 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 637s Making pep file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 637s * [Mon Mar 18 02:20:06 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 637s Making cds file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 637s transdecoder is finished. See output files /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* 637s 637s 637s 637s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 266, 796 637s -WARNING, comp1008_c0_seq1 has no genome representation... skipping 637s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 637s -WARNING, comp1021_c0_seq1 has no genome representation... skipping 637s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1026_c0_seq1.p1. 637s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1037_c0_seq1.p2. 637s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 561, 1325 637s Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'contig' => 'III', 637s 'coords' => [ 637s [ 637s '1642973', 637s '1644586' 637s ] 637s ], 637s 'orient' => '-', 637s 'gene_id' => '', 637s 'asmbl' => 'comp1051_c1_seq1', 637s 'trans_id' => '' 637s }; 637s com_name: ORF type:5prime_partial (+),score=83.26 637s classification: annotated_genes 637s num_exons: 1 637s gene_length: 1616 637s is_pseudogene: 0 637s is_3prime_partial: 0 637s source: transdecoder 637s strand: + 637s mid_pt: 808 637s gene_type: protein-coding 637s TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp1051_c1_seq1 637s Model_feat_name: comp1051_c1_seq1.p1 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1616 CDS-exon: 2, 820 637s gene_span: 1-1616 637s model_span: 2-820 637s 637s Error, couldn't localize pt [1615] within coordsets: $VAR1 = [ 637s [ 637s '1642973', 637s '1644586' 637s ] 637s ]; 637s -WARNING, comp1053_c0_seq1 has no genome representation... skipping 637s Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'contig' => 'I', 637s 'coords' => [ 637s [ 637s 5095548, 637s '5095878' 637s ], 637s [ 637s 5095142, 637s '5095301' 637s ] 637s ], 637s 'orient' => '-', 637s 'gene_id' => '', 637s 'trans_id' => '', 637s 'asmbl' => 'comp1058_c0_seq1' 637s }; 637s Model_feat_name: comp1058_c0_seq1.p1 637s TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp1058_c0_seq1 637s is_3prime_partial: 0 637s source: transdecoder 637s is_pseudogene: 0 637s mid_pt: 248 637s gene_type: protein-coding 637s strand: + 637s num_exons: 1 637s com_name: ORF type:5prime_partial (+),score=32.57 637s classification: annotated_genes 637s gene_length: 496 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 496 CDS-exon: 3, 422 637s gene_span: 1-496 637s model_span: 3-422 637s 637s Error, couldn't localize pt [494] within coordsets: $VAR1 = [ 637s [ 637s 5095142, 637s '5095301' 637s ], 637s [ 637s 5095548, 637s '5095878' 637s ] 637s ]; 637s -Warning [6], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 3441, 3773 637s -WARNING, comp1075_c0_seq1 has no genome representation... skipping 637s Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'orient' => '-', 637s 'contig' => 'III', 637s 'coords' => [ 637s [ 637s 2380416, 637s '2380466' 637s ], 637s [ 637s 2379717, 637s '2380336' 637s ] 637s ], 637s 'asmbl' => 'comp1112_c0_seq1', 637s 'trans_id' => '', 637s 'gene_id' => '' 637s }; 637s com_name: ORF type:complete (+),score=155.28 637s classification: annotated_genes 637s num_exons: 1 637s gene_length: 2081 637s is_pseudogene: 0 637s source: transdecoder 637s is_3prime_partial: 0 637s strand: + 637s mid_pt: 1041 637s gene_type: protein-coding 637s TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp1112_c0_seq1 637s Model_feat_name: comp1112_c0_seq1.p1 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 2081 CDS-exon: 365, 1903 637s gene_span: 1-2081 637s model_span: 365-1903 637s 637s Error, couldn't localize pt [1717] within coordsets: $VAR1 = [ 637s [ 637s 2379717, 637s '2380336' 637s ], 637s [ 637s 2380416, 637s '2380466' 637s ] 637s ]; 637s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 637s -WARNING, comp1124_c0_seq1 has no genome representation... skipping 637s Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'trans_id' => '', 637s 'asmbl' => 'comp1198_c0_seq1', 637s 'gene_id' => '', 637s 'orient' => '-', 637s 'contig' => 'II', 637s 'coords' => [ 637s [ 637s 402195, 637s '402246' 637s ], 637s [ 637s 402017, 637s '402141' 637s ], 637s [ 637s 401844, 637s '401910' 637s ], 637s [ 637s 401352, 637s '401683' 637s ] 637s ] 637s }; 637s Model_feat_name: comp1198_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp1198_c0_seq1 637s TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 637s mid_pt: 299 637s gene_type: protein-coding 637s strand: + 637s is_3prime_partial: 0 637s source: transdecoder 637s is_pseudogene: 0 637s gene_length: 597 637s num_exons: 1 637s com_name: ORF type:internal (+),score=37.56 637s classification: annotated_genes 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 597 CDS-exon: 2, 595 637s gene_span: 1-597 637s model_span: 2-595 637s 637s Error, couldn't localize pt [596] within coordsets: $VAR1 = [ 637s [ 637s 401352, 637s '401683' 637s ], 637s [ 637s 401844, 637s '401910' 637s ], 637s [ 637s 402017, 637s '402141' 637s ], 637s [ 637s 402195, 637s '402246' 637s ] 637s ]; 637s Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'contig' => 'III', 637s 'coords' => [ 637s [ 637s 368840, 637s '369008' 637s ], 637s [ 637s 367430, 637s '368790' 637s ] 637s ], 637s 'orient' => '-', 637s 'gene_id' => '', 637s 'trans_id' => '', 637s 'asmbl' => 'comp1210_c0_seq1' 637s }; 637s is_5prime_partial: 0 637s asmbl_id: comp1210_c0_seq1 637s TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 637s Model_feat_name: comp1210_c0_seq1.p1 637s gene_length: 1554 637s com_name: ORF type:5prime_partial (+),score=12.16 637s classification: annotated_genes 637s num_exons: 1 637s strand: + 637s mid_pt: 777 637s gene_type: protein-coding 637s is_pseudogene: 0 637s source: transdecoder 637s is_3prime_partial: 0 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1554 CDS-exon: 2, 781 637s gene_span: 1-1554 637s model_span: 2-781 637s 637s Error, couldn't localize pt [1553] within coordsets: $VAR1 = [ 637s [ 637s 367430, 637s '368790' 637s ], 637s [ 637s 368840, 637s '369008' 637s ] 637s ]; 637s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 637s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 637s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 3, 392 637s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 637s Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'orient' => '-', 637s 'contig' => 'II', 637s 'coords' => [ 637s [ 637s '3840968', 637s '3841303' 637s ] 637s ], 637s 'trans_id' => '', 637s 'asmbl' => 'comp366_c0_seq1', 637s 'gene_id' => '' 637s }; 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s gene_type: protein-coding 637s mid_pt: 170 637s strand: - 637s num_exons: 1 637s classification: annotated_genes 637s com_name: ORF type:internal (-),score=12.83 637s gene_length: 340 637s Model_feat_name: comp366_c0_seq1.p1 637s TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 637s asmbl_id: comp366_c0_seq1 637s is_5prime_partial: 0 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 340, 1 CDS-exon: 339, 1 637s gene_span: 340-1 637s model_span: 339-1 637s 637s Error, couldn't localize pt [340] within coordsets: $VAR1 = [ 637s [ 637s '3840968', 637s '3841303' 637s ] 637s ]; 637s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 1, 384 637s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 3, 347 637s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 1, 492 637s -WARNING, comp504_c0_seq1 has no genome representation... skipping 637s -WARNING, comp576_c0_seq1 has no genome representation... skipping 637s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp583_c0_seq1.p1. 637s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. 637s Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'asmbl' => 'comp610_c0_seq1', 637s 'trans_id' => '', 637s 'contig' => 'I', 637s 'coords' => [ 637s [ 637s '5471264', 637s '5472770' 637s ] 637s ], 637s 'orient' => '-' 637s }; 637s TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 637s asmbl_id: comp610_c0_seq1 637s is_5prime_partial: 0 637s Model_feat_name: comp610_c0_seq1.p1 637s num_exons: 1 637s classification: annotated_genes 637s com_name: ORF type:5prime_partial (+),score=50.55 637s gene_length: 1509 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s gene_type: protein-coding 637s mid_pt: 755 637s strand: + 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1509 CDS-exon: 2, 1210 637s gene_span: 1-1509 637s model_span: 2-1210 637s 637s Error, couldn't localize pt [1508] within coordsets: $VAR1 = [ 637s [ 637s '5471264', 637s '5472770' 637s ] 637s ]; 637s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 637s CDS coords: 1441, 1941 637s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. 637s Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'trans_id' => '', 637s 'asmbl' => 'comp645_c0_seq1', 637s 'coords' => [ 637s [ 637s '4333088', 637s '4336727' 637s ] 637s ], 637s 'contig' => 'I', 637s 'orient' => '-' 637s }; 637s Model_feat_name: comp645_c0_seq1.p1 637s TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 637s asmbl_id: comp645_c0_seq1 637s is_5prime_partial: 0 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s gene_type: protein-coding 637s mid_pt: 1827 637s strand: + 637s num_exons: 1 637s classification: annotated_genes 637s com_name: ORF type:5prime_partial (+),score=273.35 637s gene_length: 3653 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 3653 CDS-exon: 2, 3571 637s gene_span: 1-3653 637s model_span: 2-3571 637s 637s Error, couldn't localize pt [3652] within coordsets: $VAR1 = [ 637s [ 637s '4333088', 637s '4336727' 637s ] 637s ]; 637s Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'asmbl' => 'comp688_c0_seq1', 637s 'trans_id' => '', 637s 'contig' => 'II', 637s 'coords' => [ 637s [ 637s 380308, 637s '380560' 637s ], 637s [ 637s 380624, 637s '381243' 637s ] 637s ], 637s 'orient' => '+' 637s }; 637s is_pseudogene: 0 637s source: transdecoder 637s is_3prime_partial: 0 637s strand: + 637s mid_pt: 1392 637s gene_type: protein-coding 637s com_name: ORF type:complete (+),score=172.54 637s classification: annotated_genes 637s num_exons: 1 637s gene_length: 2784 637s Model_feat_name: comp688_c0_seq1.p1 637s TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp688_c0_seq1 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 2784 CDS-exon: 83, 2578 637s gene_span: 1-2784 637s model_span: 83-2578 637s 637s Error, couldn't localize pt [2578] within coordsets: $VAR1 = [ 637s [ 637s 380308, 637s '380560' 637s ], 637s [ 637s 380624, 637s '381243' 637s ] 637s ]; 637s -WARNING, comp701_c0_seq1 has no genome representation... skipping 637s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp703_c0_seq1.p2. 637s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp707_c0_seq1.p2. 637s -WARNING, comp831_c0_seq1 has no genome representation... skipping 637s Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'asmbl' => 'comp856_c0_seq1', 637s 'trans_id' => '', 637s 'contig' => 'II', 637s 'coords' => [ 637s [ 637s 3753910, 637s '3754392' 637s ], 637s [ 637s 3754438, 637s '3755057' 637s ] 637s ], 637s 'orient' => '+' 637s }; 637s TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 637s asmbl_id: comp856_c0_seq1 637s is_5prime_partial: 0 637s Model_feat_name: comp856_c0_seq1.p1 637s num_exons: 1 637s classification: annotated_genes 637s com_name: ORF type:complete (+),score=71.94 637s gene_length: 1569 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s gene_type: protein-coding 637s mid_pt: 785 637s strand: + 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1569 CDS-exon: 161, 1504 637s gene_span: 1-1569 637s model_span: 161-1504 637s 637s Error, couldn't localize pt [1504] within coordsets: $VAR1 = [ 637s [ 637s 3753910, 637s '3754392' 637s ], 637s [ 637s 3754438, 637s '3755057' 637s ] 637s ]; 637s Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'coords' => [ 637s [ 637s 3727877, 637s '3728121' 637s ], 637s [ 637s 3727705, 637s '3727810' 637s ], 637s [ 637s 3726988, 637s '3727657' 637s ] 637s ], 637s 'contig' => 'II', 637s 'orient' => '-', 637s 'gene_id' => '', 637s 'trans_id' => '', 637s 'asmbl' => 'comp873_c0_seq2' 637s }; 637s asmbl_id: comp873_c0_seq2 637s is_5prime_partial: 0 637s TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 637s Model_feat_name: comp873_c0_seq2.p1 637s gene_length: 1025 637s classification: annotated_genes 637s com_name: ORF type:5prime_partial (+),score=8.59 637s num_exons: 1 637s strand: + 637s gene_type: protein-coding 637s mid_pt: 513 637s is_pseudogene: 0 637s is_3prime_partial: 0 637s source: transdecoder 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1025 CDS-exon: 3, 677 637s gene_span: 1-1025 637s model_span: 3-677 637s 637s Error, couldn't localize pt [1023] within coordsets: $VAR1 = [ 637s [ 637s 3726988, 637s '3727657' 637s ], 637s [ 637s 3727705, 637s '3727810' 637s ], 637s [ 637s 3727877, 637s '3728121' 637s ] 637s ]; 637s Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'asmbl' => 'comp888_c0_seq1', 637s 'trans_id' => '', 637s 'coords' => [ 637s [ 637s 1268244, 637s '1268583' 637s ], 637s [ 637s 1267938, 637s '1268172' 637s ] 637s ], 637s 'contig' => 'III', 637s 'orient' => '-' 637s }; 637s TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 637s asmbl_id: comp888_c0_seq1 637s is_5prime_partial: 0 637s Model_feat_name: comp888_c0_seq1.p1 637s classification: annotated_genes 637s com_name: ORF type:5prime_partial (+),score=23.94 637s num_exons: 1 637s gene_length: 589 637s is_pseudogene: 0 637s is_3prime_partial: 0 637s source: transdecoder 637s strand: + 637s gene_type: protein-coding 637s mid_pt: 295 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 589 CDS-exon: 2, 355 637s gene_span: 1-589 637s model_span: 2-355 637s 637s Error, couldn't localize pt [588] within coordsets: $VAR1 = [ 637s [ 637s 1267938, 637s '1268172' 637s ], 637s [ 637s 1268244, 637s '1268583' 637s ] 637s ]; 637s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp924_c0_seq1.p2. 637s -WARNING, comp932_c0_seq1 has no genome representation... skipping 637s Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'gene_id' => '', 637s 'asmbl' => 'comp940_c0_seq1', 637s 'trans_id' => '', 637s 'contig' => 'III', 637s 'coords' => [ 637s [ 637s 105641, 637s '105736' 637s ], 637s [ 637s 105785, 637s '106404' 637s ] 637s ], 637s 'orient' => '+' 637s }; 637s Model_feat_name: comp940_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp940_c0_seq1 637s TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 637s mid_pt: 1065 637s gene_type: protein-coding 637s strand: + 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s gene_length: 2129 637s num_exons: 1 637s com_name: ORF type:complete (+),score=94.37 637s classification: annotated_genes 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 2129 CDS-exon: 40, 1731 637s gene_span: 1-2129 637s model_span: 40-1731 637s 637s Error, couldn't localize pt [1731] within coordsets: $VAR1 = [ 637s [ 637s 105641, 637s '105736' 637s ], 637s [ 637s 105785, 637s '106404' 637s ] 637s ]; 637s Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: 637s $VAR1 = { 637s 'trans_id' => '', 637s 'asmbl' => 'comp983_c0_seq1', 637s 'gene_id' => '', 637s 'orient' => '-', 637s 'contig' => 'I', 637s 'coords' => [ 637s [ 637s 4100066, 637s '4100163' 637s ], 637s [ 637s 4098246, 637s '4100014' 637s ] 637s ] 637s }; 637s Model_feat_name: comp983_c0_seq1.p1 637s TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 637s is_5prime_partial: 0 637s asmbl_id: comp983_c0_seq1 637s source: transdecoder 637s is_3prime_partial: 0 637s is_pseudogene: 0 637s mid_pt: 935 637s gene_type: protein-coding 637s strand: + 637s num_exons: 1 637s com_name: ORF type:5prime_partial (+),score=143.65 637s classification: annotated_genes 637s gene_length: 1870 637s gene_synonyms: 637s mRNA_coords 637s CDS_coords 637s RNA-exon: 1, 1870 CDS-exon: 2, 1810 637s gene_span: 1-1870 637s model_span: 2-1810 637s 637s Error, couldn't localize pt [1869] within coordsets: $VAR1 = [ 637s [ 637s 4098246, 637s '4100014' 637s ], 637s [ 637s 4100066, 637s '4100163' 637s ] 637s ]; 637s -WARNING, comp995_c0_seq1 has no genome representation... skipping 637s 637s 637s Done. 646 / 679 transcript orfs could be propagated to the genome 637s 637s make[1]: Leaving directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 637s Running example in $... 637s make[1]: Entering directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 637s ./runMe.sh 637s #!/bin/bash -ve 637s 637s export PERL_HASH_SEED=0 637s 637s 637s 637s ## generate alignment gff3 formatted output 637s ../../util/gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3 638s 638s 638s ## generate transcripts fasta file 638s # not including the genome here... too big, but here's how you'd do it. 638s #../../util/gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta 638s 638s ## Extract the long ORFs 638s ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S 639s CMD: mkdir -p /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir 639s * [Mon Mar 18 02:20:07 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat 639s 639s 639s -first extracting base frequencies, we'll need them later. 641s 641s 641s - extracting ORFs from transcripts. 641s -total transcripts to examine: 3501 651s [100/3501] = 2.86% done [200/3501] = 5.71% done [300/3501] = 8.57% done [400/3501] = 11.43% done [500/3501] = 14.28% done [600/3501] = 17.14% done [700/3501] = 19.99% done [800/3501] = 22.85% done [900/3501] = 25.71% done [1000/3501] = 28.56% done [1100/3501] = 31.42% done [1200/3501] = 34.28% done [1300/3501] = 37.13% done [1400/3501] = 39.99% done [1500/3501] = 42.84% done [1600/3501] = 45.70% done [1700/3501] = 48.56% done [1800/3501] = 51.41% done [1900/3501] = 54.27% done [2000/3501] = 57.13% done [2100/3501] = 59.98% done [2200/3501] = 62.84% done [2300/3501] = 65.70% done [2400/3501] = 68.55% done [2500/3501] = 71.41% done [2600/3501] = 74.26% done [2700/3501] = 77.12% done [2800/3501] = 79.98% done [2900/3501] = 82.83% done [3000/3501] = 85.69% done [3100/3501] = 88.55% done [3200/3501] = 91.40% done [3300/3501] = 94.26% done [3400/3501] = 97.12% done [3500/3501] = 99.97% done CMD: touch /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 651s 651s 651s ################################# 651s ### Done preparing long ORFs. ### 651s ################################## 651s 651s Use file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. 651s 651s Then, run TransDecoder.Predict for your final coding region predictions. 651s 651s 651s 651s 651s ## Predict likely ORFs 651s 651s ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS 651s * [Mon Mar 18 02:20:20 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 651s * [Mon Mar 18 02:20:20 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 652s -skipping training candidate: NM_198270.p1, not unique enough 652s -skipping training candidate: NR_104391.p1, not unique enough 652s -skipping training candidate: NR_104395.p1, not unique enough 652s -skipping training candidate: NM_001282622.p1, not unique enough 652s -skipping training candidate: MSTRG.376.1.p1, not unique enough 652s -skipping training candidate: MSTRG.839.3.p1, not unique enough 652s -skipping training candidate: NR_104394.p1, not unique enough 652s -skipping training candidate: MSTRG.397.18.p1, not unique enough 652s -skipping training candidate: NM_020717.p1, not unique enough 652s -skipping training candidate: MSTRG.505.14.p1, not unique enough 652s -skipping training candidate: NM_001136024.p1, not unique enough 652s -skipping training candidate: MSTRG.538.2.p1, not unique enough 652s -skipping training candidate: NM_001291868.p1, not unique enough 652s -skipping training candidate: MSTRG.236.1.p1, not unique enough 652s -skipping training candidate: MSTRG.404.8.p1, not unique enough 652s -skipping training candidate: NM_001555.p1, not unique enough 652s -skipping training candidate: NM_001282224.p1, not unique enough 652s -skipping training candidate: NM_001170962.p1, not unique enough 652s -skipping training candidate: NM_001291416.p1, not unique enough 652s -skipping training candidate: NM_021140.p1, not unique enough 652s -skipping training candidate: MSTRG.376.9.p1, not unique enough 652s -skipping training candidate: NM_014710.p1, not unique enough 652s -skipping training candidate: NM_001099411.p1, not unique enough 652s -skipping training candidate: NM_001184727.p1, not unique enough 652s -skipping training candidate: NM_001146702.p1, not unique enough 652s -skipping training candidate: MSTRG.258.8.p1, not unique enough 652s -skipping training candidate: NM_005096.p1, not unique enough 652s -skipping training candidate: MSTRG.258.9.p1, not unique enough 652s -skipping training candidate: MSTRG.502.3.p1, not unique enough 652s -skipping training candidate: NM_001171162.p1, not unique enough 652s -skipping training candidate: MSTRG.502.2.p1, not unique enough 652s -skipping training candidate: MSTRG.502.1.p1, not unique enough 652s -skipping training candidate: NM_001291417.p1, not unique enough 652s -skipping training candidate: NM_001168360.p1, not unique enough 652s -skipping training candidate: NM_032969.p1, not unique enough 652s -skipping training candidate: NM_001168363.p1, not unique enough 652s -skipping training candidate: MSTRG.236.3.p1, not unique enough 652s -skipping training candidate: NM_001168362.p1, not unique enough 652s -skipping training candidate: NM_001291418.p1, not unique enough 652s -skipping training candidate: NM_001169123.p1, not unique enough 652s -skipping training candidate: MSTRG.570.10.p1, not unique enough 652s -skipping training candidate: NR_111960.p1, not unique enough 652s -skipping training candidate: NM_001169122.p1, not unique enough 652s -skipping training candidate: NM_001169124.p1, not unique enough 652s -skipping training candidate: NM_001169125.p1, not unique enough 652s -skipping training candidate: MSTRG.848.14.p1, not unique enough 652s -skipping training candidate: NM_001042749.p1, not unique enough 652s -skipping training candidate: MSTRG.848.13.p1, not unique enough 652s -skipping training candidate: MSTRG.848.7.p1, not unique enough 652s -skipping training candidate: MSTRG.848.12.p1, not unique enough 652s -skipping training candidate: NM_000425.p1, not unique enough 652s -skipping training candidate: NM_024003.p1, not unique enough 652s -skipping training candidate: NM_001143963.p1, not unique enough 652s -skipping training candidate: MSTRG.477.3.p1, not unique enough 652s -skipping training candidate: NM_012310.p1, not unique enough 652s -skipping training candidate: MSTRG.848.11.p1, not unique enough 652s -skipping training candidate: NM_001042751.p1, not unique enough 652s -skipping training candidate: NM_006603.p1, not unique enough 652s -skipping training candidate: MSTRG.848.1.p1, not unique enough 652s -skipping training candidate: MSTRG.848.4.p1, not unique enough 652s -skipping training candidate: MSTRG.848.2.p1, not unique enough 652s -skipping training candidate: NM_001282418.p1, not unique enough 652s -skipping training candidate: MSTRG.848.6.p1, not unique enough 652s -skipping training candidate: NM_004022.p1, not unique enough 652s -skipping training candidate: NM_004013.p1, not unique enough 652s -skipping training candidate: MSTRG.570.9.p1, not unique enough 652s -skipping training candidate: MSTRG.147.2.p1, not unique enough 652s -skipping training candidate: NM_006044.p1, not unique enough 652s -skipping training candidate: MSTRG.331.3.p1, not unique enough 652s -skipping training candidate: MSTRG.331.2.p1, not unique enough 652s -skipping training candidate: MSTRG.331.4.p1, not unique enough 652s -skipping training candidate: NM_001281463.p1, not unique enough 652s -skipping training candidate: NM_001122670.p1, not unique enough 652s -skipping training candidate: MSTRG.147.3.p1, not unique enough 652s -skipping training candidate: NM_021949.p1, not unique enough 652s -skipping training candidate: MSTRG.456.2.p1, not unique enough 652s -skipping training candidate: NM_001130860.p1, not unique enough 652s -skipping training candidate: NM_001172436.p1, not unique enough 652s -skipping training candidate: MSTRG.442.1.p1, not unique enough 652s -skipping training candidate: NM_004023.p1, not unique enough 652s -skipping training candidate: MSTRG.945.2.p1, not unique enough 652s -skipping training candidate: MSTRG.945.3.p1, not unique enough 652s -skipping training candidate: MSTRG.945.8.p1, not unique enough 652s -skipping training candidate: MSTRG.518.1.p1, not unique enough 652s -skipping training candidate: NM_001010986.p1, not unique enough 652s -skipping training candidate: MSTRG.945.1.p1, not unique enough 652s -skipping training candidate: NM_004020.p1, not unique enough 652s -skipping training candidate: NM_153280.p1, not unique enough 652s -skipping training candidate: NM_001291421.p1, not unique enough 652s -skipping training candidate: NM_001105243.p1, not unique enough 652s -skipping training candidate: NM_020766.p1, not unique enough 652s -skipping training candidate: NM_007309.p1, not unique enough 652s -skipping training candidate: NM_005756.p1, not unique enough 652s -skipping training candidate: NM_001113490.p1, not unique enough 652s -skipping training candidate: NM_001079859.p1, not unique enough 652s -skipping training candidate: NM_001184833.p1, not unique enough 652s -skipping training candidate: MSTRG.945.6.p1, not unique enough 652s -skipping training candidate: NM_001168361.p1, not unique enough 652s -skipping training candidate: NM_001079860.p1, not unique enough 652s -skipping training candidate: NM_001184836.p1, not unique enough 652s -skipping training candidate: NM_001184837.p1, not unique enough 652s -skipping training candidate: NM_001257231.p1, not unique enough 652s -skipping training candidate: NM_001184835.p1, not unique enough 652s -skipping training candidate: NM_001282875.p1, not unique enough 652s -skipping training candidate: NM_003069.p1, not unique enough 652s -skipping training candidate: MSTRG.88.1.p1, not unique enough 652s -skipping training candidate: MSTRG.387.2.p1, not unique enough 652s -skipping training candidate: MSTRG.387.1.p1, not unique enough 652s -skipping training candidate: MSTRG.860.6.p1, not unique enough 652s -skipping training candidate: NM_001184834.p1, not unique enough 652s -skipping training candidate: NM_138636.p1, not unique enough 652s -skipping training candidate: NM_181673.p1, not unique enough 652s -skipping training candidate: NM_001271184.p1, not unique enough 652s -skipping training candidate: MSTRG.759.13.p1, not unique enough 652s -skipping training candidate: MSTRG.759.12.p1, not unique enough 652s -skipping training candidate: NM_001037343.p1, not unique enough 652s -skipping training candidate: NM_015107.p1, not unique enough 652s -skipping training candidate: NM_014725.p1, not unique enough 652s -skipping training candidate: NM_001142504.p1, not unique enough 652s -skipping training candidate: MSTRG.945.7.p1, not unique enough 652s -skipping training candidate: NM_001168647.p1, not unique enough 652s -skipping training candidate: NM_001099855.p1, not unique enough 652s -skipping training candidate: