0s autopkgtest [04:07:14]: starting date: 2024-03-11 0s autopkgtest [04:07:14]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [04:07:14]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9nq_5gz0/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:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade transdecoder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-10.secgroup --name adt-noble-arm64-transdecoder-20240311-040714-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/ 90s autopkgtest [04:08:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 91s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 91s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2623 kB] 91s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB] 91s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB] 91s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 91s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 91s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 91s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2967 kB] 91s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 91s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 91s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 94s Fetched 6834 kB in 2s (3951 kB/s) 94s Reading package lists... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Calculating upgrade... 98s The following packages were automatically installed and are no longer required: 98s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 98s Use 'sudo apt autoremove' to remove them. 98s The following packages will be REMOVED: 98s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 98s The following NEW packages will be installed: 98s libgdbm-compat4t64 libgdbm6t64 98s The following packages have been kept back: 98s libperl5.38 98s The following packages will be upgraded: 98s perl-base perl-modules-5.38 99s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 99s Need to get 4928 kB of archives. 99s After this operation, 4158 kB disk space will be freed. 99s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 99s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 99s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 99s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 100s Fetched 4928 kB in 1s (6618 kB/s) 100s (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 ... 74748 files and directories currently installed.) 100s Removing dpkg-dev (1.22.4ubuntu5) ... 100s Removing libdpkg-perl (1.22.4ubuntu5) ... 100s Removing perl (5.38.2-3) ... 100s (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 ... 74167 files and directories currently installed.) 100s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 100s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 101s Setting up perl-base (5.38.2-3.2) ... 101s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 101s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 101s man-db depends on libgdbm6 (>= 1.16). 101s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 101s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 101s 101s (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 ... 74167 files and directories currently installed.) 101s Removing libgdbm6:arm64 (1.23-5) ... 101s Selecting previously unselected package libgdbm6t64:arm64. 101s (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 ... 74162 files and directories currently installed.) 101s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 101s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 101s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 101s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 101s 101s (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 ... 74168 files and directories currently installed.) 101s Removing libgdbm-compat4:arm64 (1.23-5) ... 101s Selecting previously unselected package libgdbm-compat4t64:arm64. 101s (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 ... 74163 files and directories currently installed.) 101s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ... 101s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 101s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 101s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 102s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 102s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 102s Setting up perl-modules-5.38 (5.38.2-3.2) ... 102s Processing triggers for man-db (2.12.0-3) ... 103s Processing triggers for libc-bin (2.39-0ubuntu2) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s The following packages will be REMOVED: 104s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 105s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 105s After this operation, 52.0 MB disk space will be freed. 105s (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 ... 74169 files and directories currently installed.) 105s Removing libperl5.38:arm64 (5.38.2-3) ... 105s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 105s Removing lto-disabled-list (47) ... 105s Removing make (4.3-4.1build1) ... 105s Removing perl-modules-5.38 (5.38.2-3.2) ... 105s Processing triggers for man-db (2.12.0-3) ... 106s Processing triggers for libc-bin (2.39-0ubuntu2) ... 107s sh: Attempting to set up Debian/Ubuntu apt sources automatically 107s sh: Distribution appears to be Ubuntu 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s eatmydata is already the newest version (131-1). 110s dbus is already the newest version (1.14.10-4ubuntu1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s rng-tools-debian is already the newest version (2.4). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s haveged is already the newest version (1.9.14-1ubuntu1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s The following additional packages will be installed: 113s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 113s make perl perl-modules-5.38 113s Suggested packages: 113s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 113s libterm-readline-gnu-perl | libterm-readline-perl-perl 113s libtap-harness-archive-perl 113s Recommended packages: 113s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 113s libfile-fcntllock-perl 113s The following packages will be REMOVED: 113s libdb5.3 113s The following NEW packages will be installed: 113s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 113s lto-disabled-list make perl perl-modules-5.38 113s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 113s Need to get 7257 kB/10.4 MB of archives. 113s After this operation, 56.1 MB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 114s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 114s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 114s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 114s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 114s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 115s Fetched 7257 kB in 1s (7262 kB/s) 115s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 115s libsasl2-modules-db:arm64 depends on libdb5.3. 115s libpython3.12-stdlib:arm64 depends on libdb5.3. 115s libpam-modules:arm64 depends on libdb5.3. 115s iproute2 depends on libdb5.3. 115s apt-utils depends on libdb5.3. 115s 115s (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 ... 72198 files and directories currently installed.) 115s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 115s Selecting previously unselected package libdb5.3t64:arm64. 115s (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 ... 72192 files and directories currently installed.) 115s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 115s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 115s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 115s Selecting previously unselected package perl-modules-5.38. 116s (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 ... 72198 files and directories currently installed.) 116s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 116s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 116s Selecting previously unselected package libgdbm-compat4t64:arm64. 116s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 116s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 116s Selecting previously unselected package libperl5.38t64:arm64. 116s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 116s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 116s Selecting previously unselected package perl. 117s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 117s Unpacking perl (5.38.2-3.2) ... 117s Selecting previously unselected package libdpkg-perl. 117s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 117s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 117s Selecting previously unselected package make. 117s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 117s Unpacking make (4.3-4.1build1) ... 117s Selecting previously unselected package lto-disabled-list. 117s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 117s Unpacking lto-disabled-list (47) ... 117s Selecting previously unselected package dpkg-dev. 117s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 117s Unpacking dpkg-dev (1.22.4ubuntu5) ... 118s Setting up lto-disabled-list (47) ... 118s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 118s Setting up make (4.3-4.1build1) ... 118s Setting up perl-modules-5.38 (5.38.2-3.2) ... 118s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 118s Setting up perl (5.38.2-3.2) ... 118s Setting up libdpkg-perl (1.22.4ubuntu5) ... 118s Setting up dpkg-dev (1.22.4ubuntu5) ... 118s Processing triggers for man-db (2.12.0-3) ... 120s Processing triggers for libc-bin (2.39-0ubuntu2) ... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s The following packages will be REMOVED: 121s cloud-init* python3-configobj* python3-debconf* 122s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 122s After this operation, 3248 kB disk space will be freed. 122s (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 ... 74750 files and directories currently installed.) 122s Removing cloud-init (24.1-0ubuntu1) ... 125s Removing python3-configobj (5.0.8-3) ... 125s Removing python3-debconf (1.5.86) ... 125s Processing triggers for man-db (2.12.0-3) ... 126s (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 ... 74361 files and directories currently installed.) 126s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 127s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 127s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s linux-generic is already the newest version (6.8.0-11.11+1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 130s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 131s Reading package lists... 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s autopkgtest [04:09:28]: rebooting testbed after setup commands that affected boot 172s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 178s autopkgtest [04:10:12]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 178s autopkgtest [04:10:12]: testbed dpkg architecture: arm64 180s autopkgtest [04:10:14]: @@@@@@@@@@@@@@@@@@@@ apt-source transdecoder 184s Get:1 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (dsc) [2260 B] 184s Get:2 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (tar) [15.0 MB] 184s Get:3 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (diff) [5940 B] 184s gpgv: Signature made Thu Sep 14 10:39:31 2023 UTC 184s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 184s gpgv: Can't check signature: No public key 184s dpkg-source: warning: cannot verify inline signature for ./transdecoder_5.7.1-2.dsc: no acceptable signature found 185s autopkgtest [04:10:19]: testing package transdecoder version 5.7.1-2 185s autopkgtest [04:10:19]: build not needed 186s autopkgtest [04:10:20]: test run-tests: preparing testbed 189s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 190s Done 190s Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 191s The following additional packages will be installed: 191s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hmmer 191s libblas3 libcairo2 libdatrie1 libdeflate0 libdivsufsort3 libfontconfig1 191s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 191s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libmbedcrypto7 libmbedtls14 191s libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 191s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 191s libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 libxcb-render0 191s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ ncbi-data 191s r-base-core transdecoder transdecoder-doc unzip x11-common xdg-utils zip 191s Suggested packages: 191s hmmer-doc tcl8.6 tk8.6 libbusiness-isbn-perl libregexp-ipv6-perl libwww-perl 191s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 191s Recommended packages: 191s r-recommended r-base-dev r-doc-html r-cran-ggplot2 r-bioc-seqlogo 191s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 191s x11-xserver-utils 191s The following NEW packages will be installed: 191s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hmmer 191s libblas3 libcairo2 libdatrie1 libdeflate0 libdivsufsort3 libfontconfig1 191s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 191s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libmbedcrypto7 libmbedtls14 191s libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 191s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 191s libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 libxcb-render0 191s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ ncbi-data 191s r-base-core transdecoder transdecoder-doc unzip x11-common xdg-utils zip 192s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 192s 1 not fully installed or removed. 192s Need to get 69.7 MB of archives. 192s After this operation, 188 MB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 liburi-perl all 5.27-1 [88.0 kB] 192s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 192s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 192s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 192s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 192s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 192s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 192s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 192s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 192s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 192s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 192s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 192s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 192s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 192s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 192s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 192s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 192s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 192s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 192s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 192s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 192s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 192s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 192s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 193s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 193s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 193s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 193s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 193s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 193s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 193s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 193s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 193s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 193s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 193s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 193s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 193s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 193s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 193s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 193s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 193s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 193s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 193s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 193s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 193s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 194s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder all 5.7.1-2 [204 kB] 194s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder-doc all 5.7.1-2 [14.9 MB] 194s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 195s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 195s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 195s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 195s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 195s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 195s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 195s Preconfiguring packages ... 195s Fetched 69.7 MB in 4s (19.6 MB/s) 196s Selecting previously unselected package liburi-perl. 196s (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 ... 74306 files and directories currently installed.) 196s Preparing to unpack .../00-liburi-perl_5.27-1_all.deb ... 196s Unpacking liburi-perl (5.27-1) ... 196s Selecting previously unselected package zip. 196s Preparing to unpack .../01-zip_3.0-13_arm64.deb ... 196s Unpacking zip (3.0-13) ... 196s Selecting previously unselected package unzip. 196s Preparing to unpack .../02-unzip_6.0-28ubuntu3_arm64.deb ... 196s Unpacking unzip (6.0-28ubuntu3) ... 196s Selecting previously unselected package libpaper1:arm64. 196s Preparing to unpack .../03-libpaper1_1.1.29_arm64.deb ... 196s Unpacking libpaper1:arm64 (1.1.29) ... 196s Selecting previously unselected package libpaper-utils. 196s Preparing to unpack .../04-libpaper-utils_1.1.29_arm64.deb ... 196s Unpacking libpaper-utils (1.1.29) ... 196s Selecting previously unselected package xdg-utils. 196s Preparing to unpack .../05-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 196s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 196s Selecting previously unselected package libblas3:arm64. 196s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 196s Unpacking libblas3:arm64 (3.12.0-3) ... 196s Selecting previously unselected package fonts-dejavu-mono. 196s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... 196s Unpacking fonts-dejavu-mono (2.37-8) ... 196s Selecting previously unselected package fonts-dejavu-core. 196s Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ... 196s Unpacking fonts-dejavu-core (2.37-8) ... 196s Selecting previously unselected package fontconfig-config. 196s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 196s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 196s Selecting previously unselected package libfontconfig1:arm64. 196s Preparing to unpack .../10-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 196s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 196s Selecting previously unselected package libpixman-1-0:arm64. 196s Preparing to unpack .../11-libpixman-1-0_0.42.2-1_arm64.deb ... 196s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 196s Selecting previously unselected package libxcb-render0:arm64. 196s Preparing to unpack .../12-libxcb-render0_1.15-1_arm64.deb ... 196s Unpacking libxcb-render0:arm64 (1.15-1) ... 196s Selecting previously unselected package libxcb-shm0:arm64. 196s Preparing to unpack .../13-libxcb-shm0_1.15-1_arm64.deb ... 196s Unpacking libxcb-shm0:arm64 (1.15-1) ... 196s Selecting previously unselected package libxrender1:arm64. 196s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 196s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 196s Selecting previously unselected package libcairo2:arm64. 196s Preparing to unpack .../15-libcairo2_1.18.0-1_arm64.deb ... 196s Unpacking libcairo2:arm64 (1.18.0-1) ... 196s Selecting previously unselected package libgomp1:arm64. 196s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 196s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 196s Selecting previously unselected package libjpeg-turbo8:arm64. 196s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 196s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 196s Selecting previously unselected package libjpeg8:arm64. 196s Preparing to unpack .../18-libjpeg8_8c-2ubuntu11_arm64.deb ... 196s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 197s Selecting previously unselected package libgfortran5:arm64. 197s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 197s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 197s Selecting previously unselected package liblapack3:arm64. 197s Preparing to unpack .../20-liblapack3_3.12.0-3_arm64.deb ... 197s Unpacking liblapack3:arm64 (3.12.0-3) ... 197s Selecting previously unselected package fontconfig. 197s Preparing to unpack .../21-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 197s Unpacking fontconfig (2.15.0-1ubuntu1) ... 197s Selecting previously unselected package libgraphite2-3:arm64. 197s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 197s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 197s Selecting previously unselected package libharfbuzz0b:arm64. 197s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 197s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 197s Selecting previously unselected package libthai-data. 197s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 197s Unpacking libthai-data (0.1.29-2) ... 197s Selecting previously unselected package libdatrie1:arm64. 197s Preparing to unpack .../25-libdatrie1_0.2.13-3_arm64.deb ... 197s Unpacking libdatrie1:arm64 (0.2.13-3) ... 197s Selecting previously unselected package libthai0:arm64. 197s Preparing to unpack .../26-libthai0_0.1.29-2_arm64.deb ... 197s Unpacking libthai0:arm64 (0.1.29-2) ... 197s Selecting previously unselected package libpango-1.0-0:arm64. 197s Preparing to unpack .../27-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 197s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 197s Selecting previously unselected package libpangoft2-1.0-0:arm64. 197s Preparing to unpack .../28-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 197s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 197s Selecting previously unselected package libpangocairo-1.0-0:arm64. 197s Preparing to unpack .../29-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 197s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 197s Selecting previously unselected package libtcl8.6:arm64. 197s Preparing to unpack .../30-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 197s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 197s Selecting previously unselected package libdeflate0:arm64. 197s Preparing to unpack .../31-libdeflate0_1.19-1_arm64.deb ... 197s Unpacking libdeflate0:arm64 (1.19-1) ... 197s Selecting previously unselected package libjbig0:arm64. 197s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 197s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 197s Selecting previously unselected package liblerc4:arm64. 197s Preparing to unpack .../33-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 197s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 197s Selecting previously unselected package libsharpyuv0:arm64. 197s Preparing to unpack .../34-libsharpyuv0_1.3.2-0.4_arm64.deb ... 197s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 197s Selecting previously unselected package libwebp7:arm64. 197s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 197s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 197s Selecting previously unselected package libtiff6:arm64. 197s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 197s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 197s Selecting previously unselected package libxft2:arm64. 197s Preparing to unpack .../37-libxft2_2.3.6-1_arm64.deb ... 197s Unpacking libxft2:arm64 (2.3.6-1) ... 197s Selecting previously unselected package x11-common. 197s Preparing to unpack .../38-x11-common_1%3a7.7+23ubuntu2_all.deb ... 197s Unpacking x11-common (1:7.7+23ubuntu2) ... 197s Selecting previously unselected package libxss1:arm64. 197s Preparing to unpack .../39-libxss1_1%3a1.2.3-1build2_arm64.deb ... 197s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 197s Selecting previously unselected package libtk8.6:arm64. 197s Preparing to unpack .../40-libtk8.6_8.6.13-2_arm64.deb ... 197s Unpacking libtk8.6:arm64 (8.6.13-2) ... 197s Selecting previously unselected package libice6:arm64. 197s Preparing to unpack .../41-libice6_2%3a1.0.10-1build2_arm64.deb ... 197s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 197s Selecting previously unselected package libsm6:arm64. 197s Preparing to unpack .../42-libsm6_2%3a1.2.3-1build2_arm64.deb ... 197s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 197s Selecting previously unselected package libxt6:arm64. 197s Preparing to unpack .../43-libxt6_1%3a1.2.1-1.1_arm64.deb ... 197s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 197s Selecting previously unselected package r-base-core. 197s Preparing to unpack .../44-r-base-core_4.3.2-1build1_arm64.deb ... 197s Unpacking r-base-core (4.3.2-1build1) ... 198s Selecting previously unselected package transdecoder. 198s Preparing to unpack .../45-transdecoder_5.7.1-2_all.deb ... 198s Unpacking transdecoder (5.7.1-2) ... 198s Selecting previously unselected package transdecoder-doc. 198s Preparing to unpack .../46-transdecoder-doc_5.7.1-2_all.deb ... 198s Unpacking transdecoder-doc (5.7.1-2) ... 198s Selecting previously unselected package ncbi-data. 198s Preparing to unpack .../47-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 198s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 198s Selecting previously unselected package libmbedcrypto7:arm64. 198s Preparing to unpack .../48-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 198s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 198s Selecting previously unselected package libmbedx509-1:arm64. 198s Preparing to unpack .../49-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 198s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 198s Selecting previously unselected package libmbedtls14:arm64. 198s Preparing to unpack .../50-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 198s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 198s Selecting previously unselected package ncbi-blast+. 198s Preparing to unpack .../51-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 198s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 198s Selecting previously unselected package libdivsufsort3:arm64. 198s Preparing to unpack .../52-libdivsufsort3_2.0.1-6_arm64.deb ... 198s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 198s Selecting previously unselected package hmmer. 198s Preparing to unpack .../53-hmmer_3.4+dfsg-2_arm64.deb ... 198s Unpacking hmmer (3.4+dfsg-2) ... 199s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 199s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 199s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 199s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 199s Setting up libpaper1:arm64 (1.1.29) ... 199s 199s Creating config file /etc/papersize with new version 199s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 199s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 199s Setting up libdatrie1:arm64 (0.2.13-3) ... 199s Setting up libxcb-render0:arm64 (1.15-1) ... 199s Setting up unzip (6.0-28ubuntu3) ... 199s Setting up x11-common (1:7.7+23ubuntu2) ... 199s Setting up libdeflate0:arm64 (1.19-1) ... 199s Setting up libxcb-shm0:arm64 (1.15-1) ... 199s Setting up libpaper-utils (1.1.29) ... 199s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 199s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 199s Setting up transdecoder-doc (5.7.1-2) ... 199s Setting up zip (3.0-13) ... 199s Setting up libblas3:arm64 (3.12.0-3) ... 199s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 199s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 199s Setting up fonts-dejavu-mono (2.37-8) ... 199s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 199s Setting up fonts-dejavu-core (2.37-8) ... 199s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 199s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 199s Setting up libwebp7:arm64 (1.3.2-0.4) ... 199s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 199s Setting up libthai-data (0.1.29-2) ... 199s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 199s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 199s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 199s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 199s Setting up liburi-perl (5.27-1) ... 199s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 199s Setting up libice6:arm64 (2:1.0.10-1build2) ... 199s Setting up liblapack3:arm64 (3.12.0-3) ... 199s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 199s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 199s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 199s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 200s Setting up ncbi-blast+ (2.12.0+ds-4) ... 200s Setting up libthai0:arm64 (0.1.29-2) ... 200s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 200s Setting up hmmer (3.4+dfsg-2) ... 200s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 200s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 200s Setting up fontconfig (2.15.0-1ubuntu1) ... 202s Regenerating fonts cache... done. 202s Setting up libxft2:arm64 (2.3.6-1) ... 202s Setting up libtk8.6:arm64 (8.6.13-2) ... 202s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 202s Setting up libcairo2:arm64 (1.18.0-1) ... 202s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 202s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 202s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 202s Setting up r-base-core (4.3.2-1build1) ... 202s 202s Creating config file /etc/R/Renviron with new version 202s Setting up transdecoder (5.7.1-2) ... 202s Setting up autopkgtest-satdep (0) ... 202s Processing triggers for man-db (2.12.0-3) ... 203s Processing triggers for install-info (7.1-3) ... 203s Processing triggers for libc-bin (2.39-0ubuntu2) ... 207s (Reading database ... 76805 files and directories currently installed.) 207s Removing autopkgtest-satdep (0) ... 208s autopkgtest [04:10:42]: test run-tests: [----------------------- 209s Running example in $... 209s make[1]: Entering directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 209s ./runMe.sh incl_pfam_n_blast 209s 209s export PERL_HASH_SEED=0 209s 209s if [ ! -e test.genome.fasta ]; then 209s gunzip -c test.genome.fasta.gz > test.genome.fasta 209s fi 209s 209s 209s if [ ! -e transcripts.gtf ]; then 209s gunzip -c transcripts.gtf.gz > transcripts.gtf 209s fi 209s 209s if [ ! -e mini_Pfam-A.hmm ]; then 209s gunzip -c mini_Pfam-A.hmm.gz > mini_Pfam-A.hmm 209s fi 209s 209s if [ ! -e mini_sprot.db.pep ]; then 209s gunzip -c mini_sprot.db.pep.gz > mini_sprot.db.pep 209s fi 209s 209s 209s ## generate alignment gff3 formatted output 209s ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 209s 209s ## generate transcripts fasta file 209s ../../util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta 209s -parsing cufflinks output: transcripts.gtf 209s -parsing genome fasta: test.genome.fasta 209s -done parsing genome. 