NM_004014.p1, not unique enough 652s -skipping training candidate: MSTRG.110.1.p1, not unique enough 652s -skipping training candidate: NM_001282141.p1, not unique enough 652s -skipping training candidate: NM_001666.p1, not unique enough 652s -skipping training candidate: NM_001271183.p1, not unique enough 652s -skipping training candidate: NM_001257237.p1, not unique enough 652s -skipping training candidate: NM_001257230.p1, not unique enough 652s -skipping training candidate: NM_001257234.p1, not unique enough 652s -skipping training candidate: NM_001170628.p1, not unique enough 652s -skipping training candidate: NM_015075.p1, not unique enough 652s -skipping training candidate: NM_001587.p1, not unique enough 652s -skipping training candidate: NM_001184897.p1, not unique enough 652s -skipping training candidate: NM_001171879.p1, not unique enough 652s -skipping training candidate: MSTRG.759.11.p1, not unique enough 652s -skipping training candidate: MSTRG.110.4.p1, not unique enough 652s -skipping training candidate: NM_005676.p1, not unique enough 652s -skipping training candidate: MSTRG.110.5.p1, not unique enough 652s -skipping training candidate: NM_001204467.p1, not unique enough 652s -skipping training candidate: NM_031276.p1, not unique enough 652s -skipping training candidate: NM_005369.p1, not unique enough 652s -skipping training candidate: MSTRG.250.1.p1, not unique enough 652s -skipping training candidate: MSTRG.387.3.p1, not unique enough 652s -skipping training candidate: MSTRG.1005.1.p1, not unique enough 652s -skipping training candidate: NM_001300788.p1, not unique enough 652s -skipping training candidate: MSTRG.508.1.p1, not unique enough 652s -skipping training candidate: NM_001126054.p1, not unique enough 652s -skipping training candidate: NM_003588.p1, not unique enough 652s -skipping training candidate: NM_001126055.p1, not unique enough 652s -skipping training candidate: MSTRG.110.7.p1, not unique enough 652s -skipping training candidate: NM_001184965.p1, not unique enough 652s -skipping training candidate: NM_001085354.p1, not unique enough 652s -skipping training candidate: NM_001168648.p1, not unique enough 652s -skipping training candidate: NM_001079872.p1, not unique enough 652s -skipping training candidate: NM_007325.p1, not unique enough 652s -skipping training candidate: NM_014799.p1, not unique enough 652s -skipping training candidate: MSTRG.110.8.p1, not unique enough 652s -skipping training candidate: MSTRG.855.3.p1, not unique enough 652s -skipping training candidate: NM_001171184.p1, not unique enough 652s -skipping training candidate: MSTRG.110.6.p1, not unique enough 652s -skipping training candidate: NM_001184898.p1, not unique enough 652s -skipping training candidate: MSTRG.276.2.p1, not unique enough 652s -skipping training candidate: NM_024597.p1, not unique enough 652s -skipping training candidate: MSTRG.839.4.p1, not unique enough 652s -skipping training candidate: NM_007156.p1, not unique enough 652s -skipping training candidate: MSTRG.759.1.p1, not unique enough 652s -skipping training candidate: MSTRG.759.21.p1, not unique enough 652s -skipping training candidate: MSTRG.759.22.p1, not unique enough 652s -skipping training candidate: NM_182540.p1, not unique enough 652s -skipping training candidate: NM_001171878.p1, not unique enough 652s -skipping training candidate: NM_152633.p1, not unique enough 652s -skipping training candidate: MSTRG.442.2.p1, not unique enough 652s -skipping training candidate: NM_001173516.p1, not unique enough 652s -skipping training candidate: MSTRG.921.2.p1, not unique enough 652s -skipping training candidate: NM_001204466.p1, not unique enough 652s -skipping training candidate: NM_152856.p1, not unique enough 652s -skipping training candidate: MSTRG.759.20.p1, not unique enough 652s -skipping training candidate: MSTRG.855.4.p1, not unique enough 652s -skipping training candidate: NM_001168649.p1, not unique enough 652s -skipping training candidate: NM_001077445.p1, not unique enough 652s -skipping training candidate: MSTRG.839.6.p1, not unique enough 652s -skipping training candidate: NM_001144004.p1, not unique enough 652s -skipping training candidate: NM_001144010.p1, not unique enough 652s -skipping training candidate: NM_001144003.p1, not unique enough 652s -skipping training candidate: NM_001144009.p1, not unique enough 652s -skipping training candidate: NM_001144005.p1, not unique enough 652s -skipping training candidate: NM_001144006.p1, not unique enough 652s -skipping training candidate: NM_032539.p1, not unique enough 652s -skipping training candidate: NM_139289.p1, not unique enough 652s -skipping training candidate: MSTRG.839.5.p1, not unique enough 652s -skipping training candidate: NM_001173517.p1, not unique enough 652s -skipping training candidate: NM_001184875.p1, not unique enough 652s -skipping training candidate: NM_138437.p1, not unique enough 652s -skipping training candidate: NM_001199818.p1, not unique enough 652s -skipping training candidate: NM_001004051.p1, not unique enough 652s -skipping training candidate: NM_001184874.p1, not unique enough 652s -skipping training candidate: MSTRG.110.11.p1, not unique enough 652s -skipping training candidate: NM_001184749.p1, not unique enough 652s -skipping training candidate: NM_173078.p1, not unique enough 652s -skipping training candidate: MSTRG.759.24.p1, not unique enough 652s -skipping training candidate: NM_018977.p1, not unique enough 652s -skipping training candidate: NM_001184966.p1, not unique enough 652s -skipping training candidate: NM_014735.p1, not unique enough 652s -skipping training candidate: NM_001171877.p1, not unique enough 652s -skipping training candidate: NM_001282146.p1, not unique enough 652s -skipping training candidate: NM_001282145.p1, not unique enough 652s -skipping training candidate: NM_020742.p1, not unique enough 652s -skipping training candidate: NM_001127898.p1, not unique enough 652s -skipping training candidate: NM_001005332.p1, not unique enough 652s -skipping training candidate: NM_001166660.p1, not unique enough 652s -skipping training candidate: MSTRG.189.10.p1, not unique enough 652s -skipping training candidate: NM_001178085.p1, not unique enough 652s -skipping training candidate: MSTRG.189.1.p1, not unique enough 652s -skipping training candidate: NM_001178084.p1, not unique enough 652s -skipping training candidate: NM_003410.p1, not unique enough 652s -skipping training candidate: MSTRG.189.7.p1, not unique enough 652s -skipping training candidate: MSTRG.921.3.p1, not unique enough 652s -skipping training candidate: MSTRG.110.10.p1, not unique enough 652s -skipping training candidate: NM_001287242.p1, not unique enough 652s -skipping training candidate: MSTRG.76.2.p1, not unique enough 652s -skipping training candidate: MSTRG.279.6.p1, not unique enough 652s -skipping training candidate: MSTRG.279.1.p1, not unique enough 652s -skipping training candidate: MSTRG.189.11.p1, not unique enough 652s -skipping training candidate: MSTRG.189.9.p1, not unique enough 652s -skipping training candidate: NM_153380.p1, not unique enough 652s -skipping training candidate: MSTRG.279.11.p1, not unique enough 652s -skipping training candidate: MSTRG.279.2.p1, not unique enough 652s -skipping training candidate: MSTRG.279.3.p1, not unique enough 652s -skipping training candidate: NM_007130.p1, not unique enough 652s -skipping training candidate: MSTRG.279.10.p1, not unique enough 652s -skipping training candidate: NM_006986.p1, not unique enough 652s -skipping training candidate: MSTRG.1005.3.p1, not unique enough 652s -skipping training candidate: NM_001271696.p1, not unique enough 652s -skipping training candidate: MSTRG.279.8.p1, not unique enough 652s -skipping training candidate: MSTRG.279.7.p1, not unique enough 652s -skipping training candidate: NM_024778.p1, not unique enough 652s -skipping training candidate: NM_032591.p1, not unique enough 652s -skipping training candidate: NM_152780.p1, not unique enough 652s -skipping training candidate: NM_013423.p1, not unique enough 652s -skipping training candidate: NM_032512.p1, not unique enough 652s -skipping training candidate: MSTRG.166.5.p1, not unique enough 652s -skipping training candidate: NM_001282163.p1, not unique enough 652s -skipping training candidate: NM_006125.p1, not unique enough 652s -skipping training candidate: MSTRG.604.2.p1, not unique enough 652s -skipping training candidate: NM_001243963.p1, not unique enough 652s -skipping training candidate: NM_001184782.p1, not unique enough 652s -skipping training candidate: NM_001272061_dup1.p1, not unique enough 652s -skipping training candidate: MSTRG.654.4.p1, not unique enough 652s -skipping training candidate: NM_006733.p1, not unique enough 652s -skipping training candidate: MSTRG.654.1.p1, not unique enough 652s -skipping training candidate: MSTRG.925.2.p1, not unique enough 652s -skipping training candidate: NM_001163280.p1, not unique enough 652s -skipping training candidate: NR_033717.p1, not unique enough 652s -skipping training candidate: NM_001177466.p1, not unique enough 652s -skipping training candidate: NM_001271698.p1, not unique enough 652s -skipping training candidate: NM_000084.p1, not unique enough 652s -skipping training candidate: MSTRG.654.3.p1, not unique enough 652s -skipping training candidate: NM_001272062.p1, not unique enough 652s -skipping training candidate: NM_001272063.p1, not unique enough 652s -skipping training candidate: MSTRG.308.3.p1, not unique enough 652s -skipping training candidate: NM_030801_dup1.p1, not unique enough 652s -skipping training candidate: NM_177535_dup1.p1, not unique enough 652s -skipping training candidate: NM_177537.p1, not unique enough 652s -skipping training candidate: NM_177537_dup1.p1, not unique enough 652s -skipping training candidate: MSTRG.572.4.p1, not unique enough 652s -skipping training candidate: NM_001271699.p1, not unique enough 652s -skipping training candidate: NM_001271697.p1, not unique enough 652s -skipping training candidate: MSTRG.308.4.p1, not unique enough 652s -skipping training candidate: NM_001163335.p1, not unique enough 652s -skipping training candidate: NM_138780.p1, not unique enough 652s -skipping training candidate: NM_001271835.p1, not unique enough 652s -skipping training candidate: NM_001163323.p1, not unique enough 652s -skipping training candidate: NM_001168466.p1, not unique enough 652s -skipping training candidate: MSTRG.147.4.p1, not unique enough 652s -skipping training candidate: MSTRG.572.5.p1, not unique enough 652s -skipping training candidate: MSTRG.759.10.p1, not unique enough 652s -skipping training candidate: MSTRG.759.2.p1, not unique enough 652s -skipping training candidate: MSTRG.759.9.p1, not unique enough 652s -skipping training candidate: NM_001166221.p1, not unique enough 652s -skipping training candidate: NM_019117.p1, not unique enough 652s -skipping training candidate: NM_001170649.p1, not unique enough 652s -skipping training candidate: MSTRG.451.1.p1, not unique enough 652s -skipping training candidate: MSTRG.929.1.p1, not unique enough 652s -skipping training candidate: MSTRG.376.2.p1, not unique enough 652s -skipping training candidate: MSTRG.161.3.p1, not unique enough 652s -skipping training candidate: NM_152787.p1, not unique enough 652s -skipping training candidate: MSTRG.208.2.p1, not unique enough 652s -skipping training candidate: MSTRG.161.2.p1, not unique enough 652s -skipping training candidate: MSTRG.376.4.p1, not unique enough 652s -skipping training candidate: NM_177556.p1, not unique enough 652s -skipping training candidate: NM_016157.p1, not unique enough 652s -skipping training candidate: NM_001173487.p1, not unique enough 652s -skipping training candidate: NM_052817.p1, not unique enough 652s -skipping training candidate: MSTRG.215.2.p1, not unique enough 652s -skipping training candidate: NM_001306193.p1, not unique enough 652s -skipping training candidate: NM_152423.p1, not unique enough 652s -skipping training candidate: NM_001163321.p1, not unique enough 652s -skipping training candidate: MSTRG.572.6.p1, not unique enough 652s -skipping training candidate: NM_001282754.p1, not unique enough 652s -skipping training candidate: NM_001171135.p1, not unique enough 652s -skipping training candidate: NM_001171136.p1, not unique enough 652s -skipping training candidate: NM_001303515.p1, not unique enough 652s -skipping training candidate: MSTRG.922.1.p1, not unique enough 652s -skipping training candidate: MSTRG.279.5.p1, not unique enough 652s -skipping training candidate: NM_022117.p1, not unique enough 652s -skipping training candidate: NM_001178107.p1, not unique enough 652s -skipping training candidate: NM_001173488.p1, not unique enough 652s -skipping training candidate: NM_144657.p1, not unique enough 652s -skipping training candidate: NM_001178108.p1, not unique enough 652s -skipping training candidate: NR_109776.p1, not unique enough 652s -skipping training candidate: NM_007150.p1, not unique enough 652s -skipping training candidate: NM_001303516.p1, not unique enough 652s -skipping training candidate: NM_198881.p1, not unique enough 652s -skipping training candidate: MSTRG.376.3.p1, not unique enough 652s -skipping training candidate: MSTRG.376.8.p1, not unique enough 652s -skipping training candidate: MSTRG.208.3.p1, not unique enough 652s -skipping training candidate: NM_001025242.p1, not unique enough 652s -skipping training candidate: MSTRG.345.1.p1, not unique enough 652s -skipping training candidate: NR_073148.p1, not unique enough 652s -skipping training candidate: NM_001168467.p1, not unique enough 652s -skipping training candidate: MSTRG.308.1.p1, not unique enough 652s -skipping training candidate: NM_001170650.p1, not unique enough 652s -skipping training candidate: NM_001721.p1, not unique enough 652s -skipping training candidate: NM_133265.p1, not unique enough 652s -skipping training candidate: NM_001303513.p1, not unique enough 652s -skipping training candidate: NM_006777.p1, not unique enough 652s -skipping training candidate: NM_001129896.p1, not unique enough 652s -skipping training candidate: NM_001174068.p1, not unique enough 652s -skipping training candidate: MSTRG.732.1.p1, not unique enough 652s -skipping training candidate: NM_004458.p1, not unique enough 652s -skipping training candidate: MSTRG.732.2.p1, not unique enough 652s -skipping training candidate: NM_133499.p1, not unique enough 652s -skipping training candidate: NM_006359.p1, not unique enough 652s -skipping training candidate: NM_033290.p1, not unique enough 652s -skipping training candidate: NM_001098624.p1, not unique enough 652s -skipping training candidate: NM_001193277.p1, not unique enough 652s -skipping training candidate: NM_001256944.p1, not unique enough 652s -skipping training candidate: NM_004192.p1, not unique enough 652s -skipping training candidate: NM_031892.p1, not unique enough 652s -skipping training candidate: NM_003828.p1, not unique enough 652s -skipping training candidate: MSTRG.508.2.p1, not unique enough 652s -skipping training candidate: NR_110311.p1, not unique enough 652s -skipping training candidate: NM_001127197.p1, not unique enough 652s -skipping training candidate: MSTRG.862.3.p1, not unique enough 652s -skipping training candidate: NM_001421.p1, not unique enough 652s -skipping training candidate: MSTRG.862.4.p1, not unique enough 652s -skipping training candidate: MSTRG.641.6.p1, not unique enough 652s -skipping training candidate: NM_001356.p1, not unique enough 652s -skipping training candidate: NM_007137.p1, not unique enough 652s -skipping training candidate: MSTRG.292.4.p1, not unique enough 652s -skipping training candidate: NM_004016.p1, not unique enough 652s -skipping 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MSTRG.601.4.p1, not unique enough 652s -skipping training candidate: NM_004018.p1, not unique enough 652s -skipping training candidate: NM_001193417.p1, not unique enough 652s -skipping training candidate: MSTRG.759.25.p1, not unique enough 652s -skipping training candidate: NM_001184767.p1, not unique enough 652s -skipping training candidate: NM_001190255.p1, not unique enough 652s -skipping training candidate: NM_004015.p1, not unique enough 652s -skipping training candidate: NM_145119.p1, not unique enough 652s -skipping training candidate: NM_001168301.p1, not unique enough 652s -skipping training candidate: NM_001168302.p1, not unique enough 652s -skipping training candidate: NM_001178086.p1, not unique enough 652s -skipping training candidate: NM_006962.p1, not unique enough 652s -skipping training candidate: MSTRG.294.4.p1, not unique enough 652s -skipping training candidate: NM_001173473.p1, not unique enough 652s -skipping training candidate: MSTRG.82.6.p1, not unique enough 652s -skipping training candidate: NM_001025243.p1, not unique enough 652s -skipping training candidate: NM_001177478.p1, not unique enough 652s -skipping training candidate: NM_002024.p1, not unique enough 652s -skipping training candidate: MSTRG.669.2.p1, not unique enough 652s -skipping training candidate: MSTRG.669.1.p1, not unique enough 652s -skipping training candidate: NM_177949.p1, not unique enough 652s -skipping training candidate: MSTRG.669.10.p1, not unique enough 652s -skipping training candidate: MSTRG.669.3.p1, not unique enough 652s -skipping training candidate: NM_014782.p1, not unique enough 652s -skipping training candidate: MSTRG.669.9.p1, not unique enough 652s -skipping training candidate: MSTRG.669.4.p1, not unique enough 652s -skipping training candidate: NM_001282231.p1, not unique enough 652s -skipping training candidate: MSTRG.456.6.p1, not unique enough 652s -skipping training candidate: MSTRG.306.3.p1, not unique enough 652s -skipping training candidate: NM_001178110.p1, not unique enough 652s -skipping training candidate: NM_004017.p1, not unique enough 652s -skipping training candidate: NM_033626.p1, not unique enough 652s -skipping training candidate: NM_001271836.p1, not unique enough 652s -skipping training candidate: NM_005032.p1, not unique enough 652s -skipping training candidate: NM_033289.p1, not unique enough 652s -skipping training candidate: NM_001024666.p1, not unique enough 652s -skipping training candidate: NM_001099686_dup1.p1, not unique enough 652s -skipping training candidate: MSTRG.376.3.p2, not unique enough 652s -skipping training candidate: MSTRG.376.4.p2, not unique enough 652s -skipping training candidate: MSTRG.376.8.p2, not unique enough 652s -skipping training candidate: NM_022053.p1, not unique enough 652s -skipping training candidate: NM_022053_dup1.p1, not unique enough 652s -skipping training candidate: MSTRG.957.10.p1, not unique enough 652s -skipping training candidate: NM_001142805.p1, not unique 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candidate: MSTRG.110.2.p1, not unique enough 652s -skipping training candidate: NM_145812.p1, not unique enough 652s -skipping training candidate: MSTRG.151.1.p1, not unique enough 652s -skipping training candidate: NM_001654.p1, not unique enough 652s -skipping training candidate: NM_201222.p1, not unique enough 652s -skipping training candidate: NM_014599.p1, not unique enough 652s -skipping training candidate: NM_177433.p1, not unique enough 652s -skipping training candidate: MSTRG.717.1.p1, not unique enough 652s -skipping training candidate: NM_080612.p1, not unique enough 652s -skipping training candidate: NM_147175.p1, not unique enough 652s -skipping training candidate: NM_030624.p1, not unique enough 652s -skipping training candidate: MSTRG.957.12.p1, not unique enough 652s -skipping training candidate: NM_001172335.p1, not unique enough 652s -skipping training candidate: NM_001325.p1, not unique enough 652s -skipping training candidate: NM_001037967.p1, not unique enough 652s -skipping training candidate: NM_001282631.p1, not unique enough 652s -skipping training candidate: MSTRG.714.3.p1, not unique enough 652s -skipping training candidate: MSTRG.365.2.p1, not unique enough 652s -skipping training candidate: NM_152226.p1, not unique enough 652s -skipping training candidate: NM_001145933.p1, not unique enough 652s -skipping training candidate: MSTRG.62.1.p1, not unique enough 652s -skipping training candidate: NM_001201539.p1, not unique enough 652s -skipping training candidate: NM_004042.p1, not unique enough 652s -skipping training candidate: NM_024921.p1, not unique enough 652s -skipping training candidate: NM_000047.p1, not unique enough 652s -skipping training candidate: MSTRG.110.9.p1, not unique enough 652s -skipping training candidate: MSTRG.338.5.p1, not unique enough 652s -skipping training candidate: MSTRG.862.1.p1, not unique enough 652s -skipping training candidate: NM_019857.p1, not unique enough 652s -skipping training candidate: NM_001144002.p1, not unique enough 652s -skipping training candidate: NM_001185082.p1, not unique enough 652s -skipping training candidate: NM_001136158.p1, not unique enough 652s -skipping training candidate: MSTRG.338.7.p1, not unique enough 652s -skipping training candidate: NM_001136157.p1, not unique enough 652s -skipping training candidate: MSTRG.338.6.p1, not unique enough 652s -skipping training candidate: NM_001282338.p1, not unique enough 652s -skipping training candidate: NM_000351.p1, not unique enough 652s -skipping training candidate: NM_001142463.p1, not unique enough 652s -skipping training candidate: NM_001184819.p1, not unique enough 652s -skipping training candidate: NM_006375.p1, not unique enough 652s -skipping training candidate: NM_001281736.p1, not unique enough 652s -skipping training candidate: NM_004484.p1, not unique enough 652s -skipping training candidate: MSTRG.159.5.p1, not unique enough 652s -skipping training candidate: MSTRG.872.2.p1, not unique enough 652s -skipping training candidate: NM_001306209.p1, not unique enough 652s -skipping training candidate: MSTRG.75.10.p1, not unique enough 652s -skipping training candidate: MSTRG.75.6.p1, not unique enough 652s -skipping training candidate: MSTRG.75.9.p1, not unique enough 652s -skipping training candidate: NM_001139466.p1, not unique enough 652s -skipping training candidate: NM_001190417.p1, not unique enough 652s -skipping training candidate: NM_001146291.p1, not unique enough 652s -skipping training candidate: NM_001037968.p1, not unique enough 652s -skipping training candidate: NM_001139514.p1, not unique enough 652s -skipping training candidate: NM_001170460.p1, not unique enough 652s -skipping training candidate: NM_001282283.p1, not unique enough 652s -skipping training candidate: NM_001170760.p1, not unique enough 652s -skipping training candidate: NM_001128172.p1, not unique enough 652s -skipping training candidate: NM_001164618.p1, not unique enough 652s -skipping training candidate: NM_001079855.p1, not unique enough 652s -skipping training candidate: MSTRG.305.6.p1, not unique enough 652s -skipping training candidate: NM_001184702.p1, not unique enough 652s -skipping training candidate: NM_001128173.p1, not unique enough 652s -skipping training candidate: NM_001168479.p1, not unique enough 652s -skipping training candidate: NM_001168480.p1, not unique enough 652s -skipping training candidate: MSTRG.680.5.p1, not unique enough 652s -skipping training candidate: NM_001168485.p1, not unique enough 652s -skipping training candidate: NM_022838.p1, not unique enough 652s -skipping training candidate: NM_001168482.p1, not unique enough 652s -skipping training candidate: NM_001145140_dup1.p1, not unique enough 652s -skipping training candidate: NM_001145139_dup1.p1, not unique enough 652s -skipping training candidate: NM_001145139.p1, not unique enough 652s -skipping training candidate: MSTRG.945.9.p1, not unique enough 652s -skipping training candidate: NM_001448.p1, not unique enough 652s -skipping training candidate: MSTRG.340.2.p1, not unique enough 652s -skipping training candidate: NM_001128127.p1, not unique enough 652s -skipping training candidate: NM_015507.p1, not unique enough 652s -skipping training candidate: NM_001167.p1, not unique enough 652s -skipping training candidate: NM_001142529.p1, not unique enough 652s -skipping training candidate: NM_030639.p1, not unique enough 652s -skipping training candidate: NM_001142528.p1, not unique enough 652s -skipping training candidate: NM_001142530.p1, not unique enough 652s -skipping training candidate: NM_001142526.p1, not unique enough 652s -skipping training candidate: NM_001142527.p1, not unique enough 652s -skipping training candidate: NM_001142524.p1, not unique enough 652s -skipping training candidate: NM_001142391.p1, not unique enough 652s -skipping training candidate: NM_000402.p1, not unique enough 652s -skipping training candidate: NM_001128166.p1, not unique enough 652s -skipping training candidate: NM_001128167.p1, not unique enough 652s -skipping training candidate: NM_002578.p1, not unique enough 652s -skipping training candidate: MSTRG.275.2.p1, not unique enough 652s -skipping training candidate: NM_001145934.p1, not unique enough 652s -skipping training candidate: NM_017711.p1, not unique enough 652s -skipping training candidate: NM_001204401.p1, not unique enough 652s -skipping training candidate: MSTRG.326.1.p1, not unique enough 652s -skipping training candidate: MSTRG.957.16.p1, not unique enough 652s -skipping training candidate: NM_001282607.p1, not unique enough 652s -skipping training candidate: NM_001170761.p1, not unique enough 652s -skipping training candidate: NM_001282202.p1, not unique enough 652s -skipping training candidate: NR_033348.p1, not unique enough 652s -skipping training candidate: NM_001172743.p1, not unique enough 652s -skipping training candidate: NM_203391.p1, not unique enough 652s -skipping training candidate: NR_033349.p1, not unique enough 652s -skipping training candidate: NM_001172739.p1, not unique enough 652s -skipping training candidate: NM_001271815.p1, not unique enough 652s -skipping training candidate: MSTRG.865.1.p1, not unique enough 652s -skipping training candidate: MSTRG.75.4.p1, not unique enough 652s -skipping training candidate: NM_001139467.p1, not unique enough 652s -skipping training candidate: NM_001139468.p1, not unique enough 652s -skipping training candidate: MSTRG.75.8.p1, not unique enough 652s -skipping training candidate: MSTRG.75.7.p1, not unique enough 652s -skipping training candidate: NM_001164619.p1, not unique enough 652s -skipping training candidate: NM_001184703.p1, not unique enough 652s -skipping training candidate: NM_000167.p1, not unique enough 652s -skipping training candidate: NM_203475.p1, not unique enough 652s -skipping training candidate: NM_002186.p1, not unique enough 652s -skipping training candidate: NM_000377.p1, not unique enough 652s -skipping training candidate: NM_001142806.p1, not unique enough 652s -skipping training candidate: NM_001109878.p1, not unique enough 652s -skipping training candidate: MSTRG.1040.3.p1, not unique enough 652s -skipping training candidate: NM_145802.p1, not unique enough 652s -skipping training candidate: NM_203473.p1, not unique enough 652s -skipping training candidate: NM_001185081.p1, not unique enough 652s -skipping training candidate: NM_015185.p1, not unique enough 652s -skipping training candidate: NM_013955.p1, not unique enough 652s -skipping training candidate: NM_145799.p1, not unique enough 652s -skipping training candidate: NM_145800.p1, not unique enough 652s -skipping training candidate: MSTRG.266.5.p1, not unique enough 652s -skipping training candidate: MSTRG.266.4.p1, not unique enough 652s -skipping training candidate: NM_020730.p1, not unique enough 652s -skipping training candidate: MSTRG.17.2.p1, not unique enough 652s -skipping training candidate: MSTRG.17.6.p1, not unique enough 652s -skipping training candidate: NM_022825.p1, not unique enough 652s -skipping training candidate: NM_007131.p1, not unique enough 652s -skipping training candidate: NM_001193270.p1, not unique enough 652s -skipping training candidate: MSTRG.496.3.p1, not unique enough 652s -skipping training candidate: NM_001167972.p1, not unique enough 652s -skipping training candidate: NM_001167970.p1, not unique enough 652s -skipping training candidate: NM_024917.p1, not unique enough 652s -skipping training candidate: MSTRG.1036.1.p1, not unique enough 652s -skipping training candidate: NR_104109.p1, not unique enough 652s -skipping training candidate: NM_001289109.p1, not unique enough 652s -skipping training candidate: NM_033018.p1, not unique enough 652s -skipping training candidate: MSTRG.326.2.p1, not unique enough 652s -skipping training candidate: MSTRG.496.5.p1, not unique enough 652s -skipping training candidate: NM_001166460.p1, not unique enough 652s -skipping training candidate: MSTRG.137.3.p1, not unique enough 652s -skipping training candidate: NM_001166461.p1, not unique enough 652s -skipping training candidate: NM_005089.p1, not unique enough 652s -skipping training candidate: MSTRG.838.6.p1, not unique enough 652s -skipping training candidate: MSTRG.275.3.p1, not unique enough 652s -skipping training candidate: MSTRG.275.4.p1, not unique enough 652s -skipping training candidate: MSTRG.275.7.p1, not unique enough 652s -skipping training candidate: MSTRG.275.6.p1, not unique enough 652s -skipping training candidate: MSTRG.961.3.p1, not unique enough 652s -skipping training candidate: MSTRG.991.7.p1, not unique enough 652s -skipping training candidate: NM_001171163.p1, not unique enough 652s -skipping training candidate: MSTRG.443.4.p1, not unique enough 652s -skipping training candidate: MSTRG.443.1.p1, not unique enough 652s -skipping training candidate: MSTRG.443.2.p1, not unique enough 652s -skipping training candidate: MSTRG.443.5.p1, not unique enough 652s -skipping training candidate: NM_001288747.p1, not unique enough 652s -skipping training candidate: NM_001184745.p1, not unique enough 652s -skipping training candidate: MSTRG.496.4.p1, not unique enough 652s -skipping training candidate: NM_001193279.p1, not unique enough 652s -skipping training candidate: NM_198511.p1, not unique enough 652s -skipping training candidate: MSTRG.431.1.p1, not unique enough 652s -skipping training candidate: NM_004992.p1, not unique enough 652s -skipping training candidate: NM_017883.p1, not unique enough 652s -skipping training candidate: MSTRG.977.4.p1, not unique enough 652s -skipping training candidate: NM_001287345.p1, not unique enough 652s -skipping training candidate: NM_001172732.p1, not unique enough 652s -skipping training candidate: NM_019848.p1, not unique enough 652s -skipping training candidate: MSTRG.570.8.p1, not unique enough 652s -skipping training candidate: MSTRG.209.8.p1, not unique enough 652s -skipping training candidate: NM_033518.p1, not unique enough 652s -skipping training candidate: MSTRG.301.2.p1, not unique enough 652s -skipping training candidate: MSTRG.503.1.p1, not unique enough 652s -skipping training candidate: NM_001145409.p1, not unique enough 652s -skipping training candidate: NM_007363.p1, not unique enough 652s -skipping training candidate: MSTRG.503.2.p1, not unique enough 652s -skipping training candidate: MSTRG.496.7.p1, not unique enough 652s -skipping training candidate: NM_023010.p1, not unique enough 652s -skipping training candidate: NM_001282142.p1, not unique enough 652s -skipping training candidate: NM_001145252.p1, not unique enough 652s -skipping training candidate: NM_001178113.p1, not unique enough 652s -skipping training candidate: NM_203474.p1, not unique enough 652s -skipping training candidate: NM_001282401.p1, not unique enough 652s -skipping training candidate: MSTRG.672.4.p1, not unique enough 652s -skipping training candidate: NM_001282400.p1, not unique enough 652s -skipping training candidate: MSTRG.804.4.p1, not unique enough 652s -skipping training candidate: MSTRG.496.6.p1, not unique enough 652s -skipping training candidate: NM_006140.p1, not unique enough 652s -skipping training candidate: NM_001173479.p1, not unique enough 652s -skipping training candidate: NM_001166550.p1, not unique enough 652s -skipping training candidate: NM_001171193.p1, not unique enough 652s -skipping training candidate: NM_001171191.p1, not unique enough 652s -skipping training candidate: MSTRG.957.9.p1, not unique enough 652s -skipping training candidate: NM_001167971.p1, not unique enough 652s -skipping training candidate: NM_001114377.p1, not unique enough 652s -skipping training candidate: NM_000868.p1, not unique enough 652s -skipping training candidate: NM_001143982.p1, not unique enough 652s -skipping training candidate: NM_001271804.p1, not unique enough 652s -skipping training candidate: NM_145234.p1, not 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candidate: NM_001114123.p1, not unique enough 652s -skipping training candidate: NM_001184960.p1, not unique enough 652s -skipping training candidate: MSTRG.804.3.p1, not unique enough 652s -skipping training candidate: NM_002893.p1, not unique enough 652s -skipping training candidate: NM_001177466.p2, not unique enough 652s -skipping training candidate: NM_005491.p2, not unique enough 652s -skipping training candidate: NM_001171080.p1, not unique enough 652s -skipping training candidate: NM_001164415_dup1.p1, not unique enough 652s -skipping training candidate: NM_016153.p1, not unique enough 652s -skipping training candidate: NM_016153_dup1.p1, not unique enough 652s -skipping training candidate: NM_001136159.p1, not unique enough 652s -skipping training candidate: NM_003639.p1, not unique enough 652s -skipping training candidate: NM_001099857.p1, not unique enough 652s -skipping training candidate: MSTRG.921.6.p1, not unique enough 652s -skipping training candidate: NM_016542.p1, 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training candidate: NM_001007523.p1, not unique enough 652s -skipping training candidate: NM_001007523_dup1.p1, not unique enough 652s -skipping training candidate: MSTRG.961.2.p1, not unique enough 652s -skipping training candidate: NM_001278000.p1, not unique enough 653s -skipping training candidate: NM_021048.p1, not unique enough 653s -skipping training candidate: NM_001011543.p1, not unique enough 653s -skipping training candidate: MSTRG.1041.9.p1, not unique enough 653s -skipping training candidate: NM_017518.p1, not unique enough 653s -skipping training candidate: MSTRG.480.4.p1, not unique enough 653s -skipping training candidate: NM_001135740.p1, not unique enough 653s -skipping training candidate: MSTRG.222.1.p1, not unique enough 653s -skipping training candidate: NM_004019.p1, not unique enough 653s -skipping training candidate: MSTRG.222.2.p1, not unique enough 653s -skipping training candidate: MSTRG.17.7.p1, not unique enough 653s -skipping training candidate: NM_032458.p1, not unique enough 653s -skipping training candidate: NM_001015877.p1, not unique enough 653s -skipping training candidate: NM_002765.p1, not unique enough 653s -skipping training candidate: NM_032946.p1, not unique enough 653s -skipping training candidate: NM_001008222.p1, not unique enough 653s -skipping training candidate: NM_001306145.p1, not unique enough 653s -skipping training candidate: NM_001171942.p1, not unique enough 653s -skipping training candidate: MSTRG.320.5.p1, not unique enough 653s -skipping training candidate: NM_007075.p1, not unique enough 653s -skipping training candidate: MSTRG.320.2.p1, not unique enough 653s -skipping training candidate: NM_178151.p1, not unique enough 653s -skipping training candidate: NR_045864.p1, not unique enough 653s -skipping training candidate: NM_001029896.p1, not unique enough 653s -skipping training candidate: NM_007250.p1, not unique enough 653s -skipping training candidate: NM_178129.p1, not unique enough 653s -skipping training candidate: MSTRG.268.2.p1, not unique enough 653s -skipping training candidate: MSTRG.268.1.p1, not unique enough 653s -skipping training candidate: NM_153488.p1, not unique enough 653s -skipping training candidate: MSTRG.51.1.p1, not unique enough 653s -skipping training candidate: MSTRG.921.7.p1, not unique enough 653s -skipping training candidate: NM_001042452.p1, not unique enough 653s -skipping training candidate: MSTRG.1042.3.p1, not unique enough 653s -skipping training candidate: MSTRG.91.8.p1, not unique enough 653s -skipping training candidate: NM_006800.p1, not unique enough 653s -skipping training candidate: NM_015075.p2, not unique enough 653s -skipping training candidate: MSTRG.889.3.p1, not unique enough 653s -skipping training candidate: MSTRG.889.13.p1, not unique enough 653s -skipping training candidate: NM_018388.p1, not unique enough 653s -skipping training candidate: MSTRG.889.1.p1, not unique enough 653s -skipping training candidate: NM_001171132.p1, not unique enough 653s -skipping training candidate: MSTRG.651.11.p1, not unique enough 653s -skipping training candidate: MSTRG.651.10.p1, not unique enough 653s -skipping training candidate: MSTRG.651.14.p1, not unique enough 653s -skipping training candidate: MSTRG.651.9.p1, not unique enough 653s -skipping training candidate: NM_012069.p1, not unique enough 653s -skipping training candidate: NR_028477.p1, not unique enough 653s -skipping training candidate: NM_001163264.p1, not unique enough 653s -skipping training candidate: NM_001297564.p1, not unique enough 653s -skipping training candidate: NM_001297563.p1, not unique enough 653s -skipping training candidate: MSTRG.4.4.p1, not unique enough 653s -skipping training candidate: NR_027760.p1, not unique enough 653s -skipping training candidate: MSTRG.668.1.p1, not unique enough 653s -skipping training candidate: MSTRG.209.6.p1, not unique enough 653s -skipping training candidate: NR_045861.p1, not unique enough 653s -skipping training candidate: NM_002363.p1, not unique enough 653s -skipping training candidate: NM_001257403.p1, not unique enough 653s -skipping training candidate: NM_001271748.p1, not unique enough 653s -skipping training candidate: NM_177415.p1, not unique enough 653s -skipping training candidate: NM_006064.p1, not unique enough 653s -skipping training candidate: MSTRG.128.1.p1, not unique enough 653s -skipping training candidate: NM_006123.p1, not unique enough 653s -skipping training candidate: MSTRG.961.1.p1, not unique enough 653s -skipping training candidate: MSTRG.108.1.p1, not unique enough 653s -skipping training candidate: NM_001172285.p1, not unique enough 653s -skipping training candidate: NM_172247.p1, not unique enough 653s -skipping training candidate: MSTRG.549.1.p1, not unique enough 653s -skipping training candidate: NM_001178115.p1, not unique enough 653s -skipping training candidate: MSTRG.583.5.p1, not unique enough 653s -skipping training candidate: MSTRG.583.4.p1, not unique enough 653s -skipping training candidate: MSTRG.583.2.p1, not unique enough 653s -skipping training candidate: NM_198333.p1, not unique enough 653s -skipping training candidate: NM_014499.p1, not unique enough 653s -skipping training candidate: MSTRG.583.1.p1, not unique enough 653s -skipping training candidate: NM_001042453.p1, not unique enough 653s -skipping training candidate: NM_001551.p1, not unique enough 653s -skipping training candidate: MSTRG.268.4.p1, not unique enough 653s -skipping training candidate: MSTRG.705.2.p1, not unique enough 653s -skipping training candidate: NM_001282187.p1, not unique enough 653s -skipping training candidate: NM_001282188.p1, not unique enough 653s -skipping training candidate: NM_001282186.p1, not unique enough 653s -skipping training candidate: NM_205833.p1, not unique enough 653s -skipping training candidate: NM_178270.p1, not unique enough 653s -skipping training candidate: MSTRG.302.7.p1, not unique enough 653s -skipping training candidate: MSTRG.302.4.p1, not unique enough 653s -skipping training candidate: MSTRG.1001.1.p1, not unique enough 653s -skipping training candidate: MSTRG.858.4.p1, not unique enough 653s -skipping training candidate: NR_109776.p2, not unique enough 653s -skipping training candidate: NM_133486.p1, not unique enough 653s -skipping training candidate: MSTRG.586.1.p1, not unique enough 653s -skipping training candidate: NM_001282649.p1, not unique enough 653s -skipping training candidate: NM_001171186.p1, not unique enough 653s -skipping training candidate: MSTRG.209.7.p1, not unique enough 653s -skipping training candidate: NM_001163265.p1, not unique enough 653s -skipping training candidate: NM_001169574.p1, not unique enough 653s -skipping training candidate: NM_001080485.p1, not unique enough 653s -skipping training candidate: NM_012280.p1, not unique enough 653s -skipping training candidate: NM_001282198.p1, not unique enough 653s -skipping training candidate: NM_001242640.p1, not unique enough 653s -skipping training candidate: NM_001146256.p1, not unique enough 653s -skipping training candidate: NM_177439.p1, not unique enough 653s -skipping training candidate: NM_001018055.p1, not unique enough 653s -skipping training candidate: NM_001042479.p1, not unique enough 653s -skipping training candidate: MSTRG.1042.1.p1, not unique enough 653s -skipping training candidate: NM_001104544.p1, not unique enough 653s -skipping training candidate: NM_001282195.p1, not unique enough 653s -skipping training candidate: MSTRG.320.3.p1, not unique enough 653s -skipping training candidate: NR_037859.p1, not unique enough 653s -skipping training candidate: NM_001130847.p1, not unique enough 653s -skipping training candidate: NM_001166418.p1, not unique enough 653s -skipping training candidate: MSTRG.1023.3.p1, not unique enough 653s -skipping training candidate: MSTRG.4.6.p1, not unique enough 653s -skipping training candidate: NM_018390.p1, not unique 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candidate: NM_005364.p1, not unique enough 653s -skipping training candidate: NM_001011548.p1, not unique enough 653s -skipping training candidate: NM_001171133.p1, not unique enough 653s -skipping training candidate: NM_001080790_dup1.p1, not unique enough 653s -skipping training candidate: NM_005365.p1, not unique enough 653s -skipping training candidate: NM_005365_dup1.p1, not unique enough 653s -skipping training candidate: NM_005367.p1, not unique enough 653s -skipping training candidate: NM_005362.p1, not unique enough 653s -skipping training candidate: NM_175743.p1, not unique enough 653s -skipping training candidate: NM_175743_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282502_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282502.p1, not unique enough 653s -skipping training candidate: NM_005361_dup1.p1, not unique enough 653s -skipping training candidate: NM_005361.p1, not unique enough 653s -skipping training candidate: NM_001282504_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282504.p1, not unique enough 653s -skipping training candidate: NM_005363.p1, not unique enough 653s -skipping training candidate: NM_001282505_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282505.p1, not unique enough 653s -skipping training candidate: NM_001282501_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282501.p1, not unique enough 653s -skipping training candidate: NM_175742_dup1.p1, not unique enough 653s -skipping training candidate: NM_175742.p1, not unique enough 653s -skipping training candidate: NM_001166386.p1, not unique enough 653s -skipping training candidate: NM_001139457.p1, not unique enough 653s -skipping training candidate: NM_001258423.p1, not unique enough 653s -skipping training candidate: NR_104128.p1, not unique enough 653s -skipping training candidate: MSTRG.961.4.p1, not unique enough 653s -skipping training candidate: NM_032335.p1, not unique enough 653s -skipping training candidate: NR_110022.p1, not unique enough 653s -skipping training candidate: NR_110021.p1, not unique enough 653s -skipping training candidate: NM_001146151.p1, not unique enough 653s -skipping training candidate: NM_177557.p1, not unique enough 653s -skipping training candidate: MSTRG.1023.4.p1, not unique enough 653s -skipping training candidate: NM_012151.p2, not unique enough 653s -skipping training candidate: MSTRG.705.3.p1, not unique enough 653s -skipping training candidate: NM_001012755.p1, not unique enough 653s -skipping training candidate: NM_012151_dup1.p2, not unique enough 653s -skipping training candidate: MSTRG.1042.2.p1, not unique enough 653s -skipping training candidate: NM_001282401.p2, not unique enough 653s -skipping training candidate: NM_001201583.p1, not unique enough 653s -skipping training candidate: NM_001001996.p1, not unique enough 653s -skipping training candidate: NM_001100431.p1, not unique enough 653s -skipping training candidate: MSTRG.734.5.p1, not unique enough 653s -skipping training candidate: NM_001170701.p1, not unique enough 653s -skipping training candidate: MSTRG.51.3.p1, not unique enough 653s -skipping training candidate: NM_001170703.p1, not unique enough 653s -skipping training candidate: MSTRG.912.5.p1, not unique enough 653s -skipping training candidate: NM_006746.p1, not unique enough 653s -skipping training candidate: NM_001007524_dup2.p2, not unique enough 653s -skipping training candidate: NM_001012428.p1, not unique enough 653s -skipping training candidate: NM_001007523.p2, not unique enough 653s -skipping training candidate: NM_001007523_dup1.p2, not unique enough 653s -skipping training candidate: NM_001009934.p1, not unique enough 653s -skipping training candidate: NM_001303620.p1, not unique enough 653s -skipping training candidate: NM_006730.p1, not unique enough 653s -skipping training candidate: NM_001009932.p1, not unique enough 653s -skipping training candidate: MSTRG.1028.1.p1, not unique enough 653s -skipping training candidate: NM_025159.p1, not unique enough 653s -skipping training candidate: MSTRG.205.1.p1, not unique enough 653s -skipping training candidate: NM_001184771.p1, not unique enough 653s -skipping training candidate: NM_001267713.p1, not unique enough 653s -skipping training candidate: NM_019007.p1, not unique enough 653s -skipping training candidate: NM_001009584.p1, not unique enough 653s -skipping training candidate: MSTRG.651.3.p1, not unique enough 653s -skipping training candidate: MSTRG.128.5.p1, not unique enough 653s -skipping training candidate: NM_004683.p1, not unique enough 653s -skipping training candidate: NM_001171039.p1, not unique enough 653s -skipping training candidate: NM_172249.p1, not unique enough 653s -skipping training candidate: NM_001199687.p1, not unique enough 653s -skipping training candidate: MSTRG.734.3.p1, not unique enough 653s -skipping training candidate: MSTRG.1005.2.p2, not 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not unique enough 653s -skipping training candidate: NM_001242922_dup5.p1, not unique enough 653s -skipping training candidate: NM_001242922_dup1.p1, not unique enough 653s -skipping training candidate: NM_001242922_dup8.p1, not unique enough 653s -skipping training candidate: NM_001242922_dup7.p1, not unique enough 653s -skipping training candidate: MSTRG.992.1.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup9.p1, not unique enough 653s -skipping training candidate: NM_001080144.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup6.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup4.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup3.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup1.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup7.p1, not unique enough 653s -skipping training candidate: NM_001080144_dup2.p1, not unique enough 653s -skipping 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NM_001080139_dup6.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup1.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup5.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup4.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup2.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup7.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup8.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup3.p1, not unique enough 653s -skipping training candidate: NM_001080139_dup9.p1, not unique enough 653s -skipping training candidate: NR_073149.p1, not unique enough 653s -skipping training candidate: NM_000166.p1, not unique enough 653s -skipping training candidate: MSTRG.994.1.p1, not unique enough 653s -skipping training candidate: NM_030763.p1, not unique enough 653s -skipping training candidate: NM_001307944.p1, not unique enough 653s -skipping 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not unique enough 653s -skipping training candidate: NM_001130846.p1, not unique enough 653s -skipping training candidate: MSTRG.889.14.p1, not unique enough 653s -skipping training candidate: MSTRG.889.4.p1, not unique enough 653s -skipping training candidate: MSTRG.889.12.p1, not unique enough 653s -skipping training candidate: MSTRG.68.8.p1, not unique enough 653s -skipping training candidate: MSTRG.68.3.p1, not unique enough 653s -skipping training candidate: MSTRG.68.6.p1, not unique enough 653s -skipping training candidate: MSTRG.68.16.p1, not unique enough 653s -skipping training candidate: NR_034031.p1, not unique enough 653s -skipping training candidate: MSTRG.68.14.p1, not unique enough 653s -skipping training candidate: MSTRG.68.17.p1, not unique enough 653s -skipping training candidate: MSTRG.597.3.p1, not unique enough 653s -skipping training candidate: MSTRG.1041.7.p1, not unique enough 653s -skipping training candidate: MSTRG.992.2.p1, not unique enough 653s -skipping 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NM_001161532.p1, not unique enough 653s -skipping training candidate: NM_001170756.p1, not unique enough 653s -skipping training candidate: NM_017776.p1, not unique enough 653s -skipping training candidate: NM_198456.p2, not unique enough 653s -skipping training candidate: NM_001300788.p2, not unique enough 653s -skipping training candidate: NM_005710.p1, not unique enough 653s -skipping training candidate: NM_001032382.p1, not unique enough 653s -skipping training candidate: NM_001032383.p1, not unique enough 653s -skipping training candidate: NM_001032381.p1, not unique enough 653s -skipping training candidate: NM_005278.p1, not unique enough 653s -skipping training candidate: MSTRG.794.4.p1, not unique enough 653s -skipping training candidate: NM_181313.p1, not unique enough 653s -skipping training candidate: NM_001167989.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.10.