209s // processing 7000000090838467 209s 209s ## Extract the long ORFs 209s ../../TransDecoder.LongOrfs -t transcripts.fasta 209s CMD: mkdir -p /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir 209s * [Mon Mar 11 04:10:43 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 209s 209s 209s -first extracting base frequencies, we'll need them later. 209s 209s 209s - extracting ORFs from transcripts. 209s -total transcripts to examine: 64 209s CMD: touch /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 209s 209s 209s ################################# 209s ### Done preparing long ORFs. ### 209s ################################## 209s 209s Use file: /tmp/autopkgtest.B13zNQ/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. 209s 209s Then, run TransDecoder.Predict for your final coding region predictions. 209s 209s 209s 209s cmd="" 209s ## Predict likely ORFs 209s if [ "$1" == "" ]; then # always doing this now. 209s # just coding metrics 209s cmd="../../TransDecoder.Predict -t transcripts.fasta" 209s 209s else 209s 209s # this is how I would have run blast and pfam but I'm using precomputed results for ease of demonstration. 209s #BLASTDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/uniprot_sprot.pep 209s #PFAMDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/Pfam-A.hmm 209s # 209s ## run blast 209s #blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db $BLASTDB -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 209s 209s makeblastdb -in mini_sprot.db.pep -dbtype prot 209s 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 209s 209s # 209s ## run pfam 209s #hmmsearch --domtblout pfam.domtblout $PFAMDB transcripts.fasta.transdecoder_dir/longest_orfs.pep > pfam.log 209s 209s hmmpress -f mini_Pfam-A.hmm 209s hmmsearch --domtblout pfam.domtblout mini_Pfam-A.hmm transcripts.fasta.transdecoder_dir/longest_orfs.pep 209s 209s ## use pfam and blast results: 209s cmd="../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v" 209s 209s fi 209s 209s 209s Building a new DB, current time: 03/11/2024 04:10:43 209s New DB name: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/mini_sprot.db.pep 209s New DB title: mini_sprot.db.pep 209s Sequence type: Protein 209s Keep MBits: T 209s Maximum file size: 1000000000B 209s Adding sequences from FASTA; added 240 sequences in 0.00842619 seconds. 209s 209s 209s Warning: [blastp] Examining 5 or more matches is recommended 210s Working... done. 210s Pressed and indexed 118 HMMs (118 names and 118 accessions). 210s Models pressed into binary file: mini_Pfam-A.hmm.h3m 210s SSI index for binary model file: mini_Pfam-A.hmm.h3i 210s Profiles (MSV part) pressed into: mini_Pfam-A.hmm.h3f 210s Profiles (remainder) pressed into: mini_Pfam-A.hmm.h3p 210s # hmmsearch :: search profile(s) against a sequence database 210s # HMMER 3.4 (Aug 2023); http://hmmer.org/ 210s # Copyright (C) 2023 Howard Hughes Medical Institute. 210s # Freely distributed under the BSD open source license. 210s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 210s # query HMM file: mini_Pfam-A.hmm 210s # target sequence database: transcripts.fasta.transdecoder_dir/longest_orfs.pep 210s # per-dom hits tabular output: pfam.domtblout 210s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 210s 210s Query: AA_permease [M=479] 210s Accession: PF00324.20 210s Description: Amino acid permease 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 80.0 51.2 7.7e-27 7.3e-25 19 463 .. 70 500 .. 53 509 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 80.0 bits; conditional E-value: 7.7e-27 210s AA_permease 19 lgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpe....lGfviGlnylfswitvlaleltaasiliqfwelvtdlp 111 210s + + ++G++g++ ++++++++++ v +slge+a+ +p sgg y+++ +p+ l +v+G+ ++ ++t +a + as+++q + + + + 210s CUFF.38.1.p2 70 SLIFSMNCGGGGMVWSWIIGCICLIPVSISLGELASSMPTSGGLYFWIFTLASPSsrafLCWVCGYVSVLGYATIYASTVYSASSMVQALAVIGSPS 166 210s 44455689999************************************99999987222255555555555566666666666666666664444333 PP 210s 210s AA_permease 112 kawvt..........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkga..gfrflgdngsifknnlppgfakeeeg 196 210s + a +l+v+++++ + +v +++ +i + + ++ i++ii ++ ++ + +n g ++ f++++g n+ 210s CUFF.38.1.p2 167 ----YsptkyeqygiYAALLFVISAMTAIPSRVIAKVNIINITFQFLVSIILIIALAAGSDSTTRNSGSfiFGDFTNYSGW---SNM---------- 246 210s ....02345666666999**********************99999999999999996555555555553333333333333...111.......... PP 210s 210s AA_permease 197 afknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplin 293 210s +fi f + v +G+e+ a++a+E+ + +k+ P a+++ + ti+ +++++++++++ + +l +s+ + + ++ g++++ ++ 210s CUFF.38.1.p2 247 -GWAFILSFTTPVWVVSGFESSAAVAEESTNAAKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSSLGQ-PVAQVLVNNVGNKGALGIFS 341 210s .246888888899999*******************************************************99966.7888889999********** PP 210s 210s AA_permease 294 aviltaalssansslysasRvlyslakdglaP..kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388 210s +++++ +l++ +s+l++asR ++++++dg +P ++l+ ++k++vPl+aill+++ sll+ ll +n+ ais + +l++ l i+ + 210s CUFF.38.1.p2 342 LLVIALCLNC-ISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILVNVT---------AISSVFNLAIIALYIAYSG 428 210s *999999998.79************************************************99999999.........4444444444444444444 PP 210s 210s AA_permease 389 rfRkalkyqgrsieelgfkaallplgvi..lvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463 210s +++ + y++ + + + + p ++ +++ ++i++ll+ + ++ + + +++a +++ +++v++++ ++ 210s CUFF.38.1.p2 429 PLMCRFVYNKFQPGVFYVGKWSKPAALWslVWMWFMILMLLFPQYQKPNQ-----DEMNWAIVVLGFVMVFCVVYYY 500 210s 55555555555555555555666555540045555555555555555555.....6788888899999998888777 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (479 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1932.58 210s // 210s Query: AA_permease_2 [M=425] 210s Accession: PF13520.5 210s Description: Amino acid permease 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 183.8 57.6 2.7e-58 2.6e-56 1 425 [] 48 491 .. 48 491 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: 183.8 bits; conditional E-value: 2.7e-58 210s AA_permease_2 1 lsllsafalvigsv......igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf....gkkvaflsawfnwf 86 210s +s++s f+ ++gs+ +gs if +++ gg +++++i+++++ ++v++ + El+s +p+sgG+y + + ++ +++++ +++ 210s CUFF.38.1.p2 48 FSYVSIFGQSFGSMglcpamAGSLIF---SMNCGGGGMVWSWIIGCICL-IPVSISLGELASSMPTSGGLYFWIFTLAspssRAFLCWVCGYVSVL 139 210s 799***********777755555555...57888888888888888888.9*********888***********8886333356666********* PP 210s 210s AA_permease_2 87 ayvpvlasilsvaasyl..lnalg.pdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfssl.ste 178 210s +y+ as++++a s+ l ++g p++ ++++ +y+i++a+l ++ +++++ + +ak++ i +++ +l + iili ++l++++ ++ ++ s++ 210s CUFF.38.1.p2 140 GYATIYASTVYSASSMVqaLAVIGsPSYSPTKYEQYGIYAALLFVISAMTAIPSRVIAKVNIINITFQFL-VSIILI-IALAAGSDSTTRNSgSFI 233 210s ****9999888777777433345547*******************************************5.555454.566666555444334444 PP 210s 210s AA_permease_2 179 tdtffpn.gwp..g..vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsn.lgs.vaalffe 265 210s + f++ gw+ g ++l++++ +w+++Gfes+a v+ee + k +p+a++++l+++++l++ + i++++ ++ d a l++ lg+ va+++++ 210s CUFF.38.1.p2 234 FGDFTNYsGWSnmGwaFILSFTTPVWVVSGFESSAAVAEESTNaaKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSsLGQpVAQVLVN 329 210s 4444444477743133699*********************8887789*****************************999887773444569***** PP 210s 210s AA_permease_2 266 avggkvvaiivvilialsllgaintavigssrvlealardgvlP..rffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgli 359 210s +vg+k + +i++ l++++l+++ ++++i++sr ++a++rdg++P r+++ k++ p++ai l++++sl+++ll+l+ + +a++ +++++ ++l+ 210s CUFF.38.1.p2 330 NVGNKGALGIFS-LLVIALCLNCISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILV-NVTAISSVFNLAIIALY 423 210s ***999999999.8999****************************************************888877765.69*************** PP 210s 210s AA_permease_2 360 isyllliigalilrkkrphl...krpgkilvaiigalfllfllvalffppkgpatqssliytiiltval 425 210s i y ++ +++++ k +p +++ + a+ ++++ f++ +l fp+ + +q++++++i++++++ 210s CUFF.38.1.p2 424 IAYSGPLMCRFVYNKFQPGVfyvGKW-SKPAALWSLVWMWFMILMLLFPQYQKPNQDEMNWAIVVLGFV 491 210s **********9999999977444444.468**********************************99875 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (425 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1935.80 210s // 210s Query: Acetyltransf_1 [M=117] 210s Accession: PF00583.24 210s Description: Acetyltransferase (GNAT) family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 48.3 0.0 1.2e-16 5.6e-15 18 117 .] 35 129 .. 16 129 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 48.3 bits; conditional E-value: 1.2e-16 210s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 210s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 210s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 210s CUFF.34.1.p2 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 210s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 210s 210s HHHHH.TTE CS 210s Acetyltransf_1 110 rlYek.lGF 117 210s +lY + +GF 210s CUFF.34.1.p2 122 PLY-RsVGF 129 210s ***.65**9 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 48.1 0.0 1.3e-16 6.2e-15 18 117 .] 35 129 .. 16 129 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 48.1 bits; conditional E-value: 1.3e-16 210s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 210s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 210s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 210s CUFF.35.1.p1 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 210s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 210s 210s HHHHH.TTE CS 210s Acetyltransf_1 110 rlYek.lGF 117 210s +lY + +GF 210s CUFF.35.1.p1 122 PLY-RsVGF 129 210s ***.65**9 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (117 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2415.60 210s // 210s Query: Acetyltransf_10 [M=127] 210s Accession: PF13673.6 210s Description: Acetyltransferase (GNAT) domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 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- 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 70.8 0.0 1.1e-23 5.3e-22 32 127 .] 50 150 .. 28 150 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 70.8 bits; conditional E-value: 1.1e-23 210s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 210s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 210s CUFF.35.1.p1 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 210s 67888899*******9986666799***************************98888888888889999************************* PP 210s 210s Acetyltransf_10 121 vpMekel 127 210s v+M++el 210s CUFF.35.1.p1 144 VEMRLEL 150 210s ****986 PP 210s 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 65.7 0.0 4.1e-22 2e-20 32 123 .. 50 146 .] 28 146 .] 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 65.7 bits; conditional E-value: 4.1e-22 210s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 210s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 210s CUFF.34.1.p2 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 210s 67888899*******9986666799***************************98888888888889999************************* PP 210s 210s Acetyltransf_10 121 vpM 123 210s v+M 210s CUFF.34.1.p2 144 VEM 146 210s **9 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (127 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2104.17 210s // 210s Query: Acetyltransf_15 [M=210] 210s Accession: PF17013.4 210s Description: Putative acetyl-transferase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 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- 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 19.4 0.1 6.3e-08 3e-06 28 154 .. 5 149 .. 1 150 [. 0.84 210s 210s Alignments for each domain: 210s == domain 1 score: 19.4 bits; conditional E-value: 6.3e-08 210s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 210s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 210s CUFF.35.1.p1 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 210s 5578888888888888888888999999988734444479999999999999999999987777889999************************ PP 210s 210s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksgPeelkkrle 154 210s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g ++++ rle 210s CUFF.35.1.p1 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDGIPHVEMRLE 149 210s **********9888774........6789999*******99744499999998888876 PP 210s 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 17.4 0.1 2.6e-07 1.2e-05 28 145 .. 5 140 .. 1 146 [] 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 17.4 bits; conditional E-value: 2.6e-07 210s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 210s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 210s CUFF.34.1.p2 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 210s 5678888888888888888888999999988734444479999999999999999999987777889999************************ PP 210s 210s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksg 145 210s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g 210s CUFF.34.1.p2 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDG 140 210s *********99887774........5677888888888887633366655 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (210 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 882.17 210s // 210s Query: Acetyltransf_5 [M=101] 210s Accession: PF13444.5 210s Description: Acetyltransferase (GNAT) domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 22.2 0.0 2e-08 9.5e-07 1 82 [. 25 102 .. 25 123 .. 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 22.2 bits; conditional E-value: 2e-08 210s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 210s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 210s CUFF.34.1.p2 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 210s 7888888888888777......*************988889*********9999987777776666665555443555666666 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 21.7 0.0 2.7e-08 1.3e-06 1 82 [. 25 102 .. 25 106 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 21.7 bits; conditional E-value: 2.7e-08 210s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 210s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 210s CUFF.35.1.p1 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 210s 7888888888888777......*************988889*********9999877777776666665555443555677666 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (101 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 691.66 210s // 210s Query: Acetyltransf_7 [M=76] 210s Accession: PF13508.6 210s Description: Acetyltransferase (GNAT) domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 41.8 0.0 1.2e-14 5.6e-13 5 76 .] 29 131 .. 25 131 .. 0.68 210s 210s Alignments for each domain: 210s == domain 1 score: 41.8 bits; conditional E-value: 1.2e-14 210s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 210s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 210s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 210s CUFF.34.1.p2 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 210s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 210s 210s HHHHHTTEEE CS 210s Acetyltransf_7 67 kfYeklGFee 76 210s ++Y++ GF++ 210s CUFF.34.1.p2 122 PLYRSVGFKK 131 210s ********95 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 41.7 0.0 1.3e-14 6.2e-13 5 76 .] 29 131 .. 25 131 .. 0.68 210s 210s Alignments for each domain: 210s == domain 1 score: 41.7 bits; conditional E-value: 1.3e-14 210s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 210s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 210s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 210s CUFF.35.1.p1 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 210s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 210s 210s HHHHHTTEEE CS 210s Acetyltransf_7 67 kfYeklGFee 76 210s ++Y++ GF++ 210s CUFF.35.1.p1 122 PLYRSVGFKK 131 210s ********95 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (76 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1956.63 210s // 210s Query: Acetyltransf_9 [M=128] 210s Accession: PF13527.6 210s Description: Acetyltransferase (GNAT) domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 21.8 0.0 1.7e-08 8.3e-07 72 127 .. 72 131 .. 11 132 .. 0.71 210s 210s Alignments for each domain: 210s == domain 1 score: 21.8 bits; conditional E-value: 1.7e-08 210s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 210s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 210s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 210s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 210s 4567999*************************9986556666667566669******975 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 21.6 0.0 1.9e-08 9.2e-07 72 127 .. 72 131 .. 11 132 .. 0.71 210s 210s Alignments for each domain: 210s == domain 1 score: 21.6 bits; conditional E-value: 1.9e-08 210s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 210s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 210s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 210s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 210s 4567999*************************9986556666667566669******975 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (128 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 773.06 210s // 210s Query: Acetyltransf_CG [M=80] 210s Accession: PF14542.5 210s Description: GCN5-related N-acetyl-transferase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 17.2 0.0 4.8e-07 2.3e-05 8 56 .. 57 105 .. 50 108 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 17.2 bits; conditional E-value: 4.8e-07 210s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 210s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 210s CUFF.34.1.p2 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 210s 5677888888778999***************************998875 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 17.1 0.0 5.2e-07 2.5e-05 8 56 .. 57 105 .. 50 108 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 17.1 bits; conditional E-value: 5.2e-07 210s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 210s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 210s CUFF.35.1.p1 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 210s 5677888888778999***************************998875 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (80 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2266.44 210s // 210s Query: Aldo_ket_red [M=292] 210s Accession: PF00248.20 210s Description: Aldo/keto reductase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 225.3 0.0 4.8e-71 4.6e-69 1 289 [. 21 340 .. 21 342 .. 0.91 210s 210s Alignments for each domain: 210s == domain 1 score: 225.3 bits; conditional E-value: 4.8e-71 210s .EEEE-SSS-ST.......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..................... CS 210s Aldo_ket_red 1 elglGtwqlgsk......eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..................... 70 210s +l+lG +++g k ++ee+++++++a++aGi++fDtA+ Y g seel+G++++k++ +r +++i +K+ 210s CUFF.17.1.p1 21 KLILGCMSYGKKeywedwVLEDEEEVFKIMKAAYDAGIRTFDTANCYSAGVSEELVGKFIRKYEIPRSSIVILSKCffpvrkdlikifgdlssrgvh 117 210s 689999999999888663334678999*********************************************************************9 PP 210s 210s ..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH....HHTTT--EEEEE- CS 210s Aldo_ket_red 71 ..dkrdaeiksglskenieesleeslkrLgtdyvDllllHrpdpslpieevldaleelvkeGkiraiGvSnfsveqleka....kkkkkvkivavqv 161 210s d +++ gls+++i ++e+s+krLgt y+D+l++Hr dp ++ eev++al+++v++Gk+r+iG S q ++ +k++ +k+++ q+ 210s CUFF.17.1.p1 118 flDSPELANQCGLSRKHIFDAVEDSVKRLGT-YIDVLQIHRYDPHVSAEEVMRALNDVVESGKVRYIGASTMRCYQFIELqntaEKHGWHKFISMQN 213 210s 998888889999******************6.**************************************88866655566778************* PP 210s 210s B-BTTB-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------....S-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT CS 210s Aldo_ket_red 162 eynllkreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr....rtsknqdaaeelselakehgvsiaqvalryalsqpa 254 210s +nll ++ee++++++c+k gv+li++spl++Gllt+ + +e++ + +++ ++ + +++++elak+++vs+a++a ++ l + 210s CUFF.17.1.p1 214 YHNLL-YREEEREMIPYCQKTGVGLIPWSPLARGLLTRSIDANEETIRSKTD-LY-TraleFGAGYKAILSRVEELAKKYNVSMATLATAWSL--HK 305 210s *****.*******************************999988887743332.33.2479555556666799*********************..9* PP 210s 210s -SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS 210s Aldo_ket_red 255 vgivipgasnieqlednldalelklseeevaelde 289 210s + +i+g s++e+l+d l+a+elklsee++++l+e 210s CUFF.17.1.p1 306 GDYPIVGISKVERLKDALAAVELKLSEEDIKYLEE 340 210s *******************************9986 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (292 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2579.28 210s // 210s Query: Amidohydro_1 [M=344] 210s Accession: PF01979.19 210s Description: Amidohydrolase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 268.4 0.4 1.1e-83 5.3e-82 1 343 [. 55 420 .. 55 421 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 210s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 210s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 210s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 210s CUFF.26.1.p1 55 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 149 210s 79************************************************************************************9..******** PP 210s 210s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 210s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 210s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 210s CUFF.26.1.p1 150 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 238 210s ******************9988899999999999999....*******************************************9999996....67 PP 210s 210s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 210s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 210s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 210s CUFF.26.1.p1 239 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 332 210s 76.6677.8*************.************************************************************************** PP 210s 210s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 210s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 210s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 210s CUFF.26.1.p1 333 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 420 210s ***99998888.6677.89999***************6.******************972255668888********************97 PP 210s 210s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 268.4 0.4 1.1e-83 5.4e-82 1 343 [. 57 422 .. 57 423 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 210s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 210s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 210s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 210s CUFF.27.1.p1 57 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 151 210s 79************************************************************************************9..******** PP 210s 210s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 210s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 210s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 210s CUFF.27.1.p1 152 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 240 210s ******************9988899999999999999....*******************************************9999996....67 PP 210s 210s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 210s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 210s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 210s CUFF.27.1.p1 241 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 334 210s 76.6677.8*************.************************************************************************** PP 210s 210s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 210s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 210s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 210s CUFF.27.1.p1 335 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 422 210s ***99998888.6677.89999***************6.******************972255668888********************97 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (344 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1937.93 210s // 210s Query: Amidohydro_3 [M=473] 210s Accession: PF07969.10 210s Description: Amidohydrolase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 10.0 0.1 4.8e-05 0.0023 5 25 .. 51 71 .. 50 82 .. 0.86 210s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 211 421 .. 163 422 .. 0.75 210s 210s Alignments for each domain: 210s == domain 1 score: 10.0 bits; conditional E-value: 4.8e-05 210s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 210s ++G +v+PG++ H Hla 210s CUFF.26.1.p1 51 LEGHIVMPGLISLHVHLAQSL 71 210s 89**************99865 PP 210s 210s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 210s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 210s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 210s CUFF.26.1.p1 211 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 298 210s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 210s 210s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 210s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 210s CUFF.26.1.p1 299 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 389 210s 9******************.....4444444444433333333666999***************************8.***************9555 PP 210s 210s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 210s l ++p ++ v +v+dG+ + 210s CUFF.26.1.p1 390 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 421 210s 55555443333346666888899999999876 PP 210s 210s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 10.0 0.1 4.9e-05 0.0023 5 25 .. 53 73 .. 52 84 .. 0.86 210s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 213 423 .. 165 424 .. 0.75 210s 210s Alignments for each domain: 210s == domain 1 score: 10.0 bits; conditional E-value: 4.9e-05 210s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 210s ++G +v+PG++ H Hla 210s CUFF.27.1.p1 53 LEGHIVMPGLISLHVHLAQSL 73 210s 89**************99865 PP 210s 210s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 210s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 210s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 210s CUFF.27.1.p1 213 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 300 210s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 210s 210s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 210s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 210s CUFF.27.1.p1 301 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 391 210s 9******************.....4444444444433333333666999***************************8.***************9555 PP 210s 210s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 210s l ++p ++ v +v+dG+ + 210s CUFF.27.1.p1 392 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 423 210s 55555443333346666888899999999876 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (473 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 2149.74 210s // 210s Query: Aminotran_1_2 [M=363] 210s Accession: PF00155.20 210s Description: Aminotransferase class I and II 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 17.9 0.0 7.6e-08 7.3e-06 48 334 .. 65 357 .. 61 375 .. 0.71 210s 210s Alignments for each domain: 210s == domain 1 score: 17.9 bits; conditional E-value: 7.6e-08 210s HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHH...HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS 210s Aminotran_1_2 48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyk...nilrlsggevvryplyseedfhldlealeealk 140 210s e ++ lak+l+ ++++++++ +++++++++ + lk pgd++++ d +++ +l++ g+ev+ +p +e ++h ++ + ++ 210s CUFF.40.1.p1 65 ETRSLLAKLLN------ASTKDSITFTRDTTEGLNLFQRSLKWKPGDNVVILDNEHPNQGfgwIALQNDGLEVRLVP--NEGQYHANASTFAPYVD 152 210s 778999*****......45555***********************************987333568999********..77999999999*99999 PP 210s 210s THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTTSGGG-EEEEEEE CS 210s Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgn 236 210s + +tk i + s+ +G+ +++++++++ + ++++++ D + +++ ++ +v++ +++ s+ K +G++ +G ++++ 210s CUFF.40.1.p1 153 S------RTKAIGLSSVMFHSGQ---KNDVKDIANAFRPKGIHVLADLTQQVGLSK--------IDVQDLNVSACAFSCHKGLGCPT-GLGVLYVS 230 210s 9......9***********9*97...5677777777*************9999998........55555544688889999999975.58999998 PP 210s 210s H.........................HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHS.....TEEE CS 210s Aminotran_1_2 237 a.........................avvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLael.....glkv 299 210s + +++ ++ ++++ + + ++++ +al++ l+ +++ + lq + k l +eL++l g k 210s CUFF.40.1.p1 231 PlaiselrstppfvgggavedfkedlKLKLNAKYHQSALRYeHTNNAYMLITALRAYLKFLLkvGISNVERYLQGLGKDLIKELESLnvsviGYKD 326 210s 866666666666666666666666555555555555555555555666666666666555554434444444555555666666555444444444 PP 210s 210s ECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEE CS 210s Aminotran_1_2 300 lasq.sgmflltdlsaetakelskkLleevgvyvtp 334 210s ++++ s+ ++l l++e ++ L+++ gv v++ 210s CUFF.40.1.p1 327 FDKHsSHSYVLKILNPE----WFDFLRQQ-GVCVSR 357 210s 44444555555555555....44445555.666655 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (363 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1192.07 210s // 210s Query: Aminotran_5 [M=371] 210s Accession: PF00266.18 210s Description: Aminotransferase class-V 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 152.3 0.0 9.2e-49 8.8e-47 41 369 .. 59 376 .. 25 378 .. 0.89 210s 210s Alignments for each domain: 210s == domain 1 score: 152.3 bits; conditional E-value: 9.2e-49 210s HHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCHHH-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS 210s Aminotran_5 41 atkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137 210s ++ ee+r+ +a+l+na++++ i ft+ tte++nl+ +sl ++kpgd++v+ ++eh + w +l+ g++v+ +p + + + + ++++ +++ 210s CUFF.40.1.p1 59 WKERTEETRSLLAKLLNASTKDSITFTRDTTEGLNLFQRSL--KWKPGDNVVILDNEHPNQGFGWIALQ-NDGLEVRLVPNEGQYHANASTFAPYVD 152 210s 56789************************************..59***********************8.67************************* PP 210s 210s TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHHS.....SS.STTS CS 210s Aminotran_5 138 ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl...eplllggem 230 210s +tk++ ++ v +G ++v++i+++++ kg+ vl+D +q+vg +idv++l+v afs hK l PtG+Gvlyv++ ++ +l +p+ +gg+ 210s CUFF.40.1.p1 153 SRTKAIGLSSVMFHSGQKNDVKDIANAFRPKGIHVLADLTQQVGLSKIDVQDLNVSACAFSCHKgLGCPTGLGVLYVSPLAISELrstPPF-VGGGA 248 210s ****************************************************************8888*************9999774455.55555 PP 210s 210s EEEEET.....TEEEEHHTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTSSHH CS 210s Aminotran_5 231 veevsl.....eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhae 322 210s ve+ + +++++++ ++e+ + i +l+a l++l ++g++++e++ + l + l ++l+sl+ + g k+ ++s s ++k +++e 210s CUFF.40.1.p1 249 VEDFKEdlklkLNAKYHQSALRYEHTNNAYMLITALRAYLKFLLKVGISNVERYLQGLGKDLIKELESLNVSVI-G-YKDFDKHSSHSYVLKILNPE 343 210s 665554110044555999*******555578899***********************************98766.8.67899999999999999998 PP 210s 210s HHHHHHHHTTEEEEEE-TTTHHHHHHHT.S-EEEEE--TTS-HHHHH CS 210s Aminotran_5 323 dvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369 210s + +L+++g++v+ e+++R+S+++ynt++++ 210s CUFF.40.1.p1 344 WF-DFLRQQGVCVSR-------------FESGIRVSFGLYNTSKDII 376 210s 65.79******9974.............45999***********996 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (371 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1236.29 210s // 210s Query: Arginase [M=280] 210s Accession: PF00491.20 210s Description: Arginase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 298.2 0.0 3.6e-93 3.4e-91 2 277 .. 