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.2.p1, not unique enough 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MSTRG.110.2.p2, not unique enough 653s -skipping training candidate: NM_001012288.p1, not unique enough 653s -skipping training candidate: NM_001278702_dup1.p1, not unique enough 653s -skipping training candidate: NM_001278702.p1, not unique enough 653s -skipping training candidate: NM_001278697.p1, not unique enough 653s -skipping training candidate: NM_001278697_dup1.p1, not unique enough 653s -skipping training candidate: NM_001170704.p1, not unique enough 653s -skipping training candidate: MSTRG.889.15.p1, not unique enough 653s -skipping training candidate: MSTRG.889.11.p1, not unique enough 653s -skipping training candidate: MSTRG.889.18.p1, not unique enough 653s -skipping training candidate: MSTRG.889.17.p1, not unique enough 653s -skipping training candidate: MSTRG.889.16.p1, not unique enough 653s -skipping training candidate: NM_001010862.p1, not unique enough 653s -skipping training candidate: MSTRG.541.3.p1, not unique enough 653s -skipping training candidate: NM_001099681.p1, not unique enough 653s -skipping training candidate: NM_001006681.p1, not unique enough 653s -skipping training candidate: MSTRG.426.1.p1, not unique enough 653s -skipping training candidate: NM_001006683.p1, not unique enough 653s -skipping training candidate: NM_001006682.p1, not unique enough 653s -skipping training candidate: NM_017848.p2, not unique enough 653s -skipping training candidate: NM_000425.p2, not unique enough 653s -skipping training candidate: NM_024003.p2, not unique enough 653s -skipping training candidate: NM_001143963.p2, not unique enough 653s -skipping training candidate: MSTRG.222.1.p2, not unique enough 653s -skipping training candidate: MSTRG.693.4.p1, not unique enough 653s -skipping training candidate: NM_001159296.p1, not unique enough 653s -skipping training candidate: MSTRG.763.3.p1, not unique enough 653s -skipping training candidate: NM_001162491.p1, not unique enough 653s -skipping training candidate: NR_028476.p1, not unique enough 653s -skipping training candidate: NR_110023.p2, not unique enough 653s -skipping training candidate: NM_001099682.p1, not unique enough 653s -skipping training candidate: NM_012080.p1, not unique enough 653s -skipping training candidate: NM_001142389.p1, not unique enough 653s -skipping training candidate: MSTRG.651.4.p1, not unique enough 653s -skipping training candidate: MSTRG.921.7.p2, not unique enough 653s -skipping training candidate: MSTRG.921.5.p2, not unique enough 653s -skipping training candidate: MSTRG.921.6.p2, not unique enough 653s -skipping training candidate: NM_001168530.p1, not unique enough 653s -skipping training candidate: MSTRG.8.2.p1, not unique enough 653s -skipping training candidate: MSTRG.909.17.p1, not unique enough 653s -skipping training candidate: MSTRG.320.1.p1, not unique enough 653s -skipping training candidate: MSTRG.91.6.p1, not unique enough 653s -skipping training candidate: MSTRG.91.9.p1, not unique enough 653s -skipping training candidate: NM_001300884.p1, not unique enough 653s -skipping training candidate: NM_145284.p1, not unique enough 653s -skipping training candidate: NM_173698.p1, not unique enough 653s -skipping training candidate: NM_001171109.p1, not unique enough 653s -skipping training candidate: NM_181313.p2, not unique enough 653s -skipping training candidate: NM_001171111.p1, not unique enough 653s -skipping training candidate: NM_002139.p2, not unique enough 653s -skipping training candidate: NR_028477.p2, not unique enough 653s -skipping training candidate: NM_001166599.p1, not unique enough 653s -skipping training candidate: MSTRG.909.16.p1, not unique enough 653s -skipping training candidate: MSTRG.265.4.p1, not unique enough 653s -skipping training candidate: MSTRG.664.1.p1, not unique enough 653s -skipping training candidate: NR_037916.p1, not unique enough 653s -skipping training candidate: NM_005745.p1, not unique enough 653s -skipping training candidate: NM_001139441.p1, not unique enough 653s 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MSTRG.980.5.p1, not unique enough 653s -skipping training candidate: NM_001104545.p1, not unique enough 653s -skipping training candidate: MSTRG.459.5.p1, not unique enough 653s -skipping training candidate: NM_006950.p2, not unique enough 653s -skipping training candidate: MSTRG.110.9.p2, not unique enough 653s -skipping training candidate: MSTRG.1029.2.p1, not unique enough 653s -skipping training candidate: NM_000116.p2, not unique enough 653s -skipping training candidate: MSTRG.1029.4.p1, not unique enough 653s -skipping training candidate: NM_181312.p2, not unique enough 653s -skipping training candidate: MSTRG.68.9.p1, not unique enough 653s -skipping training candidate: MSTRG.222.2.p2, not unique enough 653s -skipping training candidate: MSTRG.268.7.p1, not unique enough 653s -skipping training candidate: MSTRG.268.3.p1, not unique enough 653s -skipping training candidate: NM_001267053.p1, not unique enough 653s -skipping training candidate: NR_132647.p2, not unique enough 653s -skipping training candidate: NM_001163321.p2, not unique enough 653s -skipping training candidate: MSTRG.1037.1.p1, not unique enough 653s -skipping training candidate: NM_001169125.p2, not unique enough 653s -skipping training candidate: NM_001169122.p2, not unique enough 653s -skipping training candidate: NM_005342.p1, not unique enough 653s -skipping training candidate: MSTRG.858.1.p1, not unique enough 653s -skipping training candidate: NM_001271835.p2, not unique enough 653s -skipping training candidate: NM_033626.p2, not unique enough 653s -skipping training candidate: NM_001271836.p2, not unique enough 653s -skipping training candidate: NM_001163323.p2, not unique enough 653s -skipping training candidate: MSTRG.651.12.p1, not unique enough 653s -skipping training candidate: MSTRG.651.15.p1, not unique enough 653s -skipping training candidate: MSTRG.651.13.p1, not unique enough 653s -skipping training candidate: NM_001301229.p1, not unique enough 653s -skipping training 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NM_033053.p1, not unique enough 653s -skipping training candidate: NM_033053_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.909.7.p1, not unique enough 653s -skipping training candidate: NM_001305004.p1, not unique enough 653s -skipping training candidate: NM_005834.p1, not unique enough 653s -skipping training candidate: MSTRG.664.2.p1, not unique enough 653s -skipping training candidate: NM_001301231.p1, not unique enough 653s -skipping training candidate: NM_178175.p1, not unique enough 653s -skipping training candidate: NM_001256119.p1, not unique enough 653s -skipping training candidate: NM_001171581.p1, not unique enough 653s -skipping training candidate: NM_001144885.p1, not unique enough 653s -skipping training candidate: NM_001291529.p1, not unique enough 653s -skipping training candidate: NM_000950.p1, not unique enough 653s -skipping training candidate: NM_001277710.p1, not unique enough 653s -skipping training candidate: NM_001282648.p1, not unique 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NM_007130.p2, not unique enough 653s -skipping training candidate: MSTRG.279.1.p2, not unique enough 653s -skipping training candidate: MSTRG.279.5.p2, not unique enough 653s -skipping training candidate: MSTRG.279.10.p2, not unique enough 653s -skipping training candidate: MSTRG.279.4.p2, not unique enough 653s -skipping training candidate: NM_001178136.p1, not unique enough 653s -skipping training candidate: NM_001171689.p1, not unique enough 653s -skipping training candidate: NM_013346.p1, not unique enough 653s -skipping training candidate: NM_001291543_dup2.p1, not unique enough 653s -skipping training candidate: NM_001291543.p1, not unique enough 653s -skipping training candidate: NM_001291543_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.1025.2.p1, not unique enough 653s -skipping training candidate: NM_004840.p2, not unique enough 653s -skipping training candidate: MSTRG.929.1.p2, not unique enough 653s -skipping training candidate: MSTRG.142.5.p1, not unique enough 653s -skipping training candidate: NM_001037536.p1, not unique enough 653s -skipping training candidate: NM_001037535.p1, not unique enough 653s -skipping training candidate: MSTRG.1025.3.p1, not unique enough 653s -skipping training candidate: MSTRG.1025.6.p1, not unique enough 653s -skipping training candidate: MSTRG.912.5.p2, not unique enough 653s -skipping training candidate: MSTRG.980.6.p1, not unique enough 653s -skipping training candidate: NM_024689.p1, not unique enough 653s -skipping training candidate: MSTRG.405.7.p1, not unique enough 653s -skipping training candidate: MSTRG.405.5.p1, not unique enough 653s -skipping training candidate: MSTRG.405.4.p1, not unique enough 653s -skipping training candidate: NM_013452.p1, not unique enough 653s -skipping training candidate: NR_104114.p1, not unique enough 653s -skipping training candidate: MSTRG.268.6.p1, not unique enough 653s -skipping training candidate: NM_001256188.p1, not unique enough 653s -skipping training candidate: MSTRG.994.4.p1, not unique enough 653s -skipping training candidate: MSTRG.718.5.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.11.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.4.p2, not unique enough 653s -skipping training candidate: MSTRG.1005.3.p2, not unique enough 653s -skipping training candidate: NM_181762.p1, not unique enough 653s -skipping training candidate: NM_004651.p2, not unique enough 653s -skipping training candidate: MSTRG.714.3.p2, not unique enough 653s -skipping training candidate: MSTRG.697.2.p1, not unique enough 653s -skipping training candidate: NM_001291277.p2, not unique enough 653s -skipping training candidate: NM_004251.p1, not unique enough 653s -skipping training candidate: NM_001178032.p1, not unique enough 653s -skipping training candidate: NR_045044.p1, not unique enough 653s -skipping training candidate: NM_001243804.p1, not unique enough 653s -skipping training candidate: NM_032926.p1, not unique enough 653s -skipping training candidate: NM_001006933.p1, not unique enough 653s -skipping training candidate: MSTRG.232.1.p1, not unique enough 653s -skipping training candidate: MSTRG.232.2.p1, not unique enough 653s -skipping training candidate: MSTRG.337.1.p1, not unique enough 653s -skipping training candidate: MSTRG.305.1.p2, not unique enough 653s -skipping training candidate: NM_003916.p1, not unique enough 653s -skipping training candidate: NM_001139498.p1, not unique enough 653s -skipping training candidate: NM_001666.p2, not unique enough 653s -skipping training candidate: MSTRG.1005.1.p2, not unique enough 653s -skipping training candidate: MSTRG.1024.2.p2, not unique enough 653s -skipping training candidate: NM_001129899.p1, not unique enough 653s -skipping training candidate: NM_001166422.p1, not unique enough 653s -skipping training candidate: MSTRG.459.1.p1, not unique enough 653s -skipping training candidate: NM_176786.p2, not unique enough 653s -skipping training candidate: MSTRG.124.2.p1, not unique enough 653s -skipping training candidate: MSTRG.124.3.p1, not unique enough 653s -skipping training candidate: NM_001159703.p1, not unique enough 653s -skipping training candidate: NM_001168361.p2, not unique enough 653s -skipping training candidate: NM_001195214.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.6.p2, not unique enough 653s -skipping training candidate: NM_004143.p1, not unique enough 653s -skipping training candidate: NM_001144886.p1, not unique enough 653s -skipping training candidate: NM_001129900.p1, not unique enough 653s -skipping training candidate: NM_001282157.p1, not unique enough 653s -skipping training candidate: MSTRG.51.1.p2, not unique enough 653s -skipping training candidate: NM_033642.p1, not unique enough 653s -skipping training candidate: MSTRG.4.3.p2, not unique enough 653s -skipping training candidate: NM_018390.p2, not unique enough 653s -skipping training candidate: NM_144968.p1, not unique enough 653s -skipping training candidate: NM_001142.p1, not unique enough 653s -skipping training candidate: MSTRG.1029.12.p1, not unique enough 653s -skipping training candidate: NM_134445.p1, not unique enough 653s -skipping training candidate: NM_001170757.p1, not unique enough 653s -skipping training candidate: NM_001007551_dup2.p1, not unique enough 653s -skipping training candidate: NM_001007551_dup1.p1, not unique enough 653s -skipping training candidate: NM_001007551.p1, not unique enough 653s -skipping training candidate: NM_001184808.p1, not unique enough 653s -skipping training candidate: NM_001291540_dup2.p1, not unique enough 653s -skipping training candidate: NM_001291540.p1, not unique enough 653s -skipping training candidate: NM_001291540_dup1.p1, not unique enough 653s -skipping training candidate: NM_001017436.p1, not unique enough 653s -skipping training candidate: NM_001291535.p1, not unique enough 653s -skipping training candidate: NM_001291535_dup1.p1, not unique enough 653s -skipping training candidate: NM_152582_dup1.p1, not unique enough 653s -skipping training candidate: NM_152582_dup2.p1, not unique enough 653s -skipping training candidate: NM_001172288_dup2.p1, not unique enough 653s -skipping training candidate: NM_001172288_dup1.p1, not unique enough 653s -skipping training candidate: NM_001172288.p1, not unique enough 653s -skipping training candidate: NM_001017438_dup1.p1, not unique enough 653s -skipping training candidate: NM_001017438_dup2.p1, not unique enough 653s -skipping training candidate: NM_001017438.p1, not unique enough 653s -skipping training candidate: NM_001291528.p1, not unique enough 653s -skipping training candidate: NM_175723.p1, not unique enough 653s -skipping training candidate: MSTRG.327.3.p1, not unique enough 653s -skipping training candidate: NM_003173.p2, not unique enough 653s -skipping training candidate: MSTRG.520.6.p1, not unique enough 653s -skipping training candidate: NM_005635.p1, not unique enough 653s -skipping training candidate: NM_005636.p1, not unique enough 653s -skipping training candidate: MSTRG.82.6.p2, not unique enough 653s -skipping training candidate: NR_109776.p3, not unique enough 653s -skipping training candidate: NM_013427.p2, not unique enough 653s -skipping training candidate: NM_001034832.p1, not unique enough 653s -skipping training candidate: NM_001034832_dup1.p1, not unique enough 653s -skipping training candidate: NM_020766.p2, not unique enough 653s -skipping training candidate: NM_001105243.p2, not unique enough 653s -skipping training candidate: NM_001256197.p1, not unique enough 653s -skipping training candidate: NM_016379.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.3.p2, not unique enough 653s -skipping training candidate: NM_001184875.p2, not unique enough 653s -skipping training candidate: NM_138437.p2, not unique enough 653s -skipping training candidate: NM_001199818.p2, not unique enough 653s -skipping 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NM_001098791.p1, not unique enough 653s -skipping training candidate: NM_021242.p1, not unique enough 653s -skipping training candidate: NM_001098790.p1, not unique enough 653s -skipping training candidate: NR_051952.p1, not unique enough 653s -skipping training candidate: NM_001025242.p2, not unique enough 653s -skipping training candidate: NM_001025243.p2, not unique enough 653s -skipping training candidate: NM_014060.p1, not unique enough 653s -skipping training candidate: NM_001141920.p1, not unique enough 653s -skipping training candidate: NM_198511.p2, not unique enough 653s -skipping training candidate: NM_001327.p1, not unique enough 653s -skipping training candidate: NM_139250_dup1.p1, not unique enough 653s -skipping training candidate: NM_139250.p1, not unique enough 653s -skipping training candidate: MSTRG.508.1.p2, not unique enough 653s -skipping training candidate: MSTRG.508.2.p2, not unique enough 653s -skipping training candidate: NM_175569.p1, not unique enough 653s 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MSTRG.664.1.p2, not unique enough 653s -skipping training candidate: MSTRG.664.2.p2, not unique enough 653s -skipping training candidate: NM_001171907.p1, not unique enough 653s -skipping training candidate: NM_182681.p2, not unique enough 653s -skipping training candidate: NR_026710.p1, not unique enough 653s -skipping training candidate: NR_033772_dup1.p1, not unique enough 653s -skipping training candidate: NM_001282302.p1, not unique enough 653s -skipping training candidate: MSTRG.459.2.p1, not unique enough 653s -skipping training candidate: NR_033773_dup1.p1, not unique enough 653s -skipping training candidate: NR_033773.p1, not unique enough 653s -skipping training candidate: MSTRG.1041.6.p2, not unique enough 653s -skipping training candidate: MSTRG.1041.7.p2, not unique enough 653s -skipping training candidate: MSTRG.387.3.p2, not unique enough 653s -skipping training candidate: NM_001184896.p2, not unique enough 653s -skipping training candidate: NM_001170569.p1, not unique 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NM_001079900_dup1.p1, not unique enough 653s -skipping training candidate: NM_001654.p2, not unique enough 653s -skipping training candidate: NM_001256196.p2, not unique enough 653s -skipping training candidate: MSTRG.76.2.p2, not unique enough 653s -skipping training candidate: NM_001281463.p2, not unique enough 653s -skipping training candidate: MSTRG.739.4.p1, not unique enough 653s -skipping training candidate: NM_000425.p3, not unique enough 653s -skipping training candidate: NM_024003.p3, not unique enough 653s -skipping training candidate: NM_001143963.p3, not unique enough 653s -skipping training candidate: MSTRG.205.2.p1, not unique enough 653s -skipping training candidate: MSTRG.338.6.p2, not unique enough 653s -skipping training candidate: NM_001136157.p2, not unique enough 653s -skipping training candidate: NM_001136159.p2, not unique enough 653s -skipping training candidate: MSTRG.994.1.p2, not unique enough 653s -skipping training candidate: NR_033772_dup1.p2, not unique 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NM_001278740.p1, not unique enough 653s -skipping training candidate: NM_001278741.p1, not unique enough 653s -skipping training candidate: MSTRG.324.2.p1, not unique enough 653s -skipping training candidate: NR_104107.p2, not unique enough 653s -skipping training candidate: NM_001184897.p2, not unique enough 653s -skipping training candidate: NM_015107.p3, not unique enough 653s -skipping training candidate: MSTRG.387.3.p3, not unique enough 653s -skipping training candidate: NM_001184896.p3, not unique enough 653s -skipping training candidate: MSTRG.387.1.p2, not unique enough 653s -skipping training candidate: NM_001282462.p1, not unique enough 653s -skipping training candidate: NM_001282461.p1, not unique enough 653s -skipping training candidate: NM_001012755.p2, not unique enough 653s -skipping training candidate: MSTRG.705.2.p2, not unique enough 653s -skipping training candidate: MSTRG.705.4.p2, not unique enough 653s -skipping training candidate: MSTRG.718.6.p1, not unique 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candidate: MSTRG.1012.4.p2, not unique enough 653s -skipping training candidate: NM_005334.p2, not unique enough 653s -skipping training candidate: MSTRG.1012.3.p2, not unique enough 653s -skipping training candidate: MSTRG.68.10.p2, not unique enough 653s -skipping training candidate: NM_015075.p3, not unique enough 653s -skipping training candidate: NR_030774.p2, not unique enough 653s -skipping training candidate: MSTRG.34.8.p1, not unique enough 653s -skipping training candidate: MSTRG.34.3.p1, not unique enough 653s -skipping training candidate: NM_001164619.p2, not unique enough 653s -skipping training candidate: NM_001164618.p2, not unique enough 653s -skipping training candidate: NM_001164617.p2, not unique enough 653s -skipping training candidate: MSTRG.663.1.p1, not unique enough 653s -skipping training candidate: MSTRG.734.6.p1, not unique enough 653s -skipping training candidate: NM_017698.p1, not unique enough 653s -skipping training candidate: NM_001005613.p1, not unique enough 653s -skipping training candidate: MSTRG.1029.12.p2, not unique enough 653s -skipping training candidate: MSTRG.216.5.p3, not unique enough 653s -skipping training candidate: NM_021242.p3, not unique enough 653s -skipping training candidate: MSTRG.994.4.p2, not unique enough 653s -skipping training candidate: NM_001130997.p2, not unique enough 653s -skipping training candidate: NM_016120.p2, not unique enough 653s -skipping training candidate: MSTRG.537.1.p2, not unique enough 653s -skipping training candidate: NM_183353.p2, not unique enough 653s -skipping training candidate: MSTRG.867.6.p1, not unique enough 653s -skipping training candidate: NM_001272062.p3, not unique enough 653s -skipping training candidate: NM_001272063.p2, not unique enough 653s -skipping training candidate: NM_177537.p3, not unique enough 653s -skipping training candidate: MSTRG.973.2.p1, not unique enough 653s -skipping training candidate: MSTRG.973.1.p1, not unique enough 653s -skipping training candidate: NM_001171909.p1, not unique enough 653s -skipping training candidate: MSTRG.963.2.p1, not unique enough 653s -skipping training candidate: MSTRG.963.3.p2, not unique enough 653s -skipping training candidate: MSTRG.963.1.p2, not unique enough 653s -skipping training candidate: NM_001097604_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.268.3.p2, not unique enough 653s -skipping training candidate: NM_001272061_dup1.p2, not unique enough 653s -skipping training candidate: NM_030801_dup1.p2, not unique enough 653s -skipping training candidate: NM_177535_dup1.p3, not unique enough 653s -skipping training candidate: NM_177537_dup1.p3, not unique enough 653s -skipping training candidate: NM_001097594_dup1.p1, not unique enough 653s -skipping training candidate: NM_001097594.p1, not unique enough 653s -skipping training candidate: NM_020717.p3, not unique enough 653s -skipping training candidate: MSTRG.302.6.p1, not unique enough 653s -skipping training candidate: MSTRG.1025.5.p1, not unique enough 653s -skipping training candidate: NM_001287760.p2, not unique enough 653s -skipping training candidate: NM_033641.p2, not unique enough 653s -skipping training candidate: NM_001847.p2, not unique enough 653s -skipping training candidate: MSTRG.131.6.p1, not unique enough 653s -skipping training candidate: MSTRG.131.5.p1, not unique enough 653s -skipping training candidate: NM_001303465.p2, not unique enough 653s -skipping training candidate: MSTRG.1029.3.p2, not unique enough 653s -skipping training candidate: NM_206917.p1, not unique enough 653s -skipping training candidate: NM_031407.p2, not unique enough 653s -skipping training candidate: MSTRG.397.21.p2, not unique enough 653s -skipping training candidate: MSTRG.397.6.p2, not unique enough 653s -skipping training candidate: MSTRG.397.7.p2, not unique enough 653s -skipping training candidate: MSTRG.397.5.p2, not unique enough 653s -skipping training candidate: MSTRG.397.18.p2, not unique enough 653s -skipping training candidate: MSTRG.397.26.p2, not unique enough 653s -skipping training candidate: MSTRG.397.17.p2, not unique enough 653s -skipping training candidate: MSTRG.397.24.p2, not unique enough 653s -skipping training candidate: MSTRG.397.2.p2, not unique enough 653s -skipping training candidate: MSTRG.397.27.p2, not unique enough 653s -skipping training candidate: MSTRG.397.8.p2, not unique enough 653s -skipping training candidate: MSTRG.397.23.p2, not unique enough 653s -skipping training candidate: MSTRG.397.12.p2, not unique enough 653s -skipping training candidate: MSTRG.397.19.p2, not unique enough 653s -skipping training candidate: MSTRG.397.22.p2, not unique enough 653s -skipping training candidate: MSTRG.397.9.p2, not unique enough 653s -skipping training candidate: MSTRG.397.14.p2, not unique enough 653s -skipping training candidate: MSTRG.397.25.p2, not unique enough 653s -skipping training candidate: MSTRG.397.10.p2, not unique enough 653s -skipping training candidate: MSTRG.397.11.p2, not unique enough 653s -skipping training candidate: MSTRG.397.15.p2, not unique enough 653s -skipping training candidate: MSTRG.397.4.p2, not unique enough 653s -skipping training candidate: MSTRG.397.28.p2, not unique enough 653s -skipping training candidate: MSTRG.397.3.p2, not unique enough 653s -skipping training candidate: MSTRG.397.20.p2, not unique enough 653s -skipping training candidate: MSTRG.397.16.p2, not unique enough 653s -skipping training candidate: NR_045560.p1, not unique enough 653s -skipping training candidate: MSTRG.268.7.p2, not unique enough 653s -skipping training candidate: NM_001291421.p3, not unique enough 653s -skipping training candidate: NM_001291417.p2, not unique enough 653s -skipping training candidate: NM_021140.p2, not unique enough 653s -skipping training candidate: NM_001291418.p2, not unique enough 653s -skipping training candidate: NM_001291416.p2, not unique enough 653s -skipping training candidate: NM_001291415.p2, not unique enough 653s -skipping training candidate: NM_001256187.p1, not unique enough 653s -skipping training candidate: MSTRG.305.1.p3, not unique enough 653s -skipping training candidate: MSTRG.459.3.p2, not unique enough 653s -skipping training candidate: NM_021783.p2, not unique enough 653s -skipping training candidate: MSTRG.459.1.p3, not unique enough 653s -skipping training candidate: NM_020994.p2, not unique enough 653s -skipping training candidate: NM_001282621.p1, not unique enough 653s -skipping training candidate: NM_001146257.p1, not unique enough 653s -skipping training candidate: MSTRG.109.1.p1, not unique enough 653s -skipping training candidate: NM_001168649.p2, not unique enough 653s -skipping training candidate: NM_014927.p2, not unique enough 653s -skipping training candidate: NM_001168647.p2, not unique enough 653s -skipping training candidate: NM_001242617.p1, not unique enough 653s -skipping training candidate: NM_021029.p1, not unique enough 653s -skipping training candidate: MSTRG.68.10.p3, not unique enough 653s -skipping training candidate: MSTRG.68.8.p2, not unique enough 653s -skipping training candidate: MSTRG.68.2.p1, not unique enough 653s -skipping training candidate: MSTRG.68.16.p2, not unique enough 653s -skipping training candidate: MSTRG.258.8.p2, not unique enough 653s -skipping training candidate: MSTRG.250.5.p1, not unique enough 653s -skipping training candidate: NM_001011658.p1, not unique enough 653s -skipping training candidate: MSTRG.258.9.p2, not unique enough 653s -skipping training candidate: NM_001184898.p2, not unique enough 653s -skipping training candidate: MSTRG.992.7.p2, not unique enough 653s -skipping training candidate: MSTRG.476.2.p1, not unique enough 653s -skipping training candidate: NM_020717.p4, not unique enough 653s -skipping training candidate: NM_001256186.p1, not unique enough 653s -skipping training candidate: NM_017711.p3, not unique enough 653s -skipping training candidate: NM_017883.p2, not unique enough 653s -skipping training candidate: NM_001171192.p3, not unique enough 653s -skipping training candidate: NM_001282621.p2, not unique enough 653s -skipping training candidate: MSTRG.921.1.p2, not unique enough 653s -skipping training candidate: MSTRG.921.3.p2, not unique enough 653s -skipping training candidate: MSTRG.921.2.p2, not unique enough 653s -skipping training candidate: MSTRG.718.1.p1, not unique enough 653s -skipping training candidate: NM_001184819.p2, not unique enough 653s -skipping training candidate: MSTRG.641.8.p1, not unique enough 653s -skipping training candidate: NM_001099857.p2, not unique enough 653s -skipping training candidate: NM_001008534.p1, not unique enough 653s -skipping training candidate: NM_001278742.p1, not unique enough 653s -skipping training candidate: MSTRG.305.6.p2, not unique enough 653s -skipping training candidate: MSTRG.306.1.p2, not unique enough 653s -skipping training candidate: NM_014725.p2, not unique enough 653s -skipping training candidate: NM_001142504.p2, not unique enough 653s -skipping training candidate: NM_001271183.p2, not unique enough 653s -skipping training candidate: MSTRG.404.8.p2, not unique enough 653s -skipping training candidate: NM_001271184.p2, not unique enough 653s -skipping training candidate: NM_001172739.p2, not unique enough 653s -skipping training candidate: MSTRG.734.6.p2, not unique enough 653s -skipping training candidate: NM_017698.p2, not unique enough 653s -skipping training candidate: MSTRG.734.5.p2, not unique enough 653s -skipping training candidate: MSTRG.734.3.p2, not unique enough 653s -skipping training candidate: MSTRG.734.2.p2, not unique enough 653s -skipping training candidate: NM_001005609.p2, not unique enough 653s -skipping training candidate: MSTRG.438.2.p1, not unique enough 653s -skipping training candidate: NR_001564.p1, not unique enough 653s -skipping training candidate: MSTRG.531.1.p1, not unique enough 653s -skipping training candidate: MSTRG.531.3.p1, not unique enough 653s -skipping training candidate: MSTRG.275.3.p3, not unique enough 653s -skipping training candidate: NM_001170460.p2, not unique enough 653s -skipping training candidate: MSTRG.275.2.p2, not unique enough 653s -skipping training candidate: MSTRG.275.4.p3, not unique enough 653s -skipping training candidate: MSTRG.275.7.p2, not unique enough 653s -skipping training candidate: MSTRG.275.6.p2, not unique enough 653s -skipping training candidate: NM_006201.p2, not unique enough 653s -skipping training candidate: MSTRG.615.2.p1, not unique enough 653s -skipping training candidate: MSTRG.615.1.p1, not unique enough 653s -skipping training candidate: MSTRG.16.1.p6, not unique enough 653s -skipping training candidate: NM_000495.p2, not unique enough 653s -skipping training candidate: MSTRG.992.3.p1, not unique enough 653s -skipping training candidate: NR_073156.p2, not unique enough 653s -skipping training candidate: MSTRG.62.2.p2, not unique enough 653s -skipping training candidate: MSTRG.62.1.p2, not unique enough 653s -skipping training candidate: NM_006521.p2, not unique enough 653s -skipping training candidate: MSTRG.488.1.p1, not unique enough 653s -skipping training candidate: NR_033212.p1, not unique enough 653s -skipping training candidate: NM_145305.p2, not unique enough 653s -skipping training candidate: NM_001005610.p1, not unique enough 653s -skipping training candidate: NR_001564.p2, not unique enough 653s -skipping training candidate: MSTRG.531.1.p2, not unique enough 653s -skipping training candidate: MSTRG.531.3.p2, not unique enough 653s -skipping training candidate: MSTRG.275.4.p4, not unique enough 653s -skipping training candidate: NM_006201.p3, not unique enough 653s -skipping training candidate: NM_001300788.p3, not unique enough 653s -skipping training candidate: NM_001144003.p2, not unique enough 653s -skipping training candidate: MSTRG.284.1.p3, not unique enough 653s -skipping training candidate: MSTRG.963.2.p2, not unique enough 653s -skipping training candidate: NM_001039582.p2, not unique enough 653s -skipping training candidate: NM_001144005.p2, not unique enough 653s -skipping training candidate: MSTRG.933.1.p2, not unique enough 653s -skipping training candidate: NM_001005609.p3, not unique enough 653s -skipping training candidate: NM_001005612.p2, not unique enough 653s -skipping training candidate: NM_001005612.p3, not unique enough 653s -skipping training candidate: MSTRG.759.10.p2, not unique enough 653s -skipping training candidate: MSTRG.759.2.p2, not unique enough 653s -skipping training candidate: MSTRG.759.21.p2, not unique enough 653s -skipping training candidate: MSTRG.759.11.p2, not unique enough 653s -skipping training candidate: NM_001168385.p1, not unique enough 653s -skipping training candidate: NM_001143982.p2, not unique enough 653s -skipping training candidate: MSTRG.305.8.p2, not unique enough 653s -skipping training candidate: NM_145234.p2, not unique enough 653s -skipping training candidate: MSTRG.641.7.p1, not unique enough 653s -skipping training candidate: NM_001145252.p2, not unique enough 653s -skipping training candidate: NM_001143981.p2, not unique enough 653s -skipping training candidate: NM_174951.p2, not unique enough 653s -skipping training candidate: NR_027383.p4, not unique enough 653s -skipping training candidate: MSTRG.32.4.p4, not unique enough 653s -skipping training candidate: MSTRG.327.3.p3, not unique enough 653s -skipping training candidate: NM_003173.p3, not unique enough 653s -skipping training candidate: NR_024048.p2, not unique enough 653s -skipping training candidate: NM_001123385.p2, not unique enough 653s -skipping training candidate: NM_130467.p1, not unique enough 653s -skipping training candidate: NM_005676.p2, not unique enough 653s -skipping training candidate: NM_001204468.p2, not unique enough 653s -skipping training candidate: NR_029427.p3, not unique enough 653s -skipping training candidate: MSTRG.325.4.p2, not unique enough 653s -skipping training candidate: NM_001166426.p2, not unique enough 653s -skipping training candidate: NM_017883.p3, not unique enough 653s -skipping training candidate: NM_001080851.p2, not unique enough 653s -skipping training candidate: NM_001278743.p1, not unique enough 653s -skipping training candidate: MSTRG.822.4.p1, not unique enough 653s -skipping training candidate: NM_033053.p2, not unique enough 653s -skipping training candidate: NM_033053_dup1.p2, not unique enough 653s -skipping training candidate: NM_005647.p3, not unique enough 653s -skipping training candidate: MSTRG.1023.3.p2, not unique enough 653s -skipping training candidate: MSTRG.1023.2.p2, not unique enough 653s -skipping training candidate: NM_001166700.p1, not unique enough 653s -skipping training candidate: MSTRG.1074.8.p2, not unique enough 653s -skipping training candidate: NR_026594.p1, not unique enough 653s -skipping training candidate: NR_110830.p3, not unique enough 653s -skipping training candidate: NM_001080485.p2, not unique enough 653s -skipping training candidate: MSTRG.1025.5.p2, not unique enough 653s -skipping training candidate: NM_001166701.p1, not unique enough 653s -skipping training candidate: NM_138362.p1, not unique enough 653s -skipping training candidate: NM_001256119.p2, not unique enough 653s -skipping training candidate: NM_001256120.p2, not unique enough 653s -skipping training candidate: NM_005676.p3, not unique enough 653s -skipping training candidate: NM_001204466.p2, not unique enough 653s -skipping training candidate: NM_001204468.p3, not unique enough 653s -skipping training candidate: NM_152856.p2, not unique enough 653s -skipping training candidate: NM_021949.p2, not unique enough 653s -skipping training candidate: MSTRG.109.7.p1, not unique enough 653s -skipping training candidate: NM_001168401.p1, not unique enough 653s -skipping training candidate: NM_032621.p1, not unique enough 653s -skipping training candidate: NM_003918.p2, not unique enough 653s -skipping training candidate: MSTRG.913.3.p1, not unique enough 653s -skipping training candidate: NM_001129826_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.502.3.p2, not unique enough 653s -skipping training candidate: NM_001171162.p2, not unique enough 653s -skipping training candidate: NM_005096.p2, not unique enough 653s -skipping training candidate: MSTRG.502.2.p2, not unique enough 653s -skipping training candidate: MSTRG.502.1.p2, not unique enough 653s -skipping training candidate: MSTRG.9.3.p2, not unique enough 653s -skipping training candidate: MSTRG.654.2.p2, not unique enough 653s -skipping training candidate: MSTRG.654.1.p2, not unique enough 653s -skipping training candidate: MSTRG.654.3.p2, not unique enough 653s -skipping training candidate: MSTRG.794.2.p2, not unique enough 653s -skipping training candidate: NM_001109879.p2, not unique enough 653s -skipping training candidate: MSTRG.230.7.p2, not unique enough 653s -skipping training candidate: NM_001145140_dup1.p2, not unique enough 653s -skipping training candidate: NM_001145139_dup1.p2, not unique enough 653s -skipping training candidate: NM_001145139.p2, not unique enough 653s -skipping training candidate: NM_001303624.p2, not unique enough 653s -skipping training candidate: NM_001114937.p1, not unique enough 653s -skipping training candidate: NM_001291868.p2, not unique enough 653s -skipping training candidate: MSTRG.405.3.p2, not unique enough 653s -skipping training candidate: MSTRG.405.4.p2, not unique enough 653s -skipping training candidate: NM_001291867.p2, not unique enough 653s -skipping training candidate: NM_001136024.p2, not unique enough 653s -skipping training candidate: NM_000166.p2, not unique enough 653s -skipping training candidate: MSTRG.324.2.p2, not unique enough 653s -skipping training candidate: NM_001168302.p2, not unique enough 653s -skipping training candidate: MSTRG.311.2.p2, not unique enough 653s -skipping training candidate: MSTRG.921.5.p3, not unique enough 653s -skipping training candidate: MSTRG.921.6.p3, not unique enough 653s -skipping training candidate: NM_000425.p5, not unique enough 653s -skipping training candidate: NM_024003.p5, not unique enough 653s -skipping training candidate: NM_001143963.p5, not unique enough 653s -skipping training candidate: NM_019863.p2, not unique enough 653s -skipping training candidate: NM_001242310.p2, not unique enough 653s -skipping training candidate: MSTRG.363.1.p1, not unique enough 653s -skipping training candidate: NM_001037343.p2, not unique enough 653s -skipping training candidate: MSTRG.76.2.p3, not unique enough 653s -skipping training candidate: NM_001204811.p1, not unique enough 653s -skipping training candidate: MSTRG.992.5.p2, not unique enough 653s -skipping training candidate: MSTRG.992.3.p2, not unique enough 653s -skipping training candidate: MSTRG.602.3.p1, not unique enough 653s -skipping training candidate: NM_001146256.p2, not unique enough 653s -skipping training candidate: NM_001146257.p2, not unique enough 653s -skipping training candidate: MSTRG.208.3.p2, not unique enough 653s -skipping training candidate: NM_152787.p2, not unique enough 653s -skipping training candidate: MSTRG.208.2.p2, not unique enough 653s -skipping training candidate: NM_021048.p2, not unique enough 653s -skipping training candidate: NM_001011543.p2, not unique enough 653s -skipping training candidate: MSTRG.147.4.p2, not unique enough 653s -skipping training candidate: NM_001170931.p2, not unique enough 653s -skipping training candidate: MSTRG.1041.5.p1, not unique enough 653s -skipping training candidate: MSTRG.794.3.p2, not unique enough 653s -skipping training candidate: NM_001356.p3, not unique enough 653s -skipping training candidate: MSTRG.68.1.p2, not unique enough 653s -skipping training candidate: MSTRG.68.18.p3, not unique enough 653s -skipping training candidate: MSTRG.68.10.p4, not unique enough 653s -skipping training candidate: MSTRG.68.8.p3, not unique enough 653s -skipping training candidate: MSTRG.68.5.p2, not unique enough 653s -skipping training candidate: MSTRG.68.3.p2, not unique enough 653s -skipping training candidate: MSTRG.68.6.p2, not unique enough 653s -skipping training candidate: MSTRG.68.16.p3, not unique enough 653s -skipping training candidate: NR_034031.p2, not unique enough 653s -skipping training candidate: MSTRG.68.14.p3, not unique enough 653s -skipping training candidate: MSTRG.68.17.p2, not unique enough 653s -skipping training candidate: NR_027401.p1, not unique enough 653s -skipping training candidate: NM_001303513.p2, not unique enough 653s -skipping training candidate: MSTRG.258.9.p3, not unique enough 653s -skipping training candidate: NM_001037536.p2, not unique enough 653s -skipping training candidate: NM_001037540.p2, not unique enough 653s -skipping training candidate: NM_001037535.p2, not unique enough 653s -skipping training candidate: NM_006746.p2, not unique enough 653s -skipping training candidate: MSTRG.541.3.p2, not unique enough 653s -skipping training candidate: NM_005088.p3, not unique enough 653s -skipping training candidate: NM_001080485.p3, not unique enough 653s -skipping training candidate: NM_020922.p2, not unique enough 653s -skipping training candidate: MSTRG.604.2.p2, not unique enough 653s -skipping training candidate: MSTRG.311.3.p1, not unique enough 653s -skipping training candidate: NM_001080425.p1, not unique enough 653s -skipping training candidate: MSTRG.68.17.p3, not unique enough 653s -skipping training candidate: NR_130733.p1, not unique enough 653s -skipping training candidate: NM_001282535.p3, not unique enough 653s -skipping training candidate: NM_001282607.p2, not unique enough 653s -skipping training candidate: NR_026551.p2, not unique enough 653s -skipping training candidate: NM_013423.p2, not unique enough 653s -skipping training candidate: NM_001287242.p2, not unique enough 653s -skipping training candidate: NM_013427.p3, not unique enough 653s -skipping training candidate: NR_015353.p2, not unique enough 653s -skipping training candidate: MSTRG.438.2.p2, not unique enough 653s -skipping training candidate: NM_001282161.p2, not unique enough 653s -skipping training candidate: MSTRG.397.11.p3, not unique enough 653s -skipping training candidate: MSTRG.68.4.p2, not unique enough 653s -skipping training candidate: MSTRG.921.5.p4, not unique enough 653s -skipping training candidate: NM_001139466.p2, not unique enough 653s -skipping training candidate: NR_033714.p1, not unique enough 653s -skipping training candidate: MSTRG.4.3.p5, not unique enough 653s -skipping training candidate: NM_018390.p5, not unique enough 653s -skipping training candidate: NR_028057.p2, not unique enough 653s -skipping training candidate: MSTRG.109.9.p1, not unique enough 653s -skipping training candidate: NM_001257291.p2, not unique enough 653s -skipping training candidate: NM_001170703.p2, not unique enough 653s -skipping training candidate: MSTRG.889.4.p3, not unique enough 653s -skipping training candidate: MSTRG.889.3.p2, not unique enough 653s -skipping training candidate: MSTRG.889.2.p2, not unique enough 653s -skipping training candidate: NM_133486.p2, not unique enough 653s -skipping training candidate: NM_018388.p2, not unique enough 653s -skipping training candidate: NM_001170701.p2, not unique enough 653s -skipping training candidate: NM_001170702.p2, not unique enough 653s -skipping training candidate: MSTRG.889.1.p2, not unique enough 653s -skipping training candidate: NR_033835.p2, not unique enough 653s -skipping training candidate: NM_178151.p2, not unique enough 653s -skipping training candidate: MSTRG.4.3.p6, not unique enough 653s -skipping training candidate: NM_018390.p6, not unique enough 653s -skipping training candidate: NM_001171706.p1, not unique enough 653s -skipping training candidate: NR_104390.p2, not unique enough 653s -skipping training candidate: NR_104395.p3, not unique enough 653s -skipping training candidate: NR_104393.p2, not unique enough 653s -skipping training candidate: NR_104389.p2, not unique enough 653s -skipping training candidate: NR_104392.p3, not unique enough 653s -skipping training candidate: NR_104387.p2, not unique enough 653s -skipping training candidate: NR_104391.p3, not unique enough 653s -skipping training candidate: NR_104394.p3, not unique enough 653s -skipping training candidate: NR_104388.p2, not unique enough 653s -skipping training candidate: NM_178153.p2, not unique enough 653s -skipping training candidate: MSTRG.76.2.p4, not unique enough 653s -skipping training candidate: NM_000555.p2, not unique enough 653s -skipping training candidate: NM_001195553.p2, not unique enough 653s -skipping training candidate: MSTRG.992.2.p2, not unique enough 653s -skipping training candidate: NM_001168399.p2, not unique enough 653s -skipping training candidate: MSTRG.216.5.p4, not unique enough 653s -skipping training candidate: NM_001098791.p3, not unique enough 653s -skipping training candidate: NM_021242.p4, not unique enough 653s -skipping training candidate: NM_001098790.p3, not unique enough 653s -skipping training candidate: NM_001127199_dup3.p1, not unique enough 653s -skipping training candidate: NM_001127199_dup6.p1, not unique enough 653s -skipping training candidate: NM_001127199.p1, not unique enough 653s -skipping training candidate: NM_001127199_dup5.p1, not unique enough 653s -skipping training candidate: NM_001127199_dup2.p1, not unique enough 653s -skipping training candidate: NM_001127199_dup4.p1, not unique enough 653s -skipping training candidate: NM_001127199_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098407.p1, not unique enough 653s -skipping training candidate: NM_001476.p1, not unique enough 653s -skipping training candidate: NM_001476_dup1.p1, not unique enough 653s -skipping training candidate: NM_001476_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098418_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098418_dup3.p1, not unique enough 653s -skipping training candidate: NM_001098418_dup5.p1, not unique enough 653s -skipping training candidate: NM_001098418.p1, not unique enough 653s -skipping training candidate: NM_001098418_dup4.p1, not unique enough 653s -skipping training candidate: NM_001098418_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098409_dup3.p1, not unique enough 653s -skipping training candidate: NM_001098409_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098409.p1, not unique enough 653s -skipping training candidate: NM_001098409_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098409_dup4.p1, not unique enough 653s -skipping training candidate: NM_001098409_dup5.p1, not unique enough 653s -skipping training candidate: MSTRG.68.2.p2, not unique enough 653s -skipping training candidate: MSTRG.68.7.p2, not unique enough 653s -skipping training candidate: MSTRG.68.19.p1, not unique enough 653s -skipping training candidate: NM_001306144.p3, not unique enough 653s -skipping training candidate: NM_003828.p2, not unique enough 653s -skipping training candidate: MSTRG.921.6.p4, not unique enough 653s -skipping training candidate: NM_012196.p1, not unique enough 653s -skipping training candidate: NM_001474_dup1.p1, not unique enough 653s -skipping training candidate: NM_001474_dup2.p1, not unique enough 653s -skipping training candidate: NM_001474.p1, not unique enough 653s -skipping training candidate: NM_001271187.p1, not unique enough 653s -skipping training candidate: MSTRG.887.3.p1, not unique enough 653s -skipping training candidate: MSTRG.887.8.p2, not unique enough 653s -skipping training candidate: NM_001098406.p1, not unique enough 653s -skipping training candidate: NM_013453.p1, not unique enough 653s -skipping training candidate: NM_001006684.p1, not unique enough 653s -skipping training candidate: NM_021949.p3, not unique enough 653s -skipping training candidate: NM_001127345.p1, not unique enough 653s -skipping training candidate: NM_001127345_dup1.p1, not unique enough 653s -skipping training candidate: NM_001127345_dup2.p1, not unique enough 653s -skipping training candidate: NM_001477.p1, not unique enough 653s -skipping training candidate: NM_001477_dup1.p1, not unique enough 653s -skipping training candidate: NM_001477_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098408.p1, not unique enough 653s -skipping training candidate: NM_001098408_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098408_dup5.p1, not unique enough 653s -skipping training candidate: NM_001098408_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098408_dup3.p1, not unique enough 653s -skipping training candidate: NM_001098408_dup4.p1, not unique enough 653s -skipping training candidate: NM_001475_dup1.p1, not unique enough 653s -skipping training candidate: NM_001475_dup2.p1, not unique enough 653s -skipping training candidate: NM_001475.p1, not unique enough 653s -skipping training candidate: NM_021123_dup2.p1, not unique enough 653s -skipping training candidate: NM_021123_dup1.p1, not unique enough 653s -skipping training candidate: NM_021123.p1, not unique enough 653s -skipping training candidate: NM_001456.p2, not unique enough 653s -skipping training candidate: NM_001098410_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098410_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098410_dup3.p1, not unique enough 653s -skipping training candidate: NM_001098410.p1, not unique enough 653s -skipping training candidate: NM_001040663.p1, not unique enough 653s -skipping training candidate: NM_001127200.p1, not unique enough 653s -skipping training candidate: NM_145662_dup1.p1, not unique enough 653s -skipping training candidate: NM_145662.p1, not unique enough 653s -skipping training candidate: NM_080720_dup1.p1, not unique enough 653s -skipping training candidate: NM_001098412.p1, not unique enough 653s -skipping training candidate: NM_001017990.p1, not unique enough 653s -skipping training candidate: NM_001098405_dup2.p1, not unique enough 653s -skipping training candidate: NM_001098405.p1, not unique enough 653s -skipping training candidate: NM_001098405_dup5.p1, not unique enough 653s -skipping training candidate: NM_001098405_dup3.p1, not unique enough 653s -skipping training candidate: NM_001098405_dup4.p1, not unique enough 653s -skipping training candidate: NM_001098405_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.1055.2.p1, not unique enough 653s -skipping training candidate: MSTRG.275.3.p5, not unique enough 653s -skipping training candidate: NM_001170460.p3, not unique enough 653s -skipping training candidate: MSTRG.275.2.p3, not unique enough 653s -skipping training candidate: MSTRG.275.4.p5, not unique enough 653s -skipping training candidate: MSTRG.275.7.p3, not unique enough 653s -skipping training candidate: MSTRG.275.6.p3, not unique enough 653s -skipping training candidate: NM_006201.p4, not unique enough 653s -skipping training candidate: MSTRG.443.1.p2, not unique enough 653s -skipping training candidate: NM_001173480.p2, not unique enough 653s -skipping training candidate: MSTRG.443.3.p2, not unique enough 653s -skipping training candidate: MSTRG.443.2.p2, not unique enough 653s -skipping training candidate: NM_001173479.p2, not unique enough 653s -skipping training candidate: MSTRG.443.9.p2, not unique enough 653s -skipping training candidate: NM_015185.p2, not unique enough 653s -skipping training candidate: MSTRG.443.5.p3, not unique enough 653s -skipping training candidate: NM_001472.p1, not unique enough 653s -skipping training candidate: NM_001199687.p2, not unique enough 653s -skipping training candidate: MSTRG.459.4.p2, not unique enough 653s -skipping training candidate: MSTRG.459.2.p3, not unique enough 653s -skipping training candidate: NM_015075.p4, not unique enough 653s -skipping training candidate: NM_016542.p2, not unique enough 653s -skipping training candidate: NM_001127212.p1, not unique enough 653s -skipping training candidate: NR_037859.p3, not unique enough 653s -skipping training candidate: NM_145799.p2, not unique enough 653s -skipping training candidate: MSTRG.1005.2.p4, not unique enough 653s -skipping training candidate: NM_001128166.p2, not unique enough 653s -skipping training candidate: NM_001129896.p2, not unique enough 653s -skipping training candidate: MSTRG.68.5.p3, not unique enough 653s -skipping training candidate: MSTRG.68.3.p3, not unique enough 653s -skipping training candidate: MSTRG.68.7.p3, not unique enough 653s -skipping training candidate: MSTRG.68.17.p4, not unique enough 653s -skipping training candidate: MSTRG.718.3.p1, not unique enough 653s -skipping training candidate: NM_001170780.p1, not unique enough 653s -skipping training candidate: NM_001178106.p2, not unique enough 653s -skipping training candidate: NM_016542.p3, not unique enough 653s -skipping training candidate: NM_001174068.p2, not unique enough 653s -skipping training candidate: NM_001017991_dup2.p1, not unique enough 653s -skipping training candidate: NM_001017991_dup1.p1, not unique enough 653s -skipping training candidate: NM_001017991.p1, not unique enough 653s -skipping training candidate: NM_001097605.p1, not unique enough 653s -skipping training candidate: NM_001304990.p3, not unique enough 653s -skipping training candidate: NM_181762.p2, not unique enough 653s -skipping training candidate: NM_003336.p2, not unique enough 653s -skipping training candidate: NM_001080485.p4, not unique enough 653s -skipping training candidate: NM_001184875.p3, not unique enough 653s -skipping training candidate: NM_138437.p3, not unique enough 653s -skipping training candidate: NM_001199818.p3, not unique enough 653s -skipping training candidate: NM_001004051.p3, not unique enough 653s -skipping training candidate: NM_001184874.p3, not unique enough 653s -skipping training candidate: NM_004135.p2, not unique enough 653s -skipping training candidate: NM_001830.p2, not unique enough 653s -skipping training candidate: NM_001103151.p2, not unique enough 653s -skipping training candidate: NM_001282875.p2, not unique enough 653s -skipping training candidate: NM_001282874.p2, not unique enough 653s -skipping training candidate: NM_001166703.p1, not unique enough 653s -skipping training candidate: NM_001204402.p1, not unique enough 653s -skipping training candidate: NM_001081550.p2, not unique enough 653s -skipping training candidate: MSTRG.839.4.p2, not unique enough 653s -skipping training candidate: MSTRG.839.5.p2, not unique enough 653s -skipping training candidate: MSTRG.839.3.p2, not unique enough 653s -skipping training candidate: NM_001142386.p2, not unique enough 653s -skipping training candidate: MSTRG.456.6.p2, not unique enough 653s -skipping training candidate: NM_014799.p2, not unique enough 653s -skipping training candidate: NM_001282141.p2, not unique enough 653s -skipping training candidate: NM_138737.p2, not unique enough 653s -skipping training candidate: MSTRG.456.2.p2, not unique enough 653s -skipping training candidate: NM_001449.p2, not unique enough 653s -skipping training candidate: NM_001159703.p2, not unique enough 653s -skipping training candidate: NM_001103150.p2, not unique enough 653s -skipping training candidate: NM_001097596_dup1.p1, not unique enough 653s -skipping training candidate: NM_001097596.p1, not unique enough 653s -skipping training candidate: MSTRG.1041.8.p2, not unique enough 653s -skipping training candidate: MSTRG.906.2.p1, not unique enough 653s -skipping training candidate: MSTRG.933.1.p3, not unique enough 653s -skipping training candidate: MSTRG.992.1.p3, not unique enough 653s -skipping training candidate: NM_052926.p2, not unique enough 653s -skipping training candidate: NM_013364.p3, not unique enough 653s -skipping training candidate: NM_031892.p2, not unique enough 653s -skipping training candidate: MSTRG.151.5.p2, not unique enough 653s -skipping training candidate: NM_006521.p3, not unique enough 653s -skipping training candidate: NM_182680.p2, not unique enough 653s -skipping training candidate: NM_001142.p2, not unique enough 653s -skipping training candidate: NM_001017931.p1, not unique enough 653s -skipping training candidate: NM_001199974.p2, not unique enough 653s -skipping training candidate: NR_033349.p2, not unique enough 653s -skipping training candidate: NM_001171252.p1, not unique enough 653s -skipping training candidate: NM_001078173.p1, not unique enough 653s -skipping training candidate: MSTRG.438.4.p1, not unique enough 653s -skipping training candidate: NM_001304990.p4, not unique enough 653s -skipping training candidate: NR_034116_dup1.p1, not unique enough 653s -skipping training candidate: NM_002414.p2, not unique enough 653s -skipping training candidate: NM_001277710.p2, not unique enough 653s -skipping training candidate: NM_001654.p3, not unique enough 653s -skipping training candidate: NM_001256196.