75 373 .. 74 374 .] 0.93 210s 210s Alignments for each domain: 210s == domain 1 score: 298.2 bits; conditional E-value: 3.6e-93 210s EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE...SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEE......... CS 210s Arginase 2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv...leelkivdlgdvavtpvdneevleqieeavaeilkagklp......... 86 210s d+a+lG+Pfd+++s+rpGarfGP+ ire+s+rl+ + +yn+ ++ +++kivd+gd+++t +dn+ +++qie+ e+l+++ + 210s CUFF.38.1.p4 75 DIAFLGAPFDTGTSYRPGARFGPSGIREGSRRLNLYGGYNVPMETnpfNNWAKIVDCGDIPLTSYDNAVAIKQIENGHFELLTRKPTSysekdgyal 171 210s 89********************************8778888887788999******************9***************4444555555555 PP 210s 210s ........EEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSC......TTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH..HHHH CS 210s Arginase 87 ........ivlGGDHsialgilralaekygkplgvihfDAHaDlrtpe......tegsgnshGtpfrraaeegllkpkklvqiGirsvdne..eyel 167 210s i+lGGDH+i l+ilr+++++yg p+++ihfD+H+D ++p+ ++ +++hGt+f++a++egl+++++ +++Gir++ ++ +y+ 210s CUFF.38.1.p4 172 dgsvlprvITLGGDHTIVLPILRSVSRAYG-PVSIIHFDSHLDSWKPKvfgggkSSVGSINHGTYFYHASQEGLVSNDSNIHAGIRTTLSGlsDYDN 267 210s 55555666********************99.6****************99988877778********************************999999 PP 210s 210s HHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTT CS 210s Arginase 168 akelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteae 264 210s ++++g+++i++reid +g++a++++i++rvg ++ ylS+DiDvlDpa+aP+tGtpe G+t+rel+++lr+l + +lvgaD+vEv+Pa+d ae 210s CUFF.38.1.p4 268 DADCGFEIIEAREIDTIGIDAIIKRIRDRVG--DGIAYLSIDIDVLDPAYAPATGTPESAGWTTRELRTILRGLDG-IKLVGADIVEVAPAYDF-AE 360 210s 999***************************8..57***************************************99.*****************.67 PP 210s 210s HHHHHHHHHHHHH CS 210s Arginase 265 qtarlaarlvrel 277 210s t+++aa++++e+ 210s CUFF.38.1.p4 361 VTTLAAADILFEV 373 210s ***********95 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (280 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2967.30 210s // 210s Query: Asparaginase [M=191] 210s Accession: PF00710.19 210s Description: Asparaginase, N-terminal 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-1103(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 176.1 0.6 3.1e-56 2.9e-54 1 182 [. 47 233 .. 47 241 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 176.1 bits; conditional E-value: 3.1e-56 210s EEEEEEEESGGGBB-SSSS--SS-B...S-HHHHHTTSTTHHHHSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHH.HT.--EEEEE--STTHHHHH CS 210s Asparaginase 1 kvlvlatGGTiasekdesggalapa...lsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee.ydgfVvlhGTDTlaytA 92 210s +v v a+GGTia +++s + +++ + +e+l+ea+p+++ ia+++ q++n+ S+n+tpad+lkla+ i +++ + ++g+V++hGTD+l++tA 210s CUFF.15.1.p1 47 NVTVFAMGGTIAGCANSSLEIVNYIpgsVGIEKLIEAVPAIKAIANINGVQVTNMGSENLTPADVLKLAKLILAEVaKPnVHGIVITHGTDSLEETA 143 210s 599***************99999878899***********************************************7669***************** PP 210s 210s HHHHHH---.-S-EEEE--SS-TTSTT-SHHHHHHHHHHHHHSGG.TTS-SEEEETTEEEETTT-EE-BSSSSS-EE-TTT--SEEEETTE CS 210s Asparaginase 93 saLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasse.riagvlvvfngkllranrvtKvhtssldaFespnlgplaevegsk 182 210s ++L+l++ + +kp+v++G++rp++++++Dgp+Nll+A++va+s++ ++g lv +n+++ +a ++tK++ ++ld+F+s ++g+l+ v ++k 210s CUFF.15.1.p1 144 MFLDLTIST-AKPIVVVGAMRPSTAIGADGPMNLLNAVAVASSNQsMGRGTLVLLNDRIGSAFYTTKTNGNTLDTFKSYEAGSLGIVLNQK 233 210s *******99.***************************************************************************986655 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (191 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 210s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2188.01 210s // 210s Query: Asp_Glu_race [M=224] 210s Accession: PF01177.21 210s Description: Asp/Glu/Hydantoin racemase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 18.9 0.0 1.2e-07 5.8e-06 49 98 .. 157 205 .. 141 211 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 18.9 bits; conditional E-value: 1.2e-07 210s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 210s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 210s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 210s CUFF.52.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 210s 34455667**********************99.****************7 PP 210s 210s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 18.6 0.0 1.4e-07 6.9e-06 49 98 .. 157 205 .. 141 212 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 18.6 bits; conditional E-value: 1.4e-07 210s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 210s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 210s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 210s CUFF.50.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 210s 34455667**********************99.****************7 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (224 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3346.45 210s // 210s Query: Beta_elim_lyase [M=293] 210s Accession: PF01212.20 210s Description: Beta-eliminating lyase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 18.8 0.0 4.4e-08 4.2e-06 29 201 .. 619 786 .. 611 886 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 18.8 bits; conditional E-value: 4.4e-08 210s T--HHHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT........-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS 210s Beta_elim_lyase 29 gedktvnrLedavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep........ahihfdetgaiaelagvklrdlknkeaGkmdlek 113 210s g + +++L+ ++ ++g++aa f p +G a++ l+++ + ++ +++ ah+ ++ a a++ag +++++k ++G++d+++ 210s CUFF.57.1.p1 619 GYRHVIEDLQLMLTTITGFDAACFQPnSGAAGEYTGLSVIRAYQRSIGQGHRniclipvsAHG---TNPASAAMAGFTVIPVKCLNNGYLDMQD 709 210s 555667788999999*********9956*******9977765555555555445444344443...55677889*********9999******* PP 210s 210s HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH...HHHTS-CHHHHTTSSEEEEESSSTT- CS 210s Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa...kslgeivkemfsyvDsvtmslkKdll 201 210s l+++ + h++k ++ ++t G ++e+ ++ +++g ++ +DgA +na+ ++ ++ ++D++ + l K + 210s CUFF.57.1.p1 710 LKEKASK---HADKLAAFMVTYPSTF--GI--FEPDVKEALEVIHEHGGQVYFDGAN-MNAMvglC----KAGDI--GADVCHLNLHKTFC 786 210s ***9999...8889999999888887..54..44579*******************5.45552332....33333..23444444444444 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (293 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2384.85 210s // 210s Query: Chitin_synth_1 [M=163] 210s Accession: PF01644.16 210s Description: Chitin synthase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 210s 210s Alignments for each domain: 210s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 210s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 210s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 210s CUFF.60.1.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 210s 9********************************************************************************************** PP 210s 210s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 210s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 210s CUFF.60.1.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 210s ******************************************************************98 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 210s 210s Alignments for each domain: 210s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 210s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 210s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 210s CUFF.60.2.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 210s 9********************************************************************************************** PP 210s 210s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 210s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 210s CUFF.60.2.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 210s ******************************************************************98 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (163 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1805.78 210s // 210s Query: Chitin_synth_1N [M=73] 210s Accession: PF08407.10 210s Description: Chitin synthase N-terminal 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 210s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 210s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 210s CUFF.60.1.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 210s 89***********************65..9******************************8779*********9 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 210s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 210s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 210s CUFF.60.2.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 210s 89***********************65..9******************************8779*********9 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (73 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1391.55 210s // 210s Query: Chitin_synth_2 [M=527] 210s Accession: PF03142.14 210s Description: Chitin synthase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 210s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 210s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 210s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: -3.5 bits; conditional E-value: 0.33 210s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 210s + + +t y ede + +t+ s+ 210s CUFF.60.1.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 210s 3446999*****99999999986 PP 210s 210s == domain 2 score: -3.2 bits; conditional E-value: 0.27 210s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 210s G tki ++ ++++ai v++ i+++++ 210s CUFF.60.1.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 210s 38899999999999999999988887776 PP 210s 210s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 210s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 210s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 210s CUFF.60.1.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 210s 8899********************************9876543244222225789************************************9886 PP 210s 210s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 210s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 210s CUFF.60.1.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 210s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 210s 210s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 210s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 210s CUFF.60.1.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 210s 4445556778888887776522256665111344556666666666655555555 PP 210s 210s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 210s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 210s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 210s CUFF.60.1.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 210s 34558999*************************************************6 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 210s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 210s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 210s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: -3.5 bits; conditional E-value: 0.33 210s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 210s + + +t y ede + +t+ s+ 210s CUFF.60.2.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 210s 3446999*****99999999986 PP 210s 210s == domain 2 score: -3.2 bits; conditional E-value: 0.27 210s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 210s G tki ++ ++++ai v++ i+++++ 210s CUFF.60.2.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 210s 38899999999999999999988887776 PP 210s 210s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 210s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 210s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 210s CUFF.60.2.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 210s 8899********************************9876543244222225789************************************9886 PP 210s 210s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 210s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 210s CUFF.60.2.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 210s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 210s 210s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 210s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 210s CUFF.60.2.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 210s 4445556778888887776522256665111344556666666666655555555 PP 210s 210s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 210s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 210s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 210s CUFF.60.2.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 210s 34558999*************************************************6 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (527 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 210s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 210s # Mc/sec: 1407.16 210s // 210s Query: CO_dh [M=168] 210s Accession: PF02552.15 210s Description: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.3 0.0 0.091 8.6 18 41 .. 130 154 .. 125 156 .. 0.80 210s 2 ! 20.0 0.0 2.5e-08 2.4e-06 14 78 .. 194 257 .. 175 297 .. 0.74 210s 210s Alignments for each domain: 210s == domain 1 score: -1.3 bits; conditional E-value: 0.091 210s --EEE--SHHHHHHHHHS.SSEEEE CS 210s CO_dh 18 katleealkvvakmikka.krPlli 41 210s + ++ ++l+ +a +ik+a + P++i 210s CUFF.32.1.p1 130 QMEIAKKLTCAAVAIKRAeDAPVMI 154 210s 6788899999*******93468877 PP 210s 210s == domain 2 score: 20.0 bits; conditional E-value: 2.5e-08 210s XXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G. CS 210s CO_dh 14 anskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkd 78 210s s k +le+a +a++i+k ++P+l+ Gp+++ a e a++k + + + + +g + 210s CUFF.32.1.p1 194 EISDKESLEKATDIAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMP-AAKGFYS 257 210s 455677899999*******************************99887776654444.3555554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (168 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2699.09 210s // 210s Query: CRCB [M=95] 210s Accession: PF02537.14 210s Description: CrcB-like protein, Camphor Resistance (CrcB) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 56.7 7.3 1.2e-19 1.2e-17 3 92 .. 8 118 .. 6 123 .. 0.83 210s 2 ? -2.4 0.1 0.33 32 44 56 .. 166 180 .. 143 183 .. 0.58 210s 3 ! 58.0 3.7 5e-20 4.8e-18 3 93 .. 190 296 .. 188 299 .. 0.86 210s 210s Alignments for each domain: 210s == domain 1 score: 56.7 bits; conditional E-value: 1.2e-19 210s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHH.. CS 210s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkal.. 77 210s +++++lG+l+R++l ++ln+ + g l+v ++G++++g++ + ++ttGf+G+lTTfS+++l++++ +++ + ++ + 210s CUFF.14.1.p1 8 FCIMSMLGTLARLGL-TALNTYpgapFSGLLWVQFVGCVIMGFCQTesvffprpkhnatfllAITTGFCGSLTTFSSWMLQMFTGMANLDPFERRgr 103 210s 6899***********.7677777997569**************99988887777777777666*********************8877665555566 PP 210s 210s HHHHHHHHHHHHHHH CS 210s CRCB 78 lyvllsvvlgllavv 92 210s y +lsvv +++++ 210s CUFF.14.1.p1 104 GYSFLSVVSDFMVTM 118 210s 999999998887665 PP 210s 210s == domain 2 score: -2.4 bits; conditional E-value: 0.33 210s H..HHTTTHHHHH-- CS 210s CRCB 44 a..llttGflGglTT 56 210s +++ f ++TT 210s CUFF.14.1.p1 166 IcfFVGAAFYTAYTT 180 210s 122455555555555 PP 210s 210s == domain 3 score: 58.0 bits; conditional E-value: 5e-20 210s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHHHH CS 210s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkally 79 210s ++++++ al+R++l++ ln+ p+gtl++Nv++++ll ++++ +++Gf+ l+T Stf++el+++ + +a +y 210s CUFF.14.1.p1 190 SLIFSPFAALTRLYLARFLNSPqyfiPYGTLCANVFATLLLSIMYMipqithctpvsrsvmyGIQNGFCAVLSTLSTFSNELHTMP----IKRAYIY 282 210s 689************9988888***999***************99977766666655555555*********************96....4458999 PP 210s 210s HHHHHHHHHHHHHH CS 210s CRCB 80 vllsvvlgllavvl 93 210s +++sv++++ ++v+ 210s CUFF.14.1.p1 283 CIISVAISFSICVI 296 210s 9****999987765 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (95 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1774.06 210s // 210s Query: CTP_transf_like [M=143] 210s Accession: PF01467.25 210s Description: Cytidylyltransferase-like 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.4 0.0 7.3e-06 0.00069 9 43 .. 33 66 .. 29 73 .. 0.88 210s 210s Alignments for each domain: 210s == domain 1 score: 12.4 bits; conditional E-value: 7.3e-06 210s --HHHHHHHHHHHHHSSESEEEEEESSTHCCST-S CS 210s CTP_transf_like 9 iHlGHlrlleqakklleedlivgvpsdeppkkkkk 43 210s +H GH l+++ak++ e+ ++v + ++ ++ + 210s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAEK-VVVSIFVNPMQFNNPQ 66 210s 7*****************.9999999988887754 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (143 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4382.59 210s // 210s Query: Dak1 [M=307] 210s Accession: PF02733.16 210s Description: Dak1 domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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- 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 359.4 0.4 1.3e-111 6.1e-110 2 304 .. 75 396 .. 74 399 .. 0.92 210s 210s Alignments for each domain: 210s == domain 1 score: 359.4 bits; conditional E-value: 1.3e-111 210s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 210s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 210s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 210s CUFF.19.1.p1 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 210s 899*****************94444666779****************************************************************** PP 210s 210s HHHHHHHHHHHHTT--EEEEEE--B-SSS.SSTTCSSSB--THHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTEEEEEEEEE--B-TTTSSBSS-- CS 210s Dak1 95 lnfglAaekakaegikvetvvvdDDvave.dseekagrRGvagtvlveKiaGaaaeegasLeevaelaekvnenlrsigvalsactvpgagkpsfel 190 210s ++fglAae+aka g++ve v v+DDv+v+ +++ +grRG+++tvlv+KiaG aa+ g +L++va++a++v++n ++i+++l++c vpg++ +++ l 210s CUFF.19.1.p1 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGkKRGALVGRRGLGATVLVHKIAGSAAALGLDLHQVAQVAQSVIDNAATIAASLDHCAVPGRKFETN-L 267 210s ****************************9799999********************************************************8886.* PP 210s 210s -TTEEEETE-TTS---SEEEE.---HHHHHHHHHHHHHH............TT-EEEEEEEE-BSS-HHHHHHHHHHHHHHHHHTT-EEEEEEEESS CS 210s Dak1 191 eedemelGvGiHgEpGverek.lksadelveelleklled...........kgdevvllvnglGgtsllelyivarevaelleekgikvvrvlvGey 275 210s ++de+e+G+GiH+EpG+ +++ l s+ elv+e+l+ l+ + ++d+v+llvn++Gg+s+lel ++ v e+l+++gi ++r+++G++ 210s CUFF.19.1.p1 268 GPDEYEIGMGIHNEPGTFKSSpLPSIPELVTEMLSILFGEknpdnsfvefsSKDDVILLVNNMGGMSNLELGYATEVVSEQLAKRGIIPKRTMSGTF 364 210s ****************977651566789**********64356666666655********************************************* PP 210s 210s S--TTBEEEEEEEEEE-...HHHHHHHHS-EE CS 210s Dak1 276 vTsldmaGfsitllkld...dellelldapve 304 210s vT+l+++Gf itl++++ ++ +++d p++ 210s CUFF.19.1.p1 365 VTALNGPGFGITLVNASkatPDIFKYFDLPTT 396 210s ***************98444566667776665 PP 210s 210s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 170.8 1.0 3.5e-54 1.7e-52 2 125 .. 75 202 .. 74 204 .] 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: 170.8 bits; conditional E-value: 3.5e-54 210s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 210s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 210s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 210s CUFF.20.1.p2 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 210s 899*****************94444666779****************************************************************** PP 210s 210s HHHHHHHHHHHHTT--EEEEEE--B-SSSSS CS 210s Dak1 95 lnfglAaekakaegikvetvvvdDDvaveds 125 210s ++fglAae+aka g++ve v v+DDv+v+++ 210s CUFF.20.1.p2 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGKK 202 210s ****************************876 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (307 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1899.01 210s // 210s Query: Dak2 [M=174] 210s Accession: PF02734.16 210s Description: DAK2 domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -2.4 0.0 0.22 21 70 88 .. 437 455 .. 422 460 .. 0.64 210s 2 ! 146.1 2.0 5.2e-47 4.9e-45 2 173 .. 467 642 .. 466 643 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: -2.4 bits; conditional E-value: 0.22 210s TT---HHHHHHHHHHHHHH CS 210s Dak2 70 ldaedlaaalkaaleaiqa 88 210s +d + + ++lkaa++ai++ 210s CUFF.19.1.p1 437 ADPKMFTKILKAAVDAINE 455 210s 5666677777777777765 PP 210s 210s == domain 2 score: 146.1 bits; conditional E-value: 5.2e-47 210s TS-S-HHHHHHHHHHHHHHHHHC-..--SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.......TT---HHHHHHHHHHHHHHHH---T CS 210s Dak2 2 vGDGDtGtnmargaeavlkaleel..eeaslaevlkalakallsgagGtsGvlysqflralakalke..keeldaedlaaalkaaleaiqavgkarp 94 210s +GDGD+Gt++ +g ea++ka++++ + ++ + +++la ++++++gGtsG lys++l+alak ++e +el++ ++a a k al+a+ ++++ar+ 210s CUFF.19.1.p1 467 AGDGDCGTTLVNGGEAITKAINDKsiRLDDGVNGIDDLAYIVEDSMGGTSGGLYSIYLSALAKGVHEsgDSELSVHTFAFASKYALDALFKYTRARK 563 210s 8***********************9****************************************8865777************************* PP 210s 210s TSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSGGGGGGGGGTT.......S--HHHHHHHHHHHHHH CS 210s Dak2 95 gdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgrAsylgerslg.......vvDpGAvglalileala 173 210s g +T++D+++p+ve+l++ k l++aakaa++g e+T+++ a++grAsy+++++l+ +DpGA +la+il+a++ 210s CUFF.19.1.p1 564 GFRTLIDAIQPFVETLNEGKG-------LDAAAKAATEGSEQTRKMDAVVGRASYVAKEELHkldseggLPDPGAFALAAILNAIV 642 210s ******************999.......*******************************9966999999**************997 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (174 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2774.56 210s // 210s Query: DJ-1_PfpI [M=165] 210s Accession: PF01965.23 210s Description: DJ-1/PfpI family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(-) 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 49.0 0.0 9.5e-17 3e-15 12 125 .. 30 168 .. 26 239 .. 0.74 210s 210s Alignments for each domain: 210s == domain 1 score: 49.0 bits; conditional E-value: 9.5e-17 210s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 210s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 210s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 210s CUFF.46.1.p1 30 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 126 210s 5579**************************955554433134444444444444666666667777******************************* PP 210s 210s HHHHHHTT-EEEEETTTHHHHHHTT...TTTTSEE--SGGGH CS 210s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag...vlkgrrvTsypavk 125 210s ++e++++g+++ a+C+gp+lLa+ + ++g++v ++ v+ 210s CUFF.46.1.p1 127 AREVFTNGGVLSAVCHGPVLLANVKnpqSVEGKTVVYHKHVT 168 210s **********************87512245555554444443 PP 210s 210s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 48.4 0.0 1.4e-16 4.5e-15 12 111 .. 51 172 .. 47 198 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 48.4 bits; conditional E-value: 1.4e-16 210s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 210s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 210s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 210s CUFF.47.1.p1 51 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 147 210s 5579**************************955554433134444444444444666666667777******************************* PP 210s 210s HHHHHHTT-EEEEETTTHHHHHHTT CS 210s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag 111 210s ++e++++g+++ a+C+gp+lLa+ + 210s CUFF.47.1.p1 148 AREVFTNGGVLSAVCHGPVLLANVK 172 210s *********************9865 PP 210s 210s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 31.6 0.0 2.1e-11 6.7e-10 52 161 .. 75 215 .. 15 219 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 31.6 bits; conditional E-value: 2.1e-11 210s EEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH......HHTTTTTTSEE--SGGGH.HHH............. CS 210s DJ-1_PfpI 52 aslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL......aaagvlkgrrvTsypavk.dkl............. 128 210s + +d++ ++y + GG+ ++ + + + + + ++ g+++aa+C+gp++L +++kg++vT++ + +++ 210s CUFF.42.1.p2 75 KNASDINFSDYSIFFAAGGHGTLFDFPSATNLHKGAAKIYSMGGVIAAVCHGPVILpcikdsTGFSIVKGKTVTAFNEIAeQQMnlmptfekyhfkt 171 210s 445699***************9999999999999999****************99955332223469***********995556999*9*9999999 PP 210s 210s .....HHTTSEE-SS......SEEEETTEEEESSGGGHHHHHHH CS 210s DJ-1_PfpI 129 .....ekagakyvdk......rvvvdgnlvTsrgpgaaiefale 161 210s ++ag+++vd v +dg+lvT ++p +a a++ 210s CUFF.42.1.p2 172 lnklfQEAGSNFVDPqepfddFVKTDGKLVTGANPASAASTAKA 215 210s 9999999999999999***977889*********9998776665 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (165 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 3 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 616.22 210s // 210s Query: DLH [M=217] 210s Accession: PF01738.17 210s Description: Dienelactone hydrolase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-771(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 35.2 0.0 5e-13 4.8e-11 3 215 .. 41 254 .. 39 256 .. 0.72 210s 210s Alignments for each domain: 210s == domain 1 score: 35.2 bits; conditional E-value: 5e-13 210s DLH 3 aylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa........ldpndeaeaaraldelvskvaeekvlddlkaavaylks 91 210s +y ++ ++ k v + + ++fG+ ++ik+ +++la+ + +Pd++ ++ + + e+++a ++ ++k ++ +l ++ ++ 210s CUFF.18.1.p1 41 TYFTGKRSS-KVVLIGFMDVFGLSKQIKEGADQLANHELAIYLPDFLNGETasiemidpK----TIEQKEARSKFMEKISSPLHWPKLTKVIEDIER 132 210s 555566666.4455559**********************************898863332....333344444555555555566677777888888 PP 210s 210s DLH 92 vpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188 210s ++ k+g+ GfC+G+++ + + ++ ++ + ++ s+ ++ +a+++ +p+ +l + + + d+ +k e+ + + ++ + H+ 210s CUFF.18.1.p1 133 IH-GQDVKIGAYGFCWGAKVLITYPNKE-RFLRIGCAHP-SLLDPV-DAKHVHCPVCFLCSKDEDPEEVDAWKKSFENS-PYFSESYFETFGKMHHG 224 210s 88.44589****************9999.5667777899.555555.578999***99998766665555544433333.46677778888888888 PP 210s 210s DLH 189 Fandsre...syneeaaedawervlelfkq 215 210s ++++++ +n + +++ +l++fk+ 210s CUFF.18.1.p1 225 WMAARANlsdPENRKYFDLGYQIFLKFFKE 254 210s 888888766677777777778888888776 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (217 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4199.08 210s // 210s Query: DsrD [M=64] 210s Accession: PF08679.10 210s Description: Dissimilatory sulfite reductase D (DsrD) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -4.1 0.0 1 95 21 33 .. 102 114 .. 97 116 .. 0.82 210s 2 ! 10.9 0.0 2.4e-05 0.0023 2 58 .. 132 188 .. 131 192 .. 0.80 210s 210s Alignments for each domain: 210s == domain 1 score: -4.1 bits; conditional E-value: 1 210s HHHHHH-TTS-HH CS 210s DsrD 21 kDlekalPdakpr 33 210s kDl k++ d ++r 210s CUFF.17.1.p1 102 KDLIKIFGDLSSR 114 210s 7999999888877 PP 210s 210s == domain 2 score: 10.9 bits; conditional E-value: 2.4e-05 210s HHHHHHHHSSCCCSS-EEHH..HHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETTEEE CS 210s DsrD 2 kkaiveflekkkkKskfYfk..DlekalPdakpreiKkvvneLVnegkLeywSsGSTtm 58 210s +k+i + +e + k+ Y+ +++ +P +++ e+ +++n+ V+ gk+ y G +tm 210s CUFF.17.1.p1 132 RKHIFDAVEDSVKRLGTYIDvlQIHRYDPHVSAEEVMRALNDVVESGKVRYI--GASTM 188 210s 578899999999877788762245567***********************95..66666 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (64 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2462.37 210s // 210s Query: DUF1129 [M=206] 210s Accession: PF06570.10 210s Description: Protein of unknown function (DUF1129) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 9.5 0.7 3.4e-05 0.0033 88 189 .. 128 229 .. 124 236 .. 0.73 210s 2 ? -1.5 0.0 0.083 7.9 119 133 .. 451 465 .. 423 478 .. 0.59 210s 210s Alignments for each domain: 210s == domain 1 score: 9.5 bits; conditional E-value: 3.4e-05 210s DUF1129 88 llalfallfgilalfskkkqtasiGlitl.llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvl 183 210s +la++++ ++ lfs ++++ Gli+ l+++l+ G+++ ++ +lt + +k++ + + +l+++++l ++ lf+ + + N ++++ 210s CUFF.45.1.p2 128 MLAFISFAWSMTVLFSG-FMSSYGGLIATrLILGLLEGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEQVHAGNKEGWQWIY 223 210s 67778888889999998.777787988543899****************997788877777777777777777666665544444555555555555 PP 210s 210s DUF1129 184 iiigvi 189 210s i+ g + 210s CUFF.45.1.p2 224 IVEGLV 229 210s 555555 PP 210s 210s == domain 2 score: -1.5 bits; conditional E-value: 0.083 210s DUF1129 119 valvgGlamvlvyrl 133 210s + +vgGla+v++ 210s CUFF.45.1.p2 451 CVIVGGLAYVVMFFS 465 210s 345555555554332 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (206 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1659.95 210s // 210s Query: DUF1989 [M=167] 210s Accession: PF09347.9 210s Description: Domain of unknown function (DUF1989) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 186.1 0.0 2.1e-59 2e-57 2 167 .] 58 231 .. 57 231 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 186.1 bits; conditional E-value: 2.1e-59 210s DUF1989 2 tiparsgravevkaGqvlriidleGnqvvdllafnaddprerlsaadTrklqesahlttgdrlysnl..grplltiveDtv.........gvHDtlg 87 210s ++++r+g av++++ +++ i+ +eG+qv+dl+++n ++prer++aa+Tr+++ sah++t+drl+s+l rpl+ti+ D++ +vHDtlg 210s CUFF.34.1.p1 58 VCQPRTGLAVKIPQKSIFSIVVPEGPQVCDLNIWNFHNPRERFWAARTRQIH-SAHVSTYDRLWSTLpyLRPLVTIIGDSLqarhdewggRVHDTLG 153 210s 6899************************************************.************************************99****** PP 210s 210s DUF1989 88 gacdpevnellygegkeyhrnCrdnllralakyglterdvpdvlNlFmnvgvdedgrlfmeespskpGdyvelraemDll 167 210s ++cdp++ +l + gk+++ +C++nl+ra+ yglte+dv+dvlN+F+++g++e +++fme++p++ dy++++ae+Dll 210s CUFF.34.1.p1 154 TRCDPYIDKLIS--GKDNDLHCHSNLTRAIMPYGLTEFDVHDVLNVFQVTGLNEYDQYFMETCPATSKDYFQCFAEQDLL 231 210s *********999..678*************99**********************************************97 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (167 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4114.99 210s // 210s Query: DUF2157 [M=147] 210s Accession: PF09925.8 210s Description: Predicted membrane protein (DUF2157) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s ------ inclusion threshold ------ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -0.5 0.2 0.055 5.2 109 109 .. 75 75 .. 10 128 .. 0.54 210s 2 ? 10.0 3.5 3.1e-05 0.0029 34 120 .. 156 243 .. 142 265 .. 0.89 210s 210s Alignments for each domain: 210s == domain 1 score: -0.5 bits; conditional E-value: 0.055 210s DUF2157 109 a 109 210s + 210s CUFF.14.1.p1 75 C 75 210s 1 PP 210s 210s == domain 2 score: 10.0 bits; conditional E-value: 3.1e-05 210s DUF2157 34 fleallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifqls 120 210s +++ll+l ++++ +G + A+ + +r + f l+++++++ l a++++ ++ + g + + + a+ll+ + ++ qi + + 210s CUFF.14.1.p1 156 VVRVLLLLLSICFFVGAAFYTAYTTNVTHRGIGFSLIFSPFAALTRLYlARFLNSPQYFIPYGTLCANVFATLLLSIMYMIPQITHCT 243 210s 489999999***********************************99999***99999999999999999999********99997766 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (147 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1668.73 210s // 210s Query: DUF2868 [M=328] 210s Accession: PF11067.7 210s Description: Protein of unknown function (DUF2868) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.1 0.3 1.1e-05 0.001 47 74 .. 97 123 .. 92 126 .. 0.94 210s 210s Alignments for each domain: 210s == domain 1 score: 11.1 bits; conditional E-value: 1.1e-05 210s DUF2868 47 fllGalltlllllatrdlaFgWetTLnl 74 210s +llGa++ l + ++r+l++gW+ TL l 210s CUFF.9.1.p1 97 LLLGAIFPLFAESLFRRLNYGWGCTL-L 123 210s 689***********************.6 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (328 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3920.76 210s // 210s Query: DUF2976 [M=88] 210s Accession: PF11190.7 210s Description: Protein of unknown function (DUF2976) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.3 0.1 6.1e-06 0.00058 28 76 .. 