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.9.p1, not unique enough 653s -skipping training candidate: NM_001141920.p2, not unique enough 653s -skipping training candidate: NM_198511.p3, not unique enough 653s -skipping training candidate: NM_021806.p2, not unique enough 653s -skipping training candidate: NM_001282311.p2, not unique enough 653s -skipping training candidate: MSTRG.1037.1.p2, not unique enough 653s -skipping training candidate: NM_001171134.p2, not unique enough 653s -skipping training candidate: NR_120493.p1, not unique enough 653s -skipping training candidate: NR_120493_dup1.p1, not unique enough 653s -skipping training candidate: NM_002893.p3, not unique enough 653s -skipping training candidate: MSTRG.376.9.p2, not unique enough 653s -skipping training candidate: MSTRG.376.4.p3, not unique enough 653s -skipping training candidate: NM_004187.p2, not unique enough 653s -skipping training candidate: NM_001282622.p2, not unique enough 653s -skipping training candidate: MSTRG.376.2.p3, not unique enough 653s -skipping training candidate: MSTRG.376.8.p3, not unique enough 653s -skipping training candidate: MSTRG.376.1.p2, not unique enough 653s -skipping training candidate: NM_001146702.p2, not unique enough 653s -skipping training candidate: NM_014380.p1, not unique enough 653s -skipping training candidate: MSTRG.799.2.p2, not unique enough 653s -skipping training candidate: NM_001282161.p3, not unique enough 653s -skipping training candidate: NM_022117.p3, not unique enough 653s -skipping training candidate: NM_134445.p2, not unique enough 653s -skipping training candidate: NM_134446.p2, not unique enough 653s -skipping training candidate: NM_001242614.p2, not unique enough 653s -skipping training candidate: NM_001184808.p2, not unique enough 653s -skipping training candidate: NM_001291868.p3, not unique enough 653s -skipping training candidate: NM_001025242.p3, not unique enough 653s -skipping training candidate: NM_001025243.p3, not unique enough 653s -skipping training candidate: NR_033348.p3, not unique enough 653s -skipping training candidate: NM_024087.p2, not unique enough 653s -skipping training candidate: NM_001168530.p2, not unique enough 653s -skipping training candidate: NM_001159560.p1, not unique enough 653s -skipping training candidate: MSTRG.702.2.p3, not unique enough 653s -skipping training candidate: NM_001195578.p1, not unique enough 653s -skipping training candidate: NM_001195576.p1, not unique enough 653s -skipping training candidate: NM_175569.p2, not unique enough 653s -skipping training candidate: NM_000044.p2, not unique enough 653s -skipping training candidate: NM_001291867.p3, not unique 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MSTRG.763.3.p2, not unique enough 653s -skipping training candidate: MSTRG.397.6.p3, not unique enough 653s -skipping training candidate: MSTRG.397.7.p3, not unique enough 653s -skipping training candidate: MSTRG.397.5.p3, not unique enough 653s -skipping training candidate: MSTRG.397.2.p3, not unique enough 653s -skipping training candidate: MSTRG.397.8.p3, not unique enough 653s -skipping training candidate: MSTRG.397.4.p3, not unique enough 653s -skipping training candidate: MSTRG.397.3.p3, not unique enough 653s -skipping training candidate: NM_001129828.p1, not unique enough 653s -skipping training candidate: NM_001129828_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.68.19.p2, not unique enough 653s -skipping training candidate: NM_000425.p6, not unique enough 653s -skipping training candidate: NM_024003.p6, not unique enough 653s -skipping training candidate: NM_001143963.p6, not unique enough 653s -skipping training candidate: NM_001244892_dup1.p1, not unique enough 653s -skipping training candidate: NR_037927.p1, not unique enough 653s -skipping training candidate: NM_001144064_dup1.p1, not unique enough 653s -skipping training candidate: NM_001144064.p1, not unique enough 653s -skipping training candidate: NM_001145414.p1, not unique enough 653s -skipping training candidate: MSTRG.36.2.p1, not unique enough 653s -skipping training candidate: MSTRG.36.1.p1, not unique enough 653s -skipping training candidate: MSTRG.1041.5.p2, not unique enough 653s -skipping training candidate: NM_001134321.p1, not unique enough 653s -skipping training candidate: NM_033380.p4, not unique enough 653s -skipping training candidate: MSTRG.992.4.p2, not unique enough 653s -skipping training candidate: NM_001184875.p4, not unique enough 653s -skipping training candidate: NM_138437.p4, not unique enough 653s -skipping training candidate: NM_001004051.p4, not unique enough 653s -skipping training candidate: NM_001184874.p4, not unique enough 653s -skipping 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NM_001042480.p3, not unique enough 653s -skipping training candidate: NM_001042479.p2, not unique enough 653s -skipping training candidate: MSTRG.108.1.p2, not unique enough 653s -skipping training candidate: NM_017856.p2, not unique enough 653s -skipping training candidate: NM_001448.p4, not unique enough 653s -skipping training candidate: NM_001145139_dup1.p3, not unique enough 653s -skipping training candidate: NM_001145139.p3, not unique enough 653s -skipping training candidate: NM_001018024.p1, not unique enough 653s -skipping training candidate: NR_033772_dup1.p3, not unique enough 653s -skipping training candidate: NR_120499.p1, not unique enough 653s -skipping training candidate: NR_120499_dup1.p1, not unique enough 653s -skipping training candidate: MSTRG.364.2.p2, not unique enough 653s -skipping training candidate: MSTRG.364.3.p2, not unique enough 653s -skipping training candidate: NM_001171095.p2, not unique enough 653s -skipping training candidate: MSTRG.369.2.p2, not 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-skipping training candidate: MSTRG.992.5.p3, not unique enough 653s -skipping training candidate: MSTRG.331.3.p2, not unique enough 653s -skipping training candidate: MSTRG.331.1.p2, not unique enough 653s -skipping training candidate: MSTRG.331.2.p2, not unique enough 653s -skipping training candidate: MSTRG.331.4.p2, not unique enough 653s -skipping training candidate: NM_001104544.p2, not unique enough 653s -skipping training candidate: MSTRG.822.4.p2, not unique enough 653s -skipping training candidate: NM_001104545.p2, not unique enough 653s -skipping training candidate: NR_033181.p2, not unique enough 653s -skipping training candidate: NM_001128167.p3, not unique enough 653s -skipping training candidate: MSTRG.16.1.p9, not unique enough 653s -skipping training candidate: NM_001184830.p2, not unique enough 653s -skipping training candidate: MSTRG.945.1.p2, not unique enough 653s -skipping training candidate: MSTRG.887.7.p1, not unique enough 653s -skipping training candidate: NM_005676.p4, not unique enough 653s -skipping training candidate: NM_001204466.p3, not unique enough 653s -skipping training candidate: NM_001204468.p4, not unique enough 653s -skipping training candidate: NM_152856.p3, not unique enough 653s -skipping training candidate: MSTRG.973.1.p3, not unique enough 653s -skipping training candidate: NM_001171909.p2, not unique enough 653s -skipping training candidate: MSTRG.963.2.p3, not unique enough 653s -skipping training candidate: MSTRG.963.2.p4, not unique enough 653s -skipping training candidate: MSTRG.963.3.p3, not unique enough 653s -skipping training candidate: MSTRG.963.1.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.10.p2, not unique enough 653s -skipping training candidate: MSTRG.1074.1.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.2.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.5.p2, not unique enough 653s -skipping training candidate: MSTRG.1074.3.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.8.p3, not unique enough 653s -skipping training candidate: NM_198511.p4, not unique enough 653s -skipping training candidate: NM_004595.p2, not unique enough 653s -skipping training candidate: NM_001199972.p1, not unique enough 653s -skipping training candidate: NR_024499.p1, not unique enough 653s -skipping training candidate: MSTRG.74.2.p1, not unique enough 653s -skipping training candidate: MSTRG.108.1.p3, not unique enough 653s -skipping training candidate: MSTRG.862.1.p3, not unique enough 653s -skipping training candidate: NM_001127197.p2, not unique enough 653s -skipping training candidate: MSTRG.862.3.p2, not unique enough 653s -skipping training candidate: NM_001421.p2, not unique enough 653s -skipping training candidate: MSTRG.862.4.p2, not unique enough 653s -skipping training candidate: MSTRG.68.12.p2, not unique enough 653s -skipping training candidate: MSTRG.68.9.p2, not unique enough 653s -skipping training candidate: MSTRG.68.13.p2, not unique enough 653s -skipping training candidate: MSTRG.68.8.p4, not unique enough 653s -skipping training candidate: MSTRG.68.3.p4, not unique enough 653s -skipping training candidate: MSTRG.68.6.p3, not unique enough 653s -skipping training candidate: MSTRG.68.16.p5, not unique enough 653s -skipping training candidate: NR_034031.p4, not unique enough 653s -skipping training candidate: MSTRG.68.14.p4, not unique enough 653s -skipping training candidate: MSTRG.68.17.p5, not unique enough 653s -skipping training candidate: NM_001256789.p3, not unique enough 653s -skipping training candidate: MSTRG.860.1.p2, not unique enough 653s -skipping training candidate: NM_001184772.p2, not unique enough 653s -skipping training candidate: MSTRG.860.3.p2, not unique enough 653s -skipping training candidate: MSTRG.860.6.p2, not unique enough 653s -skipping training candidate: MSTRG.860.2.p2, not unique enough 653s -skipping training candidate: NM_021949.p4, not unique enough 653s -skipping training candidate: NM_001143983.p3, not unique enough 653s -skipping training candidate: NM_153280.p2, not unique enough 653s -skipping training candidate: NM_001586.p2, not unique enough 653s -skipping training candidate: NM_005183.p3, not unique enough 653s -skipping training candidate: NM_032591.p3, not unique enough 653s -skipping training candidate: MSTRG.268.7.p3, not unique enough 653s -skipping training candidate: NM_001257291.p3, not unique enough 653s -skipping training candidate: MSTRG.268.2.p2, not unique enough 653s -skipping training candidate: MSTRG.268.1.p2, not unique enough 653s -skipping training candidate: MSTRG.268.3.p3, not unique enough 653s -skipping training candidate: MSTRG.268.6.p2, not unique enough 653s -skipping training candidate: NM_001143981.p3, not unique enough 653s -skipping training candidate: MSTRG.876.1.p3, not unique enough 653s -skipping training candidate: NM_203474.p2, not unique enough 653s -skipping training candidate: NM_022825.p2, not unique enough 653s -skipping training candidate: MSTRG.305.8.p3, not unique enough 653s -skipping training candidate: MSTRG.305.6.p3, not unique enough 653s -skipping training candidate: NM_203475.p2, not unique enough 653s -skipping training candidate: NM_203473.p2, not unique enough 653s -skipping training candidate: MSTRG.305.7.p3, not unique enough 653s -skipping training candidate: NM_001282167.p3, not unique enough 653s -skipping training candidate: MSTRG.2.1.p2, not unique enough 653s -skipping training candidate: NM_007213.p3, not unique enough 653s -skipping training candidate: MSTRG.68.10.p5, not unique enough 653s -skipping training candidate: MSTRG.68.5.p4, not unique enough 653s -skipping training candidate: MSTRG.468.4.p2, not unique enough 653s -skipping training candidate: NM_032926.p3, not unique enough 653s -skipping training candidate: NM_016303.p1, not unique enough 653s -skipping training candidate: NM_001006612.p1, not unique enough 653s -skipping training candidate: NM_001006614.p1, not unique enough 653s -skipping training candidate: NM_153280.p3, not unique enough 653s -skipping training candidate: NM_000533.p2, not unique enough 653s -skipping training candidate: NM_001145140_dup1.p4, not unique enough 653s -skipping training candidate: NM_001171184.p2, not unique enough 653s -skipping training candidate: NM_014927.p3, not unique enough 653s -skipping training candidate: NM_001168647.p3, not unique enough 653s -skipping training candidate: NM_024597.p2, not unique enough 653s -skipping training candidate: MSTRG.17.6.p4, not unique enough 653s -skipping training candidate: NM_001145139_dup1.p4, not unique enough 653s -skipping training candidate: NM_001145139.p4, not unique enough 653s -skipping training candidate: NM_199478.p2, not unique enough 653s -skipping training candidate: MSTRG.889.17.p2, not unique enough 653s -skipping training candidate: NM_033215.p3, not unique enough 653s -skipping training candidate: MSTRG.549.7.p2, not unique enough 653s -skipping training candidate: NM_017848.p3, not unique enough 653s -skipping training candidate: NM_001300788.p4, not unique enough 653s -skipping training candidate: NM_134445.p3, not unique enough 653s -skipping training candidate: NM_134446.p3, not unique enough 653s -skipping training candidate: NM_001242614.p3, not unique enough 653s -skipping training candidate: NM_001184808.p3, not unique enough 653s -skipping training candidate: NR_029427.p4, not unique enough 653s -skipping training candidate: MSTRG.325.4.p3, not unique enough 653s -skipping training candidate: NM_001166426.p4, not unique enough 653s -skipping training candidate: NM_017883.p4, not unique enough 653s -skipping training candidate: MSTRG.301.3.p2, not unique enough 653s -skipping training candidate: MSTRG.301.2.p3, not unique enough 653s -skipping training candidate: MSTRG.1074.11.p2, not unique enough 653s -skipping training candidate: MSTRG.1074.9.p2, not unique enough 653s -skipping training candidate: MSTRG.1074.10.p3, not unique enough 653s -skipping training candidate: NM_014799.p3, not unique enough 653s -skipping training candidate: NM_138737.p3, not unique enough 653s -skipping training candidate: MSTRG.456.2.p3, not unique enough 653s -skipping training candidate: NM_001040663.p2, not unique enough 653s -skipping training candidate: MSTRG.862.1.p4, not unique enough 653s -skipping training candidate: NM_001127197.p3, not unique enough 653s -skipping training candidate: MSTRG.862.3.p3, not unique enough 653s -skipping training candidate: NM_001421.p3, not unique enough 653s -skipping training candidate: MSTRG.862.4.p3, not unique enough 653s -skipping training candidate: NM_206917.p2, not unique enough 653s -skipping training candidate: NM_001282157.p2, not unique enough 653s -skipping training candidate: NM_012280.p2, not unique enough 653s -skipping training candidate: NM_006013.p2, not unique enough 653s -skipping training candidate: MSTRG.1025.5.p3, not unique enough 653s -skipping training candidate: NM_001256577.p2, not unique enough 653s -skipping training candidate: NM_001303625.p2, not unique enough 653s -skipping training candidate: NM_001303624.p3, not unique enough 653s -skipping training candidate: NM_001256580.p2, not unique enough 653s -skipping training candidate: MSTRG.1025.1.p2, not unique enough 653s -skipping training candidate: NM_152634.p2, not unique enough 653s -skipping training candidate: NM_001297563.p2, not unique enough 653s -skipping training candidate: NM_000513.p2, not unique enough 653s -skipping training candidate: NM_000513_dup2.p2, not unique enough 653s -skipping training candidate: NM_001300788.p5, not unique enough 653s -skipping training candidate: NM_004651.p3, not unique enough 653s -skipping training candidate: MSTRG.597.1.p2, not unique enough 653s -skipping training candidate: MSTRG.597.3.p2, not unique enough 653s -skipping training candidate: NM_001017931.p2, not unique enough 653s -skipping training candidate: NM_001128835.p2, not unique enough 653s -skipping training candidate: NM_000451.p2, not unique enough 653s -skipping training candidate: NM_001114123.p3, not unique enough 653s -skipping training candidate: MSTRG.907.2.p1, not unique enough 653s -skipping training candidate: NM_000402.p3, not unique enough 653s -skipping training candidate: NM_001042351.p2, not unique enough 653s -skipping training candidate: NM_032539.p2, not unique enough 653s -skipping training candidate: NM_006013.p3, not unique enough 653s -skipping training candidate: MSTRG.1025.5.p4, not unique enough 653s -skipping training candidate: NM_001256577.p3, not unique enough 653s -skipping training candidate: NM_001303625.p3, not unique enough 653s -skipping training candidate: NM_001303624.p4, not unique enough 653s -skipping training candidate: NM_001256580.p3, not unique enough 653s -skipping training candidate: MSTRG.1025.1.p3, not unique enough 653s -skipping training candidate: NM_033290.p2, not unique enough 653s -skipping training candidate: MSTRG.1042.3.p2, not unique enough 653s -skipping training candidate: MSTRG.1042.1.p3, not unique enough 653s -skipping training candidate: NM_002637.p2, not unique enough 653s -skipping training candidate: NM_001172436.p2, not unique enough 653s -skipping training candidate: MSTRG.306.3.p2, not unique enough 653s -skipping training candidate: NM_001098624.p2, not unique enough 653s -skipping training candidate: MSTRG.128.4.p2, not unique enough 653s -skipping training candidate: MSTRG.1074.5.p3, not unique enough 653s -skipping training candidate: NM_033289.p2, not unique enough 653s -skipping training candidate: NM_001145255.p3, not unique enough 653s -skipping training candidate: MSTRG.1041.6.p4, not unique enough 653s -skipping training candidate: NM_003639.p2, not unique enough 653s -skipping training candidate: NM_001099857.p3, not unique enough 653s -skipping training candidate: MSTRG.1041.7.p3, not unique enough 653s -skipping training candidate: MSTRG.1041.9.p2, not unique enough 653s -skipping training candidate: NM_001099856.p2, not unique enough 653s -skipping training candidate: NM_001303465.p3, not unique enough 653s -skipping training candidate: MSTRG.1029.3.p4, not unique enough 653s -skipping training candidate: NM_001193277.p2, not unique enough 653s -skipping training candidate: NM_147175.p2, not unique enough 653s -skipping training candidate: NM_198450.p2, not unique enough 653s -skipping training candidate: MSTRG.108.1.p4, not unique enough 653s -skipping training candidate: NM_001184835.p2, not unique enough 653s -skipping training candidate: NM_001079859.p2, not unique enough 653s -skipping training candidate: NM_032498.p2, not unique enough 653s -skipping training candidate: NM_001830.p3, not unique enough 653s -skipping training candidate: MSTRG.961.7.p4, not unique enough 653s -skipping training candidate: NM_000202.p2, not unique enough 653s -skipping training candidate: MSTRG.961.3.p2, not unique enough 653s -skipping training candidate: MSTRG.961.4.p4, not unique enough 653s -skipping training candidate: NM_001166550.p2, not unique enough 653s -skipping training candidate: MSTRG.961.1.p3, not unique enough 653s -skipping training candidate: NM_001163278.p2, not unique enough 653s -skipping training candidate: NR_109985.p1, not unique enough 653s -skipping training candidate: NM_001079860.p2, not unique enough 653s -skipping training candidate: NM_007137.p2, not unique enough 653s -skipping training candidate: MSTRG.292.4.p2, not unique enough 653s -skipping training candidate: NM_014253.p2, not unique enough 653s -skipping training candidate: MSTRG.109.9.p2, not unique enough 653s -skipping training candidate: NM_001001994.p2, not unique enough 653s -skipping training candidate: NM_005278.p2, not unique enough 653s -skipping training candidate: NR_027401.p2, not unique enough 653s -skipping training candidate: MSTRG.841.1.p3, not unique enough 653s -skipping training candidate: NM_001079858.p2, not unique enough 653s -skipping training candidate: NM_001184834.p2, not unique enough 653s -skipping training candidate: NM_001449.p3, not unique enough 653s -skipping training candidate: NM_001159703.p3, not unique enough 653s -skipping training candidate: NM_005756.p2, not unique enough 653s -skipping training candidate: NM_001099685.p2, not unique enough 653s -skipping training candidate: NM_001099685_dup1.p2, not unique enough 653s -skipping training candidate: NM_001141920.p3, not unique enough 653s -skipping training candidate: NM_001142529.p2, not unique enough 653s -skipping training candidate: NM_030639.p2, not unique enough 653s -skipping training candidate: NM_001142528.p2, not unique enough 653s -skipping training candidate: NM_001142530.p2, not unique enough 653s -skipping training candidate: NM_001142526.p2, not unique enough 653s -skipping training candidate: NM_001142527.p2, not unique enough 653s -skipping training candidate: NM_001142524.p2, not unique enough 653s -skipping training candidate: NM_001184836.p2, not unique enough 653s -skipping training candidate: NM_175569.p3, not unique enough 653s -skipping training candidate: NR_026594.p2, not unique enough 653s -skipping training candidate: NM_001184837.p2, not unique enough 653s -skipping training candidate: NM_177537_dup1.p4, not unique enough 653s -skipping training candidate: NR_103770.p1, not unique enough 653s -skipping training candidate: MSTRG.945.3.p2, not unique enough 653s 653s -redundancy-minimized set includes 1645 / 4259 = 38.62% 653s 654s * [Mon Mar 18 02:20:23 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 654s PCT_GC: 46 654s * [Mon Mar 18 02:20:23 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores 657s * [Mon Mar 18 02:20:26 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 692s * [Mon Mar 18 02:21:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 692s Selecting best orfs 692s * [Mon Mar 18 02:21:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement 692s Training start codon pattern recognition* [Mon Mar 18 02:21:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 694s * [Mon Mar 18 02:21:03 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 694s -round: 1 699s -round: 2 704s -round: 3 710s -round: 4 715s -round: 5 721s * [Mon Mar 18 02:21:30 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 721s -parsing scores 728s * [Mon Mar 18 02:21:36 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 728s Error in library(ggplot2) : there is no package called ‘ggplot2’ 728s Execution halted 728s * [Mon Mar 18 02:21:37 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 728s Error in library(ggplot2) : there is no package called ‘ggplot2’ 728s Execution halted 728s * [Mon Mar 18 02:21:37 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 728s Error in library(seqLogo) : there is no package called ‘seqLogo’ 728s Execution halted 728s * [Mon Mar 18 02:21:37 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 729s Error in library(seqLogo) : there is no package called ‘seqLogo’ 729s Execution halted 729s * [Mon Mar 18 02:21:37 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced 729s num features: 336 num_incorporate: 100 729s -feature swap of score: 3.78911079353454 instead of -4.15762669956 729s -feature swap of score: 4.3075564869904 instead of -3.54241712691985 729s -feature swap of score: -1.55002091334646 instead of -2.55010664779592 729s -feature swap of score: 4.83949655109525 instead of -2.24867860418506 729s -feature swap of score: 0.392270533069581 instead of -2.32345623662297 729s -feature swap of score: 3.78855323991787 instead of -2.2988029392048 729s -feature swap of score: 3.99836372804798 instead of -2.19588732342881 729s -feature swap of score: 3.64835524788969 instead of -2.09663793619562 729s -feature swap of score: 4.88229074177495 instead of -2.0071137297779 729s -feature swap of score: -1.8083423728436 instead of -1.93321879934806 729s -feature swap of score: 3.92879192464595 instead of -1.772614249871 729s -feature swap of score: -0.465948676008031 instead of -2.00439257184315 729s -feature swap of score: 0.0546515421473758 instead of -1.60684025496409 729s -feature swap of score: 0.803622088306608 instead of -1.17227320164039 729s -feature swap of score: 4.45581598878225 instead of -1.27696269799764 729s -feature swap of score: 2.07236230159122 instead of -1.40605769767333 729s -feature swap of score: 4.02245547784082 instead of -1.5805710473436 729s -feature swap of score: 0.586330906031762 instead of -0.825175240434032 729s -feature swap of score: 3.96397529913446 instead of -0.871836639747919 729s -feature swap of score: 1.28205341901886 instead of -0.854499557546068 729s -feature swap of score: 2.51752465071796 instead of -0.880497045171406 729s -feature swap of score: 7.60013808606777 instead of -0.651902109016902 729s -feature swap of score: 5.56752159508171 instead of -0.585113517527429 729s -feature swap of score: 4.16682533874051 instead of -0.591263924699593 729s -feature swap of score: 5.98692288702727 instead of -0.550933752346117 729s -feature swap of score: 2.78461992524222 instead of -0.361642943889318 729s -feature swap of score: -0.14086687166401 instead of -0.260141330736644 729s -feature swap of score: 1.30640970749369 instead of -0.208633020456475 729s -feature swap of score: 0.305536787416525 instead of 0.0104847431676378 729s -feature swap of score: 3.55759636533095 instead of -0.120486034233916 729s -feature swap of score: 2.46987628753496 instead of -0.103803542507822 729s -feature swap of score: 2.0546736913397 instead of 0.0935269368540257 729s -feature swap of score: 1.31912484703918 instead of 0.229231280733345 729s -feature swap of score: 1.89359151880524 instead of 0.232351263114116 729s -feature swap of score: 5.43521751645765 instead of 0.195794099551117 729s -feature swap of score: 4.33834387795496 instead of -0.054616396540288 729s -feature swap of score: 6.43704991515938 instead of 0.111124242596921 729s -feature swap of score: 4.25846830983975 instead of 0.127430589246059 729s -feature swap of score: 0.771786455336691 instead of 0.285671737045457 729s -feature swap of score: 6.60911073864081 instead of 0.0418054250163035 729s -feature swap of score: 6.79809024958936 instead of 0.555671326116825 729s -feature swap of score: 7.27612094216219 instead of 0.559863976992066 729s -feature swap of score: 3.36215544495879 instead of 0.702288739001579 729s -feature swap of score: 4.38866473472805 instead of 0.440911348584446 729s -feature swap of score: 0.836843797008186 instead of 0.157766373683364 729s -feature swap of score: 2.13420236534183 instead of 0.949736946003556 729s -feature swap of score: 1.64354527137561 instead of 0.773162924133292 729s -feature swap of score: 2.38988424268632 instead of 0.941592652583747 729s -feature swap of score: 4.91107243910547 instead of 1.09251723189791 729s -feature swap of score: 2.49264242586391 instead of 0.856412735226522 729s -feature swap of score: 6.28552706210459 instead of 1.07932791455603 729s -feature swap of score: 4.67930772689507 instead of 1.27353927782704 729s -feature swap of score: 7.50973191408739 instead of 1.12100700928058 729s -feature swap of score: 5.55751937051127 instead of 1.21030026759988 729s -feature swap of score: 2.60074697345087 instead of 1.47109964978436 729s -feature swap of score: 3.74655896712747 instead of 1.48225927554747 729s -feature swap of score: 3.99301668862372 instead of 1.24561259795263 729s -feature swap of score: 1.72372236527001 instead of 1.02241527158741 729s -feature swap of score: 6.86300883201794 instead of 1.14563582053961 729s -feature swap of score: 5.54190533772704 instead of 1.28297492173032 729s -feature swap of score: 2.51308026289154 instead of 1.4180584754329 729s -feature swap of score: 3.38846514773249 instead of 1.2857641622143 729s -feature swap of score: 2.49385651598659 instead of 1.55130322997112 729s -feature swap of score: 2.65351701617127 instead of 1.23066210648887 729s -feature swap of score: 2.60425530523188 instead of 1.47665351441682 729s -feature swap of score: 7.60582369996651 instead of 1.55381032974607 729s -feature swap of score: 2.9807664000693 instead of 1.59725854839862 729s -feature swap of score: 4.52648695626297 instead of 1.66034729751211 729s -feature swap of score: 7.21055045635181 instead of 1.7858663752496 729s -feature swap of score: 4.25795336260412 instead of 1.84036163713462 729s -feature swap of score: 9.54168129081765 instead of 1.91931805946798 729s -feature swap of score: 8.89437210131165 instead of 1.47973460790513 729s -feature swap of score: 3.3622755750855 instead of 1.94740840499986 729s -feature swap of score: 6.78489489553093 instead of 1.90264556019824 729s -feature swap of score: 9.60405031469725 instead of 2.1040236037399 729s -feature swap of score: 5.57780850222194 instead of 1.85621488376428 729s -feature swap of score: 3.43303080359017 instead of 0.865435946387495 729s -feature swap of score: 2.67597182314123 instead of 1.80627212503354 729s -feature swap of score: 6.43244682385697 instead of 1.78041450678908 729s -feature swap of score: 3.95962793695356 instead of 1.84794334938432 729s -feature swap of score: 3.98432173082736 instead of 1.875580806845 729s -feature swap of score: 3.21236503540814 instead of 2.21808523494257 729s -feature swap of score: 7.03718379305501 instead of 2.08706655299514 729s -feature swap of score: 5.90582904633149 instead of 1.87026115503397 729s -feature swap of score: 5.79478155363706 instead of 1.80883534807753 729s -feature swap of score: 5.36619160368881 instead of 1.98766010735596 729s -feature swap of score: 6.07858328906771 instead of 2.06576129141207 729s -feature swap of score: 5.86937251981998 instead of 1.90511689506347 729s -feature swap of score: 3.38462816070108 instead of 2.13933881189727 729s -feature swap of score: 6.37449231938971 instead of 2.82058094033957 729s -feature swap of score: 6.72646305674668 instead of 2.83352026076865 729s -feature swap of score: 4.82560543584288 instead of 2.70443214397618 729s -feature swap of score: 4.42177781286965 instead of 2.8151180947157 729s -feature swap of score: 8.98279247275997 instead of 2.94679407717209 729s -feature swap of score: 4.60893969392588 instead of 2.9477877072234 729s -feature swap of score: 7.85133157245333 instead of 1.91369736378323 729s -feature swap of score: 5.99853031964839 instead of 2.93641177087966 729s -feature swap of score: 4.29682354807149 instead of 3.14449015818142 729s -feature swap of score: 3.52291944162443 instead of 3.13111126617467 729s -feature swap of score: 4.76551376672987 instead of 3.16811466075655 729s -num feature swaps: 100 729s * [Mon Mar 18 02:21:38 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 729s -round: 1 734s -round: 2 739s -round: 3 744s -round: 4 749s -round: 5 754s * [Mon Mar 18 02:22:03 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 754s -parsing scores 760s * [Mon Mar 18 02:22:09 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 760s Error in library(ggplot2) : there is no package called ‘ggplot2’ 760s Execution halted 760s * [Mon Mar 18 02:22:09 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 760s Error in library(ggplot2) : there is no package called ‘ggplot2’ 760s Execution halted 760s * [Mon Mar 18 02:22:09 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 761s Error in library(seqLogo) : there is no package called ‘seqLogo’ 761s Execution halted 761s * [Mon Mar 18 02:22:10 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 762s Refining start codon selections. 762s -number of revised start positions: 247 762s * [Mon Mar 18 02:22:11 2024] Running CMD: cp /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 762s copying output to final output file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Mon Mar 18 02:22:11 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 762s Making bed file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 762s * [Mon Mar 18 02:22:11 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 763s Making pep file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 764s * [Mon Mar 18 02:22:13 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 765s Making cds file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 766s transdecoder is finished. See output files /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* 766s 766s 766s 766s 766s ## convert to genome coordinates 766s ../../util/cdna_alignment_orf_to_genome_orf.pl stringtie_merged.transcripts.fasta.transdecoder.gff3 stringtie_merged.gff3 stringtie_merged.transcripts.fasta > stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 767s 768s 768s 768s Done. 3037 / 3037 transcript orfs could be propagated to the genome 768s 768s 768s 768s ## make bed files for viewing with GenomeView 768s 768s # covert cufflinks gtf to bed 768s ../../util/gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed 769s 769s # convert the genome-based gene-gff3 file to bed 769s ../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed 770s 771s 771s 771s ../../util/fasta_prot_checker.pl stringtie_merged.transcripts.fasta.transdecoder.pep 771s 771s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 771s 771s 771s exit 0 771s make[1]: Leaving directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 771s Running example in $... 771s make[1]: Entering directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 771s ./runMe.sh 771s + ../../util/gtf_to_alignment_gff3.pl supertranscripts.gtf 771s + ../../util/gtf_genome_to_cdna_fasta.pl supertranscripts.gtf supertranscripts.fasta 771s -parsing cufflinks output: supertranscripts.gtf 771s -parsing genome fasta: supertranscripts.fasta 771s -done parsing genome. 771s // processing ADD1 771s // processing ATPsyn-d 771s // processing AdipoR 771s // processing Aldh-III 771s // processing CG10082 771s // processing CG10237 771s // processing CG12581 771s // processing CG13255 771s // processing CG13284 771s // processing CG13887 771s // processing CG14995 771s // processing CG15715 771s // processing CG30438 771s // processing CG31639 771s // processing CG31948 771s // processing CG32082 771s // processing CG33125 771s // processing CG33970 771s // processing CG3530 771s // processing CG6024 771s // processing CG6091 771s // processing CG6145 771s // processing CG6424 771s // processing CG6852 771s // processing CG7564 771s // processing CG8136 771s // processing CG8312 771s // processing Calx 771s // processing CanB2 771s // processing Cdep 771s // processing Cnx99A 771s // processing Dat 771s // processing Dgk 771s // processing Eno 771s // processing Est-6 771s // processing Gale 771s // processing Galk 771s // processing His4r 771s // processing Hsc70-1 771s // processing IP3K1 771s // processing Irk2 771s // processing Klp10A 771s // processing Lip4 771s // processing Mgstl 771s // processing Myo61F 771s // processing Npl4 771s // processing RpL15 771s // processing S-Lap3 771s // processing Sec16 771s // processing Tm1 771s // processing bdg 771s // processing bic 771s // processing cdi 771s // processing ctp 771s // processing eIF5B 771s // processing eff 771s // processing gukh 771s // processing hrg 771s // processing kto 771s // processing l(1)G0193 771s // processing l(3)05822 771s // processing mGluR 771s // processing mge 771s // processing nmo 771s // processing ogre 771s // processing regucalcin 771s // processing sqd 771s // processing stas 771s // processing trc 771s + ../../TransDecoder.LongOrfs -t transcripts.fasta 771s CMD: mkdir -p /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir 771s * [Mon Mar 18 02:22:20 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 771s 771s 771s -first extracting base frequencies, we'll need them later. 771s 771s 771s - extracting ORFs from transcripts. 771s -total transcripts to examine: 279 772s [100/279] = 35.84% done [200/279] = 71.68% done CMD: touch /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 772s 772s 772s ################################# 772s ### Done preparing long ORFs. ### 772s ################################## 772s 772s Use file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. 772s 772s Then, run TransDecoder.Predict for your final coding region predictions. 772s 772s 772s + cmd='../../TransDecoder.Predict -t transcripts.fasta' 772s + '[' ']' 772s + eval ../../TransDecoder.Predict -t transcripts.fasta 772s ++ ../../TransDecoder.Predict -t transcripts.fasta 772s * [Mon Mar 18 02:22:21 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 772s * [Mon Mar 18 02:22:21 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 773s -skipping training candidate: bdg_i2.p1, not unique enough 773s -skipping training candidate: bdg_i3.p1, not unique enough 773s -skipping training candidate: bdg_i1.p1, not unique enough 773s -skipping training candidate: Dgk_i7.p1, not unique enough 773s -skipping training candidate: Cdep_i1.p1, not unique enough 773s -skipping training candidate: eIF5B_i4.p1, not unique enough 773s -skipping training candidate: eIF5B_i2.p1, not unique enough 773s -skipping training candidate: Dgk_i1.p1, not unique enough 773s -skipping training candidate: eIF5B_i5.p1, not unique enough 773s -skipping training candidate: Dgk_i3.p1, not unique enough 773s -skipping training candidate: Dgk_i6.p1, not unique enough 773s -skipping training candidate: eIF5B_i1.p1, not unique enough 773s -skipping training candidate: Myo61F_i3.p1, not unique enough 773s -skipping training candidate: Myo61F_i2.p1, not unique enough 773s -skipping training candidate: Myo61F_i4.p1, not unique enough 773s -skipping training candidate: ADD1_i3.p1, not unique enough 773s -skipping training candidate: mGluR_i3.p1, not unique enough 773s -skipping training candidate: Calx_i3.p1, not unique enough 773s -skipping training candidate: Calx_i9.p1, not unique enough 773s -skipping training candidate: Calx_i8.p1, not unique enough 773s -skipping training candidate: Calx_i4.p1, not unique enough 773s -skipping training candidate: Calx_i1.p1, not unique enough 773s -skipping training candidate: Calx_i5.p1, not unique enough 773s -skipping training candidate: Calx_i2.p1, not unique enough 773s -skipping training candidate: cdi_i1.p1, not unique enough 773s -skipping training candidate: CG8312_i4.p1, not unique enough 773s -skipping training candidate: CG8312_i2.p1, not unique enough 773s -skipping training candidate: Klp10A_i6.p1, not unique enough 773s -skipping training candidate: Klp10A_i5.p1, not unique enough 773s -skipping training candidate: Klp10A_i4.p1, not unique enough 773s -skipping training candidate: Klp10A_i3.p1, not unique enough 773s -skipping training candidate: Klp10A_i1.p1, not unique enough 773s -skipping training candidate: CG6424_i3.p1, not unique enough 773s -skipping training candidate: CG6424_i4.p1, not unique enough 773s -skipping training candidate: CG6424_i1.p1, not unique enough 773s -skipping training candidate: Dgk_i4.p1, not unique enough 773s -skipping training candidate: CG33970_i1.p1, not unique enough 773s -skipping training candidate: Dgk_i5.p1, not unique enough 773s -skipping training candidate: CG33125_i1.p1, not unique enough 773s -skipping training candidate: CG3530_i2.p1, not unique enough 773s -skipping training candidate: CG10082_i2.p1, not unique enough 773s -skipping training candidate: CG12581_i1.p1, not unique enough 773s -skipping training candidate: CG6091_i1.p1, not unique enough 773s -skipping training candidate: hrg_i3.p1, not unique enough 773s -skipping training candidate: hrg_i1.p1, not unique enough 773s -skipping training candidate: hrg_i4.p1, not unique enough 773s -skipping training candidate: Calx_i7.p1, not unique enough 773s -skipping training candidate: CG32082_i1.p1, not unique enough 773s -skipping training candidate: Npl4_i1.p1, not unique enough 773s -skipping training candidate: Npl4_i3.p1, not unique enough 773s -skipping training candidate: CG3530_i3.p1, not unique enough 773s -skipping training candidate: CG32082_i3.p1, not unique enough 773s -skipping training candidate: CG32082_i2.p1, not unique enough 773s -skipping training candidate: l(3)05822_i3.p1, not unique enough 773s -skipping training candidate: Cnx99A_i4.p1, not unique enough 773s -skipping training candidate: Cnx99A_i3.p1, not unique enough 773s -skipping training candidate: Cnx99A_i2.p1, not unique enough 773s -skipping training candidate: l(3)05822_i4.p1, not unique enough 773s -skipping training candidate: l(3)05822_i1.p1, not unique enough 773s -skipping training candidate: CG6091_i4.p1, not unique enough 773s -skipping training candidate: Aldh-III_i5.p1, not unique enough 773s -skipping training candidate: Aldh-III_i1.p1, not unique enough 773s -skipping training candidate: Aldh-III_i9.p1, not unique enough 773s -skipping training candidate: Aldh-III_i12.p1, not unique enough 773s -skipping training candidate: Hsc70-1_i2.p1, not unique enough 773s -skipping training candidate: Hsc70-1_i3.p1, not unique enough 773s -skipping training candidate: Est-6_i2.p1, not unique enough 773s -skipping training candidate: S-Lap3_i3.p1, not unique enough 773s -skipping training candidate: S-Lap3_i2.p1, not unique enough 773s -skipping training candidate: gukh_i4.p1, not unique enough 773s -skipping training candidate: mGluR_i2.p1, not unique enough 773s -skipping training candidate: CG30438_i5.p1, not unique enough 773s -skipping training candidate: CG30438_i3.p1, not unique enough 773s -skipping training candidate: CG30438_i1.p1, not unique enough 773s -skipping training candidate: CG6145_i4.p1, not unique enough 773s -skipping training candidate: CG33970_i3.p1, not unique enough 773s -skipping training candidate: Aldh-III_i11.p1, not unique enough 773s -skipping training candidate: mGluR_i1.p1, not unique enough 773s -skipping training candidate: Eno_i5.p1, not unique enough 773s -skipping training candidate: Eno_i3.p1, not unique enough 773s -skipping training candidate: Eno_i4.p1, not unique enough 773s -skipping training candidate: CG6091_i2.p1, not unique enough 773s -skipping training candidate: Aldh-III_i4.p1, not unique enough 773s -skipping training candidate: Aldh-III_i3.p1, not unique enough 773s -skipping training candidate: Aldh-III_i7.p1, not unique enough 773s -skipping training candidate: Aldh-III_i6.p1, not unique enough 773s -skipping training candidate: Aldh-III_i10.p1, not unique enough 773s -skipping training candidate: Aldh-III_i8.p1, not unique enough 773s -skipping training candidate: Galk_i4.p1, not unique enough 773s -skipping training candidate: Galk_i1.p1, not unique enough 773s -skipping training candidate: Galk_i3.p1, not unique enough 773s -skipping training candidate: CG6145_i1.p1, not unique enough 773s -skipping training candidate: CG6145_i2.p1, not unique enough 773s -skipping training candidate: Eno_i6.p1, not unique enough 773s -skipping training candidate: Eno_i1.p2, not unique enough 773s -skipping training candidate: Eno_i5.p2, not unique enough 773s -skipping training candidate: Eno_i3.p2, not unique enough 773s -skipping training candidate: Eno_i4.p2, not unique enough 773s -skipping training candidate: CG6424_i3.p2, not unique enough 773s -skipping training candidate: CG6424_i4.p2, not unique enough 773s -skipping training candidate: CG6424_i1.p2, not unique enough 773s -skipping training candidate: Eno_i6.p2, not unique enough 773s -skipping training candidate: Eno_i2.p2, not unique enough 773s -skipping training candidate: trc_i2.p1, not unique enough 773s -skipping training candidate: Irk2_i1.p1, not unique enough 773s -skipping training candidate: Irk2_i4.p1, not unique enough 773s -skipping training candidate: Lip4_i2.p1, not unique enough 773s -skipping training candidate: CG8312_i1.p1, not unique enough 773s -skipping training candidate: AdipoR_i3.p1, not unique enough 773s -skipping training candidate: AdipoR_i5.p1, not unique enough 773s -skipping training candidate: AdipoR_i4.p1, not unique enough 773s -skipping training candidate: Tm1_i14.p1, not unique enough 773s -skipping training candidate: Tm1_i5.p1, not unique enough 773s -skipping training candidate: CG8136_i4.p1, not unique enough 773s -skipping training candidate: kto_i1.p2, not unique enough 773s -skipping training candidate: CG30438_i4.p1, not unique enough 773s -skipping training candidate: Lip4_i1.p1, not unique enough 773s -skipping training candidate: nmo_i7.p1, not unique enough 773s -skipping training candidate: nmo_i6.p1, not unique enough 773s -skipping training candidate: nmo_i3.p1, not unique enough 773s -skipping training candidate: CG8136_i1.p1, not unique enough 773s -skipping training candidate: CG8136_i3.p1, not unique enough 773s -skipping training candidate: CG6145_i3.p1, not unique enough 773s -skipping training candidate: CG7564_i1.p1, not unique enough 773s -skipping training candidate: CG7564_i3.p1, not unique enough 773s -skipping training candidate: CG7564_i2.p3, not unique enough 773s -skipping training candidate: CG14995_i7.p1, not unique enough 773s -skipping training candidate: nmo_i5.p1, not unique enough 773s -skipping training candidate: nmo_i2.p1, not unique enough 773s -skipping training candidate: nmo_i4.p1, not unique enough 773s -skipping training candidate: CG14995_i3.p1, not unique enough 773s -skipping training candidate: Cdep_i4.p1, not unique enough 773s -skipping training candidate: CG14995_i2.p1, not unique enough 773s -skipping training candidate: CG6024_i1.p1, not unique enough 773s -skipping training candidate: gukh_i4.p2, not unique enough 773s -skipping training candidate: AdipoR_i1.p1, not unique enough 773s -skipping training candidate: CG14995_i4.p1, not unique enough 773s -skipping training candidate: ogre_i3.p1, not unique enough 773s -skipping training candidate: ogre_i1.p1, not unique enough 773s -skipping training candidate: ogre_i4.p1, not unique enough 773s -skipping training candidate: ogre_i6.p1, not unique enough 773s -skipping training candidate: ogre_i2.p1, not unique enough 773s -skipping training candidate: IP3K1_i2.p1, not unique enough 773s -skipping training candidate: CG14995_i1.p1, not unique enough 773s -skipping training candidate: Gale_i1.p1, not unique enough 773s -skipping training candidate: CG33125_i1.p2, not unique enough 773s -skipping training candidate: CG13284_i5.p1, not unique enough 773s -skipping training candidate: CG13284_i1.p1, not unique enough 773s -skipping training candidate: CG13284_i4.p1, not unique enough 773s -skipping training candidate: CG13284_i2.p1, not unique enough 773s -skipping training candidate: sqd_i4.p1, not unique enough 773s -skipping training candidate: Klp10A_i6.p2, not unique enough 773s -skipping training candidate: Klp10A_i5.p2, not unique enough 773s -skipping training candidate: Klp10A_i4.p2, not unique enough 773s -skipping training candidate: Klp10A_i3.p2, not unique enough 773s -skipping training candidate: Klp10A_i1.p2, not unique enough 773s -skipping training candidate: Calx_i7.p2, not unique enough 773s -skipping training candidate: sqd_i2.p1, not unique enough 773s -skipping training candidate: sqd_i1.p1, not unique enough 773s -skipping training candidate: CG10237_i5.p1, not unique enough 773s -skipping training candidate: CG10237_i4.p1, not unique enough 773s -skipping training candidate: CG31948_i2.p1, not unique enough 773s -skipping training candidate: regucalcin_i1.p1, not unique enough 773s -skipping training candidate: regucalcin_i4.p1, not unique enough 773s -skipping training candidate: regucalcin_i2.p1, not unique enough 773s -skipping training candidate: CG10237_i1.p1, not unique enough 773s -skipping training candidate: CG10237_i3.p1, not unique enough 773s -skipping training candidate: l(3)05822_i4.p2, not unique enough 773s -skipping training candidate: l(3)05822_i1.p2, not unique enough 773s -skipping training candidate: l(3)05822_i2.p2, not unique enough 773s -skipping training candidate: Tm1_i3.p1, not unique enough 773s -skipping training candidate: Tm1_i4.p1, not unique enough 773s -skipping training candidate: Tm1_i2.p1, not unique enough 773s -skipping training candidate: Tm1_i6.p1, not unique enough 773s -skipping training candidate: Tm1_i11.p1, not unique enough 773s -skipping training candidate: Tm1_i9.p1, not unique enough 773s -skipping training candidate: Npl4_i3.p2, not unique enough 773s -skipping training candidate: Npl4_i2.p2, not unique enough 773s -skipping training candidate: Sec16_i5.p2, not unique enough 773s -skipping training candidate: Sec16_i1.p2, not unique enough 773s -skipping training candidate: Sec16_i2.p2, not unique enough 773s -skipping training candidate: CG8312_i4.p2, not unique enough 773s -skipping training candidate: CG8312_i2.p2, not unique enough 773s -skipping training candidate: Dgk_i1.p2, not unique enough 773s -skipping training candidate: eIF5B_i3.p2, not unique enough 773s -skipping training candidate: eIF5B_i5.p2, not unique enough 773s -skipping training candidate: eIF5B_i4.p2, not unique enough 773s -skipping training candidate: eIF5B_i2.p2, not unique enough 773s -skipping training candidate: Dgk_i3.p2, not unique enough 773s -skipping training candidate: Dgk_i6.p2, not unique enough 773s -skipping training candidate: Dgk_i2.p2, not unique enough 773s -skipping training candidate: l(1)G0193_i2.p2, not unique enough 773s -skipping training candidate: Tm1_i12.p1, not unique enough 773s -skipping training candidate: Dgk_i7.p3, not unique enough 773s -skipping training candidate: Dgk_i1.p3, not unique enough 773s -skipping training candidate: Dat_i1.p1, not unique enough 773s -skipping training candidate: Dgk_i3.p3, not unique enough 773s -skipping training candidate: Dgk_i4.p3, not unique enough 773s -skipping training candidate: Dgk_i6.p3, not unique enough 773s -skipping training candidate: Dgk_i2.p3, not unique enough 773s -skipping training candidate: l(3)05822_i4.p3, not unique enough 773s -skipping training candidate: l(3)05822_i1.p3, not unique enough 773s -skipping training candidate: l(3)05822_i2.p3, not unique enough 773s -skipping training candidate: CG14995_i5.p1, not unique enough 773s -skipping training candidate: CG6024_i1.p2, not unique enough 773s -skipping training candidate: Sec16_i6.p2, not unique enough 773s -skipping training candidate: Sec16_i2.p3, not unique enough 773s -skipping training candidate: CG13887_i1.p1, not unique enough 773s -skipping training candidate: CG13887_i4.p1, not unique enough 773s -skipping training candidate: CG14995_i3.p2, not unique enough 773s -skipping training candidate: Dgk_i5.p3, not unique enough 773s -skipping training candidate: nmo_i1.p2, not unique enough 773s -skipping training candidate: nmo_i7.p2, not unique enough 773s -skipping training candidate: nmo_i6.p2, not unique enough 773s -skipping training candidate: nmo_i2.p2, not unique enough 773s -skipping training candidate: nmo_i4.p2, not unique enough 773s -skipping training candidate: nmo_i3.p2, not unique enough 773s -skipping training candidate: RpL15_i6.p1, not unique enough 773s -skipping training candidate: regucalcin_i1.p2, not unique enough 773s -skipping training candidate: Hsc70-1_i3.p2, not unique enough 773s -skipping training candidate: RpL15_i7.p1, not unique enough 773s -skipping training candidate: regucalcin_i3.p2, not unique enough 773s -skipping training candidate: regucalcin_i2.p2, not unique enough 773s -skipping training candidate: gukh_i4.p3, not unique enough 773s -skipping training candidate: gukh_i1.p2, not unique enough 773s -skipping training candidate: cdi_i1.p2, not unique enough 773s -skipping training candidate: Hsc70-1_i2.p2, not unique enough 773s -skipping training candidate: RpL15_i5.p1, not unique enough 773s -skipping training candidate: RpL15_i3.p1, not unique enough 773s -skipping training candidate: RpL15_i1.p1, not unique enough 773s -skipping training candidate: RpL15_i2.p1, not unique enough 773s -skipping training candidate: RpL15_i4.p1, not unique enough 773s -skipping training candidate: Npl4_i3.p3, not unique enough 773s -skipping training candidate: Npl4_i2.p3, not unique enough 773s -skipping training candidate: trc_i2.p2, not unique enough 773s -skipping training candidate: Hsc70-1_i1.p3, not unique enough 773s -skipping training candidate: Hsc70-1_i3.p3, not unique enough 773s -skipping training candidate: CG14995_i5.p2, not unique enough 773s -skipping training candidate: CG14995_i4.p2, not unique enough 773s -skipping training candidate: CG14995_i1.p2, not unique enough 773s -skipping training candidate: CG14995_i2.p2, not unique enough 773s -skipping training candidate: CG10237_i1.p2, not unique enough 773s -skipping training candidate: CG10237_i3.p2, not unique enough 773s -skipping training candidate: CG10237_i4.p2, not unique enough 773s -skipping training candidate: CG10237_i2.p2, not unique enough 773s -skipping training candidate: Eno_i2.p3, not unique enough 773s -skipping training candidate: Eno_i1.p3, not unique enough 773s -skipping training candidate: Eno_i5.p3, not unique enough 773s -skipping training candidate: Eno_i3.p3, not unique enough 773s -skipping training candidate: Eno_i4.p3, not unique enough 773s -skipping training candidate: Sec16_i1.p3, not unique enough 773s -skipping training candidate: Sec16_i4.p3, not unique enough 773s -skipping training candidate: CG14995_i7.p3, not unique enough 773s -skipping training candidate: CG14995_i3.p3, not unique enough 773s -skipping training candidate: CG13887_i3.p1, not unique enough 773s -skipping training candidate: gukh_i1.p3, not unique enough 773s -skipping training candidate: ATPsyn-d_i1.p1, not unique enough 773s -skipping training candidate: ATPsyn-d_i3.p1, not unique enough 773s -skipping training candidate: CG10082_i2.p2, not unique enough 773s -skipping training candidate: sqd_i5.p1, not unique enough 773s -skipping training candidate: CG14995_i5.p3, not unique enough 773s -skipping training candidate: CG14995_i6.p3, not unique enough 773s -skipping training candidate: CG30438_i5.p2, not unique enough 773s -skipping training candidate: CG30438_i4.p2, not unique enough 773s -skipping training candidate: CG30438_i3.p2, not unique enough 773s -skipping training candidate: CG30438_i1.p2, not unique enough 773s -skipping training candidate: CG14995_i5.p4, not unique enough 773s -skipping training candidate: stas_i1.p1, not unique enough 773s -skipping training candidate: cdi_i1.p3, not unique enough 773s -skipping training candidate: CG14995_i4.p3, not unique enough 773s -skipping training candidate: CG14995_i1.p3, not unique enough 773s -skipping training candidate: CG14995_i2.p3, not unique enough 773s -skipping training candidate: CanB2_i1.p1, not unique enough 773s -skipping training candidate: ADD1_i2.p2, not unique enough 773s -skipping training candidate: Sec16_i1.p4, not unique enough 773s -skipping training candidate: Sec16_i4.p4, not unique enough 773s -skipping training candidate: bic_i2.p1, not unique enough 773s -skipping training candidate: CG12581_i1.p2, not unique enough 773s -skipping training candidate: Mgstl_i1.p1, not unique enough 773s -skipping training candidate: ctp_i2.p1, not unique enough 773s -skipping training candidate: ctp_i4.p1, not unique enough 773s -skipping training candidate: ctp_i1.p1, not unique enough 773s -skipping training candidate: hrg_i3.p2, not unique enough 773s -skipping training candidate: hrg_i4.p2, not unique enough 773s -skipping training candidate: Eno_i2.p4, not unique enough 773s -skipping training candidate: Eno_i1.p4, not unique enough 773s -skipping training candidate: Eno_i5.p4, not unique enough 773s -skipping training candidate: Eno_i3.p4, not unique enough 773s -skipping training candidate: Eno_i4.p4, not unique enough 773s -skipping training candidate: Klp10A_i6.p3, not unique enough 773s -skipping training candidate: Klp10A_i5.p3, not unique enough 773s -skipping training candidate: Klp10A_i4.p3, not unique enough 773s -skipping training candidate: Klp10A_i3.p3, not unique enough 773s -skipping training candidate: Klp10A_i1.p3, not unique enough 773s -skipping training candidate: Calx_i1.p2, not unique enough 773s -skipping training candidate: Calx_i9.p2, not unique enough 773s -skipping training candidate: Calx_i3.p2, not unique enough 773s -skipping training candidate: Calx_i5.p2, not unique enough 773s -skipping training candidate: Calx_i7.p3, not unique enough 773s -skipping training candidate: Calx_i2.p2, not unique enough 773s -skipping training candidate: Calx_i8.p2, not unique enough 773s -skipping training candidate: Calx_i6.p2, not unique enough 773s -skipping training candidate: CG7564_i4.p2, not unique enough 773s -skipping training candidate: CG7564_i1.p2, not unique enough 773s -skipping training candidate: CG7564_i1.p3, not unique enough 773s -skipping training candidate: CG7564_i3.p3, not unique enough 773s -skipping training candidate: CG7564_i2.p4, not unique enough 773s -skipping training candidate: CG7564_i2.p5, not unique enough 773s -skipping training candidate: Gale_i1.p2, not unique enough 773s -skipping training candidate: eIF5B_i3.p3, not unique enough 773s -skipping training candidate: eIF5B_i5.p3, not unique enough 773s -skipping training candidate: eIF5B_i4.p3, not unique enough 773s -skipping training candidate: eIF5B_i2.p3, not unique enough 773s -skipping training candidate: Dgk_i7.p4, not unique enough 773s -skipping training candidate: Mgstl_i3.p2, not unique enough 773s -skipping training candidate: AdipoR_i4.p2, not unique enough 773s -skipping training candidate: CG6424_i3.p3, not unique enough 773s -skipping training