120 168 .. 107 177 .. 0.90 210s 2 ! 2.3 0.1 0.0082 0.78 39 77 .. 307 348 .. 282 351 .. 0.68 210s 3 ? -1.6 0.1 0.13 13 58 75 .. 404 421 .. 371 425 .. 0.73 210s 210s Alignments for each domain: 210s == domain 1 score: 12.3 bits; conditional E-value: 6.1e-06 210s DUF2976 28 villgLvlaavaflaVakaalkkfnevregkaewgkfgltlvvGvvllv 76 210s ++ L +a++ + V+k +l kf+++ + +++ + l+ v+G++++ 210s CUFF.25.1.p1 120 SMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIGFIVVA 168 210s 678889999*************************************996 PP 210s 210s == domain 2 score: 2.3 bits; conditional E-value: 0.0082 210s DUF2976 39 aflaVaka.alkkfnevregkaewg..kfgltlvvGvvllvv 77 210s +l V ++ +l f+ + k+ w ++++++vvG v+l++ 210s CUFF.25.1.p1 307 ILLGVGWSiLLLPFSLTSYAKNGWKnpSMIAMMVVGGVILIA 348 210s 445555441345677777778888733588888999988876 PP 210s 210s == domain 3 score: -1.6 bits; conditional E-value: 0.13 210s DUF2976 58 kaewgkfgltlvvGvvll 75 210s +w+ f t+ ++ ++ 210s CUFF.25.1.p1 404 YRDWTYFNNTMTIALCVF 421 210s 567888888888888775 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (88 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1480.00 210s // 210s Query: DUF2997 [M=47] 210s Accession: PF11211.7 210s Description: Protein of unknown function (DUF2997) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.5 0.0 1.1e-05 0.0011 10 25 .. 83 98 .. 83 103 .. 0.91 210s 210s Alignments for each domain: 210s == domain 1 score: 11.5 bits; conditional E-value: 1.1e-05 210s DUF2997 10 rVeeeveGikGksCle 25 210s +V+ +ve+i+GksCl+ 210s CUFF.54.1.p1 83 KVKLRVEDIQGKSCLT 98 210s 79************96 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (47 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2089.22 210s // 210s Query: DUF3288 [M=89] 210s Accession: PF11691.7 210s Description: Protein of unknown function (DUF3288) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(-) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 14.6 0.0 1.4e-06 0.00013 17 62 .. 72 117 .. 68 119 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 14.6 bits; conditional E-value: 1.4e-06 210s DUF3288 17 LlaeepedenlaelArLliRYegFpGardiqkdldkvlkkWqltee 62 210s L++++++ +l e++r l+R +F G +++++ l+ l +W+++++ 210s CUFF.32.1.p3 72 LIEGSANLLSLEEISRTLLRILDFVGNKNMRTYLEVPLCRWHISQA 117 210s 55667777899********************************986 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (89 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3981.09 210s // 210s Query: DUF4208 [M=96] 210s Accession: PF13907.5 210s Description: Domain of unknown function (DUF4208) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 210s 210s Alignments for each domain: 210s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 210s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 210s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 210s CUFF.48.1.p3 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 210s 5567899**************99877***********999855576 PP 210s 210s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 210s 210s Alignments for each domain: 210s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 210s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 210s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 210s CUFF.49.1.p2 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 210s 5567899**************99877***********999855576 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (96 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2818.40 210s // 210s Query: DUF705 [M=304] 210s Accession: PF05152.11 210s Description: Protein of unknown function (DUF705) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.6 0.0 8e-06 0.00076 225 270 .. 70 116 .. 58 152 .. 0.73 210s 210s Alignments for each domain: 210s == domain 1 score: 11.6 bits; conditional E-value: 8e-06 210s DUF705 225 vlditnskrl..PksvkvvlkyLsdknleffksitLvDDladnninYD 270 210s + + n+++l Pks ++v+ sd n+ f+s L DD ++n i+Y 210s CUFF.52.1.p2 70 YTATVNHEDLnePKSHEIVMLLASDGNVGSFESN-LLDDCFKNRIEYA 116 210s 555566665333********************95.78*******9874 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (304 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 5038.47 210s // 210s Query: DUF999 [M=143] 210s Accession: PF06198.10 210s Description: Protein of unknown function (DUF999) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 305.5 5.8 5e-96 2.4e-94 1 143 [] 21 163 .. 21 163 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 305.5 bits; conditional E-value: 5e-96 210s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 210s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyypdgristrs++rw+lliiwsiiiv 210s CUFF.5.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPDGRISTRSNFRWPLLIIWSIIIV 118 210s 9************************************************************************************************* PP 210s 210s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 210s +a+dkkfev++flsiwinenrfyseiw+piaiyvcllvl+ll+li 210s CUFF.5.1.p1 119 FAVDKKFEVQKFLSIWINENRFYSEIWVPIAIYVCLLVLMLLSLI 163 210s ******************************************996 PP 210s 210s >> CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 293.2 4.2 3.2e-92 1.5e-90 1 143 [] 21 163 .. 21 163 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 293.2 bits; conditional E-value: 3.2e-92 210s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 210s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyyp+grist++k+rwvlliiwsii++ 210s CUFF.3.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPNGRISTQDKSRWVLLIIWSIITI 118 210s 9************************************************************************************************* PP 210s 210s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 210s l+idkkf++ke++++wi+en+++seiwgpi+iyv+l++lll+a++ 210s CUFF.3.1.p1 119 LTIDKKFKIKESYLEWIGENQSHSEIWGPIVIYVGLFILLLSAFN 163 210s ******************************************985 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (143 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2893.10 210s // 210s Query: FAD_syn [M=158] 210s Accession: PF06574.11 210s Description: FAD synthetase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.2 0.0 6.8e-06 0.00065 18 82 .. 33 92 .. 22 109 .. 0.84 210s 2 ? -1.4 0.0 0.1 9.9 112 145 .. 141 174 .. 125 188 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 12.2 bits; conditional E-value: 6.8e-06 210s FAD_syn 18 vHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlv 82 210s +H GH +l+++a+++a+ ++vv +F + P+++ ++++ t+++ ++l++lgvd v+ 210s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAE----KVVVSIFVN-PMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYA 92 210s 7*******999998884....577888865.99999988888888899999**********9986 PP 210s 210s == domain 2 score: -1.4 bits; conditional E-value: 0.1 210s FAD_syn 112 vvGfdfrfGkkregdvellkelgaklgfevevvp 145 210s v + +fG+k +v+ +k++ + l+f +e+++ 210s CUFF.50.1.p2 141 VNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQ 174 210s 5555568999999999999999999997776654 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (158 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3045.48 210s // 210s Query: Fe-ADH [M=364] 210s Accession: PF00465.18 210s Description: Iron-containing alcohol dehydrogenase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 415.6 1.9 8e-129 7.6e-127 1 364 [] 52 414 .. 52 414 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 415.6 bits; conditional E-value: 8e-129 210s -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHH CS 210s Fe-ADH 1 PtrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtA 97 210s P+ +fgkg+l+e ++ +k g+k+ livtd+g++ k gl+dkv++ lee+ i+v+++dgv+pnpt+ +v+++++++++e++d +++GGGs++D+A 210s CUFF.50.1.p1 52 PSFNLFGKGCLAEAAKQIKMSGFKNTLIVTDPGII-KVGLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCA 147 210s 56678****************************99.************************************************************* PP 210s 210s HHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHH CS 210s Fe-ADH 98 Kaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahal 193 210s K+iall++n++ ++dy+g++k+ k++lpliai TtaGt+se+t++a+it e ++ k++i d++++P l++ Dpe +++lP+++taatg+Dal+ha+ 210s CUFF.50.1.p1 148 KGIALLATNGGkIADYEGVDKS-SKPQLPLIAINTTAGTASEMTRFAIITEETRHIKMAIIDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAV 243 210s *********956*****99987.8999***********************99999****************************************** PP 210s 210s HHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH........ CS 210s Fe-ADH 194 EayvskkanplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaa. 289 210s 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 ++ 210s CUFF.50.1.p1 244 EAYVSTAANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFYGIPHGVCNAVLLAHVQKFNSRDPr 340 210s ***********************************************************************99********************5554 PP 210s 210s ....HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHHH CS 210s Fe-ADH 290 p.erlaqlaralggesdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkdrslannpreltaedv 364 210s + +rl ++a lg +e ae++++++ +l+ e+++ +L +lgv+e+d+d l+++a+kd + a+np ++t+++v 210s CUFF.50.1.p1 341 AnARLGDIAFHLGC--EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKDFDVLVDHAMKDACGATNPIQPTHDEV 414 210s 44888888888864..699*****************************************************9986 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (364 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2874.89 210s // 210s Query: Fe-ADH_2 [M=250] 210s Accession: PF13685.5 210s Description: Iron-containing alcohol dehydrogenase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 65.9 2.6 2.4e-22 2.3e-20 2 245 .. 57 320 .. 56 323 .. 0.89 210s 2 ? -3.6 0.0 0.4 38 27 60 .. 355 388 .. 350 399 .. 0.70 210s 210s Alignments for each domain: 210s == domain 1 score: 65.9 bits; conditional E-value: 2.4e-22 210s Fe-ADH_2 2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvs.. 95 210s +g+g l + ++ +k ++k+ l+v+d ++ k+ + +kv+ l+e+ i+v++++ v++++++ +v++ +e ++++++d +v++GgG+++D ak ++ 210s CUFF.50.1.p1 57 FGKGCLAEAAKQIKMSGFKNTLIVTDPGIIKVgLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCAKGIAll 153 210s 57899999********************9999899*********************************************************98622 PP 210s 210s Fe-ADH_2 96 ................aklnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkl 173 210s +k ++p++++ T+a + +a ++++ + k + k ++P+ + D + + P +l+a+ D+l + + + + 210s CUFF.50.1.p1 154 atnggkiadyegvdksSKPQLPLIAINTTAGTASEMTRFAIITEEtrHIKMAIiDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAVEAYVSTA 250 210s 222222222222222256689*********9999999999999887788888888999*************************************** PP 210s 210s Fe-ADH_2 174 anevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalH 245 210s an +++ a + ++ v + ++++v+++k++ea +++ a l+g+++ ++ G H ++H l + H 210s CUFF.50.1.p1 251 ANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFY--GIPH 320 210s ************************************************************997666..5555 PP 210s 210s == domain 2 score: -3.6 bits; conditional E-value: 0.4 210s Fe-ADH_2 27 dentkkaagekveeslkeagikvevveeveeead 60 210s +e+t +aa +++++ + e +i++++v+ +e+d 210s CUFF.50.1.p1 355 EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKD 388 210s 5778888888888888888888887765555554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (250 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1124.67 210s // 210s Query: Fig1 [M=188] 210s Accession: PF12351.7 210s Description: Ca2+ regulator and membrane fusion protein Fig1 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.4 0.1 1.2e-05 0.0012 73 147 .. 7 79 .. 2 95 .. 0.75 210s 210s Alignments for each domain: 210s == domain 1 score: 11.4 bits; conditional E-value: 1.2e-05 210s Fig1 73 sdnvvhpyllmvaiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalwqhvassaastl 147 210s ++++ +l+m a+++++ f + lyf +ei ++ fk a++ ++v+s ++l+ + ++l++ ++ + l 210s CUFF.52.1.p2 7 KNTLTKRKLIMLALAIVFTFFAFGLYFIPHDEISVFDFKLPALQYETTVTSLDNFLIGGSTTLYTATVN--HEDL 79 210s 5566677899999999999999999998899**********7777777777777888777777765543..3555 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (188 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 4621.95 210s // 210s Query: Flavodoxin_2 [M=198] 210s Accession: PF02525.16 210s Description: Flavodoxin-like fold 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 210s 210s Alignments for each domain: 210s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 210s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 210s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 210s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 210s CUFF.48.1.p3 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 210s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 210s 210s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 210s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 210s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 210s CUFF.48.1.p3 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 210s **************999999****97777778878888899******************999999****************************9644 PP 210s 210s CCCHHHHHHHHHH CS 210s Flavodoxin_2 180 gaedeealaeale 192 210s +++ ++ a+ 210s CUFF.48.1.p3 173 NPK----VDIAVC 181 210s 443....444444 PP 210s 210s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 210s 210s Alignments for each domain: 210s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 210s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 210s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 210s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 210s CUFF.49.1.p2 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 210s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 210s 210s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 210s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 210s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 210s CUFF.49.1.p2 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 210s **************999999****97777778878888899******************999999****************************9644 PP 210s 210s CCCHHHHHHHHHH CS 210s Flavodoxin_2 180 gaedeealaeale 192 210s +++ ++ a+ 210s CUFF.49.1.p2 173 NPK----VDIAVC 181 210s 443....444444 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (198 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3239.19 210s // 210s Query: FMN_red [M=155] 210s Accession: PF03358.14 210s Description: NADPH-dependent FMN reductase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 210s 210s Alignments for each domain: 210s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 210s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 210s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 210s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 210s CUFF.48.1.p3 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 210s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 210s 210s HCH CS 210s FMN_red 96 Drl 98 210s D + 210s CUFF.48.1.p3 82 DEV 84 210s 976 PP 210s 210s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 210s 210s Alignments for each domain: 210s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 210s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 210s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 210s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 210s CUFF.49.1.p2 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 210s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 210s 210s HCH CS 210s FMN_red 96 Drl 98 210s D + 210s CUFF.49.1.p2 82 DEV 84 210s 976 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (155 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 966.60 210s // 210s Query: FPP [M=866] 210s Accession: PF05911.10 210s Description: Filament-like plant protein, long coiled-coil 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 9.9 0.1 2.1e-05 0.00099 518 597 .. 