candidate: CG6424_i4.p3, not unique enough 773s -skipping training candidate: CG6424_i1.p3, not unique enough 773s -skipping training candidate: CG6424_i1.p4, not unique enough 773s -skipping training candidate: Tm1_i13.p2, not unique enough 773s -skipping training candidate: Tm1_i14.p2, not unique enough 773s -skipping training candidate: Tm1_i5.p2, not unique enough 773s -skipping training candidate: Dgk_i6.p4, not unique enough 773s -skipping training candidate: Dgk_i2.p5, not unique enough 773s -skipping training candidate: Dgk_i7.p5, not unique enough 773s -skipping training candidate: Dgk_i1.p4, not unique enough 773s -skipping training candidate: cdi_i1.p4, not unique enough 773s -skipping training candidate: eff_i3.p1, not unique enough 773s -skipping training candidate: eff_i2.p1, not unique enough 773s -skipping training candidate: CG6852_i2.p1, not unique enough 773s -skipping training candidate: eIF5B_i3.p4, not unique enough 773s -skipping training candidate: eIF5B_i5.p4, not unique enough 773s -skipping training candidate: eIF5B_i4.p5, not unique enough 773s -skipping training candidate: eIF5B_i2.p4, not unique enough 773s -skipping training candidate: Sec16_i5.p4, not unique enough 773s -skipping training candidate: Sec16_i1.p5, not unique enough 773s -skipping training candidate: Sec16_i6.p3, not unique enough 773s -skipping training candidate: Sec16_i2.p5, not unique enough 773s -skipping training candidate: Sec16_i4.p5, not unique enough 773s -skipping training candidate: CG32082_i1.p2, not unique enough 773s -skipping training candidate: CG32082_i4.p2, not unique enough 773s -skipping training candidate: CG32082_i3.p2, not unique enough 773s -skipping training candidate: CG3530_i3.p2, not unique enough 773s -skipping training candidate: CG3530_i2.p2, not unique enough 773s -skipping training candidate: Dgk_i7.p6, not unique enough 773s -skipping training candidate: l(3)05822_i4.p4, not unique enough 773s -skipping training candidate: l(3)05822_i1.p5, not unique enough 773s -skipping training candidate: l(3)05822_i2.p4, not unique enough 773s -skipping training candidate: sqd_i1.p2, not unique enough 773s -skipping training candidate: CG7564_i1.p4, not unique enough 773s -skipping training candidate: CG7564_i3.p4, not unique enough 773s -skipping training candidate: CG7564_i2.p6, not unique enough 773s -skipping training candidate: S-Lap3_i3.p2, not unique enough 773s -skipping training candidate: S-Lap3_i2.p2, not unique enough 773s -skipping training candidate: cdi_i1.p5, not unique enough 773s -skipping training candidate: CG6091_i2.p2, not unique enough 773s -skipping training candidate: CG6091_i4.p2, not unique enough 773s -skipping training candidate: CG6091_i1.p2, not unique enough 773s -skipping training candidate: Cdep_i1.p2, not unique enough 773s -skipping training candidate: Cdep_i3.p2, not unique enough 773s -skipping training candidate: Cnx99A_i4.p2, not unique enough 773s -skipping training candidate: Cnx99A_i2.p2, not unique enough 773s -skipping training candidate: Cnx99A_i3.p2, not unique enough 773s -skipping training candidate: Sec16_i5.p5, not unique enough 773s -skipping training candidate: Sec16_i1.p6, not unique enough 773s -skipping training candidate: Sec16_i6.p4, not unique enough 773s -skipping training candidate: ogre_i6.p2, not unique enough 773s -skipping training candidate: CG6024_i1.p3, not unique enough 773s -skipping training candidate: hrg_i1.p3, not unique enough 773s -skipping training candidate: hrg_i4.p3, not unique enough 773s -skipping training candidate: ATPsyn-d_i3.p2, not unique enough 773s -skipping training candidate: CG6091_i4.p3, not unique enough 773s -skipping training candidate: CG6091_i1.p3, not unique enough 773s -skipping training candidate: ATPsyn-d_i2.p2, not unique enough 773s -skipping training candidate: CG33970_i1.p2, not unique enough 773s -skipping training candidate: CG33970_i3.p2, not unique enough 773s -skipping training candidate: eIF5B_i1.p5, not unique enough 773s -skipping training candidate: eIF5B_i3.p5, not unique enough 773s -skipping training candidate: eIF5B_i5.p5, not unique enough 773s -skipping training candidate: Aldh-III_i10.p2, not unique enough 773s -skipping training candidate: Aldh-III_i8.p2, not unique enough 773s -skipping training candidate: CG13284_i3.p2, not unique enough 773s -skipping training candidate: CG13284_i4.p2, not unique enough 773s -skipping training candidate: CG13284_i5.p2, not unique enough 773s -skipping training candidate: CG13284_i2.p2, not unique enough 773s -skipping training candidate: Lip4_i3.p2, not unique enough 773s -skipping training candidate: Lip4_i1.p2, not unique enough 773s -skipping training candidate: Dgk_i4.p4, not unique enough 773s -skipping training candidate: Dgk_i6.p5, not unique enough 773s -skipping training candidate: Dgk_i2.p7, not unique enough 773s -skipping training candidate: Dgk_i7.p7, not unique enough 773s -skipping training candidate: Dgk_i1.p5, not unique enough 773s -skipping training candidate: Dgk_i5.p4, not unique enough 773s -skipping training candidate: Tm1_i13.p3, not unique enough 773s -skipping training candidate: Tm1_i14.p3, not unique enough 773s -skipping training candidate: Tm1_i5.p3, not unique enough 773s -skipping training candidate: CG8312_i1.p2, not unique enough 773s -skipping training candidate: CG8312_i1.p3, not unique enough 773s -skipping training candidate: CG8312_i3.p3, not unique enough 773s -skipping training candidate: CG8312_i3.p4, not unique enough 773s -skipping training candidate: CG8312_i2.p3, not unique enough 773s -skipping training candidate: CG8312_i2.p4, not unique enough 773s -skipping training candidate: Klp10A_i6.p4, not unique enough 773s -skipping training candidate: Klp10A_i5.p4, not unique enough 773s -skipping training candidate: Klp10A_i4.p4, not unique enough 773s -skipping training candidate: Klp10A_i3.p4, not unique enough 773s -skipping training candidate: Klp10A_i1.p4, not unique enough 773s -skipping training candidate: eff_i3.p2, not unique enough 773s -skipping training candidate: eff_i2.p2, not unique enough 773s -skipping training candidate: CG14995_i7.p4, not unique enough 773s -skipping training candidate: CG14995_i1.p4, not unique enough 773s -skipping training candidate: CG14995_i5.p5, not unique enough 773s -skipping training candidate: CG14995_i3.p4, not unique enough 773s -skipping training candidate: CG14995_i6.p4, not unique enough 773s -skipping training candidate: CG6424_i3.p5, not unique enough 773s -skipping training candidate: CG6424_i4.p4, not unique enough 773s -skipping training candidate: CG6424_i1.p5, not unique enough 773s -skipping training candidate: CG12581_i1.p3, not unique enough 773s -skipping training candidate: CG32082_i1.p3, not unique enough 773s -skipping training candidate: CG32082_i4.p5, not unique enough 773s -skipping training candidate: CG32082_i3.p3, not unique enough 773s -skipping training candidate: Cnx99A_i2.p3, not unique enough 773s -skipping training candidate: Cnx99A_i3.p3, not unique enough 773s -skipping training candidate: Cdep_i2.p6, not unique enough 773s -skipping training candidate: Cdep_i3.p3, not unique enough 773s -skipping training candidate: Sec16_i2.p6, not unique enough 773s -skipping training candidate: CG33970_i1.p3, not unique enough 773s -skipping training candidate: CG33970_i3.p3, not unique enough 773s -skipping training candidate: Sec16_i5.p6, not unique enough 773s -skipping training candidate: Sec16_i1.p7, not unique enough 773s -skipping training candidate: Sec16_i6.p5, not unique enough 773s -skipping training candidate: Sec16_i2.p7, not unique enough 773s -skipping training candidate: Sec16_i4.p6, not unique enough 773s -skipping training candidate: Sec16_i4.p7, not unique enough 773s -skipping training candidate: mge_i3.p1, not unique enough 773s -skipping training candidate: CG6024_i1.p4, not unique enough 773s -skipping training candidate: Myo61F_i4.p2, not unique enough 773s -skipping training candidate: Myo61F_i2.p2, not unique enough 773s -skipping training candidate: Myo61F_i3.p2, not unique enough 773s -skipping training candidate: Cdep_i1.p3, not unique enough 773s -skipping training candidate: Cnx99A_i2.p4, not unique enough 773s -skipping training candidate: Cnx99A_i3.p4, not unique enough 773s -skipping training candidate: CG13887_i1.p2, not unique enough 773s -skipping training candidate: CG13887_i4.p2, not unique enough 773s -skipping training candidate: CG6145_i3.p2, not unique enough 773s -skipping training candidate: CG6145_i2.p2, not unique enough 773s -skipping training candidate: CG6145_i4.p2, not unique enough 773s -skipping training candidate: CG6145_i1.p2, not unique enough 773s -skipping training candidate: Calx_i1.p3, not unique enough 773s -skipping training candidate: Calx_i9.p3, not unique enough 773s -skipping training candidate: Calx_i3.p3, not unique enough 773s -skipping training candidate: Calx_i5.p3, not unique enough 773s -skipping training candidate: Calx_i7.p5, not unique enough 773s -skipping training candidate: Calx_i2.p3, not unique enough 773s -skipping training candidate: Calx_i8.p3, not unique enough 773s -skipping training candidate: Calx_i6.p3, not unique enough 773s -skipping training candidate: mge_i1.p2, not unique enough 773s -skipping training candidate: AdipoR_i3.p3, not unique enough 773s -skipping training candidate: AdipoR_i5.p2, not unique enough 773s -skipping training candidate: AdipoR_i4.p3, not unique enough 773s -skipping training candidate: AdipoR_i1.p2, not unique enough 773s -skipping training candidate: Aldh-III_i10.p3, not unique enough 773s -skipping training candidate: Aldh-III_i9.p2, not unique enough 773s -skipping training candidate: Aldh-III_i4.p2, not unique enough 773s -skipping training candidate: Aldh-III_i2.p2, not unique enough 773s -skipping training candidate: Aldh-III_i7.p2, not unique enough 773s -skipping training candidate: Aldh-III_i6.p2, not unique enough 773s -skipping training candidate: Cdep_i1.p4, not unique enough 773s -skipping training candidate: Cdep_i2.p9, not unique enough 773s -skipping training candidate: Cdep_i3.p4, not unique enough 773s -skipping training candidate: hrg_i3.p4, not unique enough 773s -skipping training candidate: hrg_i1.p4, not unique enough 773s -skipping training candidate: hrg_i4.p4, not unique enough 773s -skipping training candidate: CG33125_i2.p2, not unique enough 773s -skipping training candidate: Calx_i9.p4, not unique enough 773s -skipping training candidate: mge_i3.p2, not unique enough 773s -skipping training candidate: CG12581_i1.p4, not unique enough 773s -skipping training candidate: Sec16_i5.p7, not unique enough 773s -skipping training candidate: Sec16_i5.p8, not unique enough 773s -skipping training candidate: Sec16_i1.p8, not unique enough 773s -skipping training candidate: Sec16_i1.p9, not unique enough 773s -skipping training candidate: Sec16_i6.p6, not unique enough 773s -skipping training candidate: Sec16_i6.p7, not unique enough 773s -skipping training candidate: Sec16_i2.p8, not unique enough 773s -skipping training candidate: Sec16_i2.p9, not unique enough 773s -skipping training candidate: Sec16_i4.p8, not unique enough 773s -skipping training candidate: Sec16_i4.p9, not unique enough 773s -skipping training candidate: Aldh-III_i4.p3, not unique enough 773s -skipping training candidate: l(3)05822_i2.p5, not unique enough 773s -skipping training candidate: CG6091_i2.p3, not unique enough 773s -skipping training candidate: CG6091_i4.p4, not unique enough 773s -skipping training candidate: CG6091_i1.p4, not unique enough 773s -skipping training candidate: CanB2_i1.p2, not unique enough 773s -skipping training candidate: IP3K1_i1.p3, not unique enough 773s -skipping training candidate: Klp10A_i6.p5, not unique enough 773s -skipping training candidate: Klp10A_i5.p5, not unique enough 773s -skipping training candidate: Klp10A_i4.p5, not unique enough 773s -skipping training candidate: Klp10A_i3.p5, not unique enough 773s -skipping training candidate: Klp10A_i1.p6, not unique enough 773s -skipping training candidate: AdipoR_i2.p3, not unique enough 773s -skipping training candidate: Cdep_i1.p5, not unique enough 773s -skipping training candidate: Cdep_i2.p10, not unique enough 773s -skipping training candidate: Cdep_i3.p5, not unique enough 773s -skipping training candidate: Est-6_i2.p2, not unique enough 773s -skipping training candidate: Klp10A_i6.p6, not unique enough 773s -skipping training candidate: Klp10A_i5.p6, not unique enough 773s -skipping training candidate: Klp10A_i4.p6, not unique enough 773s -skipping training candidate: Klp10A_i3.p6, not unique enough 773s -skipping training candidate: Klp10A_i1.p7, not unique enough 773s -skipping training candidate: l(3)05822_i3.p5, not unique enough 773s -skipping training candidate: ADD1_i2.p3, not unique enough 773s -skipping training candidate: AdipoR_i5.p3, not unique enough 773s -skipping training candidate: Cnx99A_i4.p3, not unique enough 773s -skipping training candidate: Cnx99A_i2.p5, not unique enough 773s -skipping training candidate: Cnx99A_i3.p5, not unique enough 773s -skipping training candidate: Myo61F_i4.p3, not unique enough 773s -skipping training candidate: Myo61F_i2.p3, not unique enough 773s -skipping training candidate: Myo61F_i3.p3, not unique enough 773s -skipping training candidate: Myo61F_i4.p4, not unique enough 773s -skipping training candidate: Myo61F_i2.p4, not unique enough 773s -skipping training candidate: Myo61F_i3.p4, not unique enough 773s -skipping training candidate: bic_i2.p2, not unique enough 773s -skipping training candidate: CG10082_i2.p3, not unique enough 773s -skipping training candidate: CG32082_i1.p4, not unique enough 773s -skipping training candidate: CG32082_i4.p6, not unique enough 773s -skipping training candidate: CG32082_i3.p4, not unique enough 773s -skipping training candidate: Eno_i2.p5, not unique enough 773s -skipping training candidate: Eno_i1.p6, not unique enough 773s -skipping training candidate: Eno_i5.p6, not unique enough 773s -skipping training candidate: Eno_i3.p5, not unique enough 773s -skipping training candidate: Eno_i4.p6, not unique enough 773s -skipping training candidate: Sec16_i3.p9, not unique enough 773s -skipping training candidate: Sec16_i1.p10, not unique enough 773s -skipping training candidate: Sec16_i4.p10, not unique enough 773s -skipping training candidate: Dgk_i4.p5, not unique enough 773s -skipping training candidate: Dgk_i6.p6, not unique enough 773s -skipping training candidate: Dgk_i2.p8, not unique enough 773s -skipping training candidate: Dgk_i7.p8, not unique enough 773s -skipping training candidate: Dgk_i1.p6, not unique enough 773s -skipping training candidate: Dgk_i5.p5, not unique enough 773s -skipping training candidate: nmo_i4.p3, not unique enough 773s -skipping training candidate: CG33970_i1.p4, not unique enough 773s -skipping training candidate: sqd_i5.p3, not unique enough 773s -skipping training candidate: Dgk_i6.p7, not unique enough 773s -skipping training candidate: Dgk_i1.p7, not unique enough 773s -skipping training candidate: His4r_i4.p1, not unique enough 773s -skipping training candidate: His4r_i3.p1, not unique enough 773s -skipping training candidate: His4r_i1.p1, not unique enough 773s -skipping training candidate: Hsc70-1_i1.p4, not unique enough 773s -skipping training candidate: Hsc70-1_i3.p4, not unique enough 773s -skipping training candidate: hrg_i1.p5, not unique enough 773s -skipping training candidate: hrg_i4.p6, not unique enough 773s -skipping training candidate: CG8136_i4.p2, not unique enough 773s -skipping training candidate: CG8136_i2.p2, not unique enough 773s -skipping training candidate: CG8136_i3.p2, not unique enough 773s -skipping training candidate: Myo61F_i4.p5, not unique enough 773s -skipping training candidate: Myo61F_i2.p5, not unique enough 773s -skipping training candidate: Myo61F_i3.p5, not unique enough 773s -skipping training candidate: CG6091_i2.p4, not unique enough 773s -skipping training candidate: CG6091_i4.p5, not unique enough 773s -skipping training candidate: CG6091_i1.p5, not unique enough 773s -skipping training candidate: CG6145_i3.p3, not unique enough 773s -skipping training candidate: CG6145_i2.p3, not unique enough 773s -skipping training candidate: CG6145_i4.p3, not unique enough 773s -skipping training candidate: CG6145_i1.p3, not unique enough 773s -skipping training candidate: gukh_i1.p4, not unique enough 773s -skipping training candidate: sqd_i5.p4, not unique enough 773s -skipping training candidate: CG33125_i2.p3, not unique enough 773s -skipping training candidate: gukh_i1.p5, not unique enough 773s 773s -redundancy-minimized set includes 286 / 856 = 33.41% 773s 773s * [Mon Mar 18 02:22:22 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 773s PCT_GC: 49.4 773s * [Mon Mar 18 02:22:22 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores 774s * [Mon Mar 18 02:22:23 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 779s * [Mon Mar 18 02:22:28 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 779s Selecting best orfs 779s * [Mon Mar 18 02:22:28 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement 779s Training start codon pattern recognition* [Mon Mar 18 02:22:28 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 780s * [Mon Mar 18 02:22:28 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 780s -round: 1 785s -round: 2 790s -round: 3 795s -round: 4 800s -round: 5 805s * [Mon Mar 18 02:22:54 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 805s -parsing scores 812s * [Mon Mar 18 02:23:00 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 812s Error in library(ggplot2) : there is no package called ‘ggplot2’ 812s Execution halted 812s * [Mon Mar 18 02:23:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 812s Error in library(ggplot2) : there is no package called ‘ggplot2’ 812s Execution halted 812s * [Mon Mar 18 02:23:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 812s Error in library(seqLogo) : there is no package called ‘seqLogo’ 812s Execution halted 812s * [Mon Mar 18 02:23:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 813s Error in library(seqLogo) : there is no package called ‘seqLogo’ 813s Execution halted 813s * [Mon Mar 18 02:23:01 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 813s num features: 253 num_incorporate: 75 813s -feature swap of score: -1.36228585301376 instead of -3.33935227631382 813s -feature swap of score: -1.18403993630238 instead of -3.27184261318986 813s -feature swap of score: -2.02700666221193 instead of -3.04577529833809 813s -feature swap of score: -1.30609251018487 instead of -1.87574722095598 813s -feature swap of score: -0.992236381588456 instead of -1.32592720984861 813s -feature swap of score: -0.617071928273436 instead of -1.02930379751856 813s -feature swap of score: 1.88850525638889 instead of -2.21987116598966 813s -feature swap of score: -1.03665247806593 instead of -1.5971498774967 813s -feature swap of score: 2.43265375092124 instead of -1.44149737937444 813s -feature swap of score: 1.32802587924371 instead of -1.24521641747885 813s -feature swap of score: -0.525122207373897 instead of -1.17585525815013 813s -feature swap of score: -0.0538235158961158 instead of -0.960641666191012 813s -feature swap of score: 0.70163790258175 instead of -1.19115186104239 813s -feature swap of score: 2.01248804767062 instead of -1.13036098214049 813s -feature swap of score: 0.750618689575259 instead of -0.906280118938993 813s -feature swap of score: -0.349248785940906 instead of -1.1026784594767 813s -feature swap of score: 1.36714727220801 instead of -0.813681296459017 813s -feature swap of score: 0.153363902246392 instead of -0.574283759464449 813s -feature swap of score: -0.232777330751729 instead of -0.673173526034354 813s -feature swap of score: 3.25339625176077 instead of -0.687176177317553 813s -feature swap of score: 1.77565120603615 instead of -0.34594229611663 813s -feature swap of score: 0.0486842316706984 instead of -0.267496067982875 813s -feature swap of score: 2.77390724208467 instead of -0.380181436263324 813s -feature swap of score: -0.0620345064298571 instead of -0.435172320594316 813s -feature swap of score: -0.32768739787532 instead of -0.349626844170758 813s -feature swap of score: 1.15729358758445 instead of -0.10725674421539 813s -feature swap of score: 0.759368337152421 instead of -0.02579471124732 813s -feature swap of score: -0.00336889031837295 instead of -0.0673719148988756 813s -feature swap of score: 1.94066366693499 instead of -0.00883527661117167 813s -feature swap of score: 1.14512160822102 instead of 0.195250330045512 813s -feature swap of score: 0.181791259323352 instead of -0.0127502685282486 813s -feature swap of score: 0.16526376693912 instead of 0.0625289167075371 813s -feature swap of score: 1.6437527713989 instead of -0.019214947606608 813s -feature swap of score: 0.776488894255548 instead of 0.0160945776706917 813s -feature swap of score: 2.74633667276279 instead of 0.0718236207866946 813s -feature swap of score: 0.17452437078546 instead of -0.034014121347739 813s -feature swap of score: 2.61836914825763 instead of -0.270635325282535 813s -feature swap of score: 0.470689729056115 instead of -0.215648721785514 813s -feature swap of score: 2.1295413541611 instead of -0.154038029050987 813s -feature swap of score: 2.09533162022045 instead of -0.133579149923582 813s -feature swap of score: 0.204741479136657 instead of 0.193614223741557 813s -feature swap of score: 2.53502847177769 instead of -0.162023207923653 813s -feature swap of score: 1.00951203916073 instead of 0.0300485316243723 813s -feature swap of score: 1.69906073622626 instead of 0.0393284656189395 813s -feature swap of score: 0.679765198080688 instead of 0.271781285395621 813s -feature swap of score: 0.983977566431164 instead of 0.470803926382287 813s -feature swap of score: 0.980408558019215 instead of 0.277623308657348 813s -feature swap of score: 2.05367456249005 instead of 0.102562107827557 813s -feature swap of score: 3.06746943220492 instead of -0.218957057307602 813s -feature swap of score: 3.89479402139789 instead of 0.189232725005433 813s -feature swap of score: 0.527053721926772 instead of 0.287205488533377 813s -feature swap of score: 2.54292384394556 instead of 0.0450432208637948 813s -feature swap of score: 5.50890857918181 instead of 0.546401090296238 813s -feature swap of score: 2.58354070390181 instead of 0.0221602917930075 813s -num feature swaps: 54 813s * [Mon Mar 18 02:23:02 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 813s -round: 1 818s -round: 2 822s -round: 3 827s -round: 4 832s -round: 5 837s * [Mon Mar 18 02:23:26 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 837s -parsing scores 842s * [Mon Mar 18 02:23:31 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 843s Error in library(ggplot2) : there is no package called ‘ggplot2’ 843s Execution halted 843s * [Mon Mar 18 02:23:32 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 843s Error in library(ggplot2) : there is no package called ‘ggplot2’ 843s Execution halted 843s * [Mon Mar 18 02:23:32 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 843s Error in library(seqLogo) : there is no package called ‘seqLogo’ 843s Execution halted 843s * [Mon Mar 18 02:23:32 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 844s Refining start codon selections. 844s -number of revised start positions: 10 844s * [Mon Mar 18 02:23:32 2024] Running CMD: cp /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 844s copying output to final output file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Mon Mar 18 02:23:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 844s Making bed file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 844s * [Mon Mar 18 02:23:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 844s Making pep file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 844s * [Mon Mar 18 02:23:33 2024] Running CMD: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 844s Making cds file: /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 844s transdecoder is finished. See output files /tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* 844s 844s 844s + ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 supertranscripts.gff3 transcripts.fasta 844s 844s -Warning [1], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG10082_i1.p3. 844s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i1.p3. 844s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i2.p3. 844s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i3.p3. 844s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i4.p5. 844s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6091_i4.p2. 844s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. 844s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. 844s -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. 844s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. 844s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. 844s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. 844s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. 844s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. 844s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. 844s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i3.p5. 844s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i4.p4. 844s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Galk_i4.p2. 844s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Klp10A_i2.p3. 844s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Tm1_i14.p4. 844s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry bic_i2.p3. 844s -Warning [22], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i1.p2. 844s -Warning [23], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i3.p2. 844s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i4.p2. 844s -Warning [25], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i1.p2. 844s -Warning [26], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i2.p2. 844s -Warning [27], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i3.p2. 844s -Warning [28], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i3.p2. 844s -Warning [29], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i6.p2. 844s 844s 844s Done. 305 / 334 transcript orfs could be propagated to the genome 844s 844s + ../../util/gff3_file_to_bed.pl supertranscripts.wOrfs.gff3 844s 844s + ../../util/gff3_gene_to_gtf_format.pl supertranscripts.wOrfs.gff3 supertranscripts.fasta 844s -missing faidx file: supertranscripts.fasta.fai, extracting positions directly. 844s -Fasta_retriever:: begin initializing for supertranscripts.fasta 844s -Fasta_retriever:: done initializing for supertranscripts.fasta 844s 845s + echo Done 845s Done 845s make[1]: Leaving directory '/tmp/autopkgtest.hmQi3d/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 845s autopkgtest [02:23:34]: test run-tests: -----------------------] 846s run-tests PASS 846s autopkgtest [02:23:35]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 846s autopkgtest [02:23:35]: @@@@@@@@@@@@@@@@@@@@ summary 846s run-tests PASS 857s Creating nova instance adt-noble-arm64-transdecoder-20240318-020928-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...