171 250 .. 146 265 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 9.9 bits; conditional E-value: 2.1e-05 210s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 210s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 210s CUFF.60.1.p2 171 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 250 210s 333333333333333334444455778999************************9*******************999985 PP 210s 210s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 9.6 0.1 2.7e-05 0.0013 518 597 .. 222 301 .. 197 316 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 9.6 bits; conditional E-value: 2.7e-05 210s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 210s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 210s CUFF.60.2.p2 222 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 301 210s 333333333333333334444455778999************************9*******************999985 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (866 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 2884.48 210s // 210s Query: FR47 [M=86] 210s Accession: PF08445.9 210s Description: FR47-like protein 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 18.3 0.0 1.9e-07 9e-06 18 81 .. 70 133 .. 53 137 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: 18.3 bits; conditional E-value: 1.9e-07 210s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 210s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 210s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 210s CUFF.34.1.p2 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 210s 455578********************999999899999999999999*************9975 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 18.2 0.0 2.1e-07 9.8e-06 18 81 .. 70 133 .. 53 137 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: 18.2 bits; conditional E-value: 2.1e-07 210s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 210s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 210s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 210s CUFF.35.1.p1 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 210s 455578********************999999899999999999999*************9975 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (86 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2927.81 210s // 210s Query: Fungal_trans [M=267] 210s Accession: PF04082.17 210s Description: Fungal specific transcription factor domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+ 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 210s 210s Alignments for each domain: 210s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 210s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 210s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 210s CUFF.40.1.p2 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 210s 799*********************.*****************************9998444444....66....******..*************** PP 210s 210s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 210s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 210s CUFF.40.1.p2 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 210s ****************************************999**********************************99********9999997776 PP 210s 210s Fungal_trans 191 dlwesddase 200 210s ++e +++ 210s CUFF.40.1.p2 303 -VNEYRVNNA 311 210s .777766665 PP 210s 210s >> CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 210s 210s Alignments for each domain: 210s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 210s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 210s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 210s CUFF.41.1.p1 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 210s 799*********************.*****************************9998444444....66....******..*************** PP 210s 210s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 210s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 210s CUFF.41.1.p1 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 210s ****************************************999**********************************99********9999997776 PP 210s 210s Fungal_trans 191 dlwesddase 200 210s ++e +++ 210s CUFF.41.1.p1 303 -VNEYRVNNA 311 210s .777766665 PP 210s 210s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 87.3 5.9 1.9e-28 4.5e-27 3 234 .. 203 429 .. 201 459 .. 0.81 210s 2 ? 1.2 0.0 0.035 0.82 1 23 [. 471 492 .. 471 504 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 87.3 bits; conditional E-value: 1.9e-28 210s Fungal_trans 3 rffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLll 99 210s ++f++++ ++p + +++f+++++ ++++ l+ +l+ ++ +++ + s++ ++s ++ ++ df+ +s + +q+L 210s CUFF.38.1.p1 203 SYFQHVNWWWPTFVYNDFMYEFERLYAFGFHSNNAWLISFYSILALSSIRKRLGNSKTLAESLF------STAWVFVQKSDFFLTPS-IDKVQALIV 292 210s 8999999999999999999999666666666677777766777777778888887766666643......34777666667777777.********* PP 210s 210s Fungal_trans 100 lelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddlwesd 196 210s + y +s+ +l+ ++g a+ +a++l Lhr++s +e+ aes++R++w++++lDk i+l++G p+ ++d +i+++LP++ +l + 210s CUFF.38.1.p1 293 MTQYAAYLSSSSLCRTLCGQACLMAQQLNLHRKQSTDV------EPEK-AESWKRIFWMCYILDKNISLIFGTPSVFNDKDIDCNLPDSKYELLFGV 382 210s **********************************9988......7777.**************************99**********9998887777 PP 210s 210s Fungal_trans 197 daseetlvetk.........lsneeksrkiasfllaLkkilskiags 234 210s + + + n+ s+k ++++ a ki+ i+ + 210s CUFF.38.1.p1 383 QSGGDLIFVPTvsltiiqseIRNRLYSVKSPTQMAAREKIIIPIHQK 429 210s 77666666544667777777777777777777777766666666554 PP 210s 210s == domain 2 score: 1.2 bits; conditional E-value: 0.035 210s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpk 23 210s ++++fs+++ ++ ilh+ps +++ 210s CUFF.38.1.p1 471 MEVYFSYLNTLI-ILHRPSSSTE 492 210s 679******998.****997665 PP 210s 210s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 36.9 4.7 4.3e-13 1e-11 4 197 .. 151 329 .. 148 351 .. 0.75 210s 210s Alignments for each domain: 210s == domain 1 score: 36.9 bits; conditional E-value: 4.3e-13 210s Fungal_trans 4 ffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLlll 100 210s +f++fhp fp++h+ sf+++ + +l+++a+l++G + s + + s ++ + l + +++ w+ qs ll+ 210s CUFF.45.1.p1 151 YFEWFHPVFPFIHQASFNSEN-----VAASFLRSLVVIACLCTGIESDFSMALLFWDSGFHVL---------QLYL--QGDPERVKKAWVFQSRLLF 231 210s *********************.....4444444444555555555555555555544444433.........3333..3566667779********* PP 210s 210s Fungal_trans 101 elyektssdralher.....hhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddl 192 210s ++ ++ + ++ ++ v+ +r+ g + +v+ ++ + ++ e+ rR ++ ++l+ ++al+++ pp l+ ++++pLP ++ l 210s CUFF.45.1.p1 232 CTASLFEKT--ACFSgighvLLKDLVHESRTFGWTKLNWSVEGDTDISNLID-LECIRRSVFCLYILEWFLALIFNKPPSLSVLELQMPLPISSA-L 324 210s *99988775..55555445666666676777777666666676668888899.**************************99**************.9 PP 210s 210s Fungal_trans 193 wesdd 197 210s w+s + 210s CUFF.45.1.p1 325 WSSKE 329 210s 99875 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (267 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 210s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 4 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 210s # Mc/sec: 798.25 210s // 210s Query: GalKase_gal_bdg [M=49] 210s Accession: PF10509.8 210s Description: Galactokinase galactose-binding signature 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 13.3 0.0 2.6e-06 0.00024 12 44 .. 5 37 .. 2 41 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 13.3 bits; conditional E-value: 2.6e-06 210s EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEE CS 210s GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieldiy 44 210s +++s+PG + L GEH g l++A+ l+ y 210s CUFF.60.2.p2 5 LIVSSPGKTILFGEHAVVYGATALAAAVSLRSY 37 210s 799************************998866 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (49 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2048.15 210s // 210s Query: GDC-P [M=430] 210s Accession: PF02347.15 210s Description: Glycine cleavage system P-protein 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 665.5 0.0 1.7e-204 1.6e-202 2 430 .] 66 504 .. 65 504 .. 0.99 210s 2 ! 36.7 0.0 1.2e-13 1.2e-11 22 285 .. 529 810 .. 525 822 .. 0.77 210s 3 ? 0.7 0.0 0.01 0.96 332 373 .. 840 881 .. 836 926 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 665.5 bits; conditional E-value: 1.7e-204 210s HH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S-------............--HHHHHHHHHHHHTTB---EE--BTTB------HHHHHH CS 210s GDC-P 2 rhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleap............ksEeellaelekiasknkvvksfiGaGyydtilPaviqrn 86 210s rhigps++dq+++Le+lG+k++d+++++ +P+++++++++ ++ + +sE+e+++ +++a++nk++ksfiG+Gyy+++lPa+iqrn 210s CUFF.57.1.p1 66 RHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGsvnpneknppvnYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRN 162 210s 9******************************************9999************************************************** PP 210s 210s TTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEE CS 210s GDC-P 87 ilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqtlevlktrakglgieiv 183 210s +lenpewyt+YtPYqaEisqGrLe+++n+qt++adltGl+i+nasllDegtAa+EA++++++++kkk+k+++vdk+++p+tl+vl+tra+g+gi+i+ 210s CUFF.57.1.p1 163 VLENPEWYTQYTPYQAEISQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIYPNTLSVLRTRASGFGIKIE 259 210s ************************************************************************************************* PP 210s 210s EE-GGG--S-...S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGG CS 210s GDC-P 184 evdlteekvtdkekevagvlvqypnteGriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkekl 280 210s ++++t e +t+++k+v+g++vqyp+++G+i d+ +l+++a++ +++vv+a+dllaLt+lk+Pge+gaD++vGs+qrfG+P+gyGGPhagffA++e++ 210s CUFF.57.1.p1 260 LDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATARSFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEF 356 210s ************************************************************************************************* PP 210s 210s GGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSS CS 210s GDC-P 281 kRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffd 377 210s kRkiPGRl+G+skD+ +++a+rlalqtREqHirR+kAtsniCtaqaLlAn++a+ya+yhG++gl+eia+ri+++t++l+++l+++ ++ ++k++ffd 210s CUFF.57.1.p1 357 KRKIPGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGLQEIANRIYASTSFLKSALESSGYKIVNKSHFFD 453 210s ************************************************************************************************* PP 210s 210s EEEEE--TTTHHHHHHHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS 210s GDC-P 378 tllieveekaaekvlkkaekeglnlrkvelktvgialdEtvtkedieallkvl 430 210s tl+ieve +a+kvl+ka+++g+nlrkv++++vg++ldEtv+++di+al++++ 210s CUFF.57.1.p1 454 TLTIEVE--SADKVLAKALDHGYNLRKVDDSHVGLSLDETVCDKDIQALFSIF 504 210s ****999..889**************************************987 PP 210s 210s == domain 2 score: 36.7 bits; conditional E-value: 1.2e-13 210s SHHHHHHHHS-GGGB--S-------.....--HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG.G-HHHHHH CS 210s GDC-P 22 slddliekavPkeiklkkelkleap.....ksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE.isqGrLea 111 210s ++d+l ++P++ + +++l l++p +sE+el++ ++++ sk+ ++ + G ++l av + + np + ++ PY +E ++G + 210s CUFF.57.1.p1 529 TVDNLSICSLPENFR-RTTLYLQHPvfnryHSETELMRYIHHLQSKDLSlAHAMTPLGSCTMKLNAVTEMMPITNPLF-ANIHPYVPEeQAKGYRHV 623 210s 677888888899985.456667777777779****************987899999************9988999976.5678999963789***** PP 210s 210s HHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHH.HH-SSS.....--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-......... CS 210s GDC-P 112 llnfqtlvadltGldianasllDegtAaaEAvllaa.raskkk.....akkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd........ 194 210s + + q +++ +tG+d a + ++ Aa+E l++ ra ++ ++ ++ + h + a g+ ++ v++ +++ d 210s CUFF.57.1.p1 624 IEDLQLMLTTITGFDAA--CFQPNSGAAGEYTGLSViRAYQRSigqghRNICLIPVSAHGTN----PASAAMAGFTVIPVKCLNNGYLDmqdlkeka 714 210s **************975..6778888888877665412222221111134444444444333....3445566666666666666666666677777 PP 210s 210s ....S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG-- CS 210s GDC-P 195 ..kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiP 285 210s +++++a+ +v yp+t+G e+ +ke e ++++ v a++ a++ l g++gaD+ + + f +P g GGP +g + vk++l+ +P 210s CUFF.57.1.p1 715 skHADKLAAFMVTYPSTFGIFEPdVKEALEVIHEHGGQVYFdGANMNAMVGLCKAGDIGADVChLNLHKTFCIPHGGGGPGVGPICVKKHLADFLP 810 210s 768899**************99669*********99888763689999999***********84667889******************99988777 PP 210s 210s == domain 3 score: 0.7 bits; conditional E-value: 0.01 210s HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--S CS 210s GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkkleeelkkk 373 210s + y+ + G gl++ ++ + +++++ak l ++ + + ++k 210s CUFF.57.1.p1 840 SWAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNK 881 210s 567999*************************98755444443 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (430 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 210s # Mc/sec: 932.87 210s // 210s Query: GHMP_kinases_C [M=85] 210s Accession: PF08544.12 210s Description: GHMP kinases C terminal 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 25.9 0.0 1.1e-09 5e-08 8 66 .. 233 287 .. 221 298 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 25.9 bits; conditional E-value: 1.1e-09 210s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 210s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 210s CUFF.60.1.p2 233 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 287 210s 6678999********..899********************..*************9997 PP 210s 210s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 25.6 0.0 1.3e-09 6.2e-08 8 66 .. 284 338 .. 272 349 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 25.6 bits; conditional E-value: 1.3e-09 210s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 210s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 210s CUFF.60.2.p2 284 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 338 210s 6678999********..899********************..*************9997 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (85 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 729.22 210s // 210s Query: GHMP_kinases_N [M=66] 210s Accession: PF00288.25 210s Description: GHMP kinases N terminal domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 57.0 1.6 1.8e-19 8.7e-18 2 66 .] 75 152 .. 74 152 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 57.0 bits; conditional E-value: 1.8e-19 210s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 210s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 210s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 210s CUFF.60.1.p2 75 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 152 210s 799****************************877765543352257899999***********.************998 PP 210s 210s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? 0.1 0.1 0.11 5.2 19 40 .. 25 47 .. 22 57 .. 0.68 210s 2 ! 56.7 1.6 2.3e-19 1.1e-17 2 66 .] 126 203 .. 125 203 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 0.1 bits; conditional E-value: 0.11 210s HHHHHHHHHHHHHTTEHH.HHHH CS 210s GHMP_kinases_N 19 AlavalvaAlaallglsl.eeak 40 210s A a+a+++ l +++ l+ ++++ 210s CUFF.60.2.p2 25 ATALAAAVSLRSYCKLQTtNNNE 47 210s 77888888888999655323344 PP 210s 210s == domain 2 score: 56.7 bits; conditional E-value: 2.3e-19 210s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 210s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 210s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 210s CUFF.60.2.p2 126 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 203 210s 799****************************877765543352257899999***********.************998 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (66 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1921.20 210s // 210s Query: GLEYA [M=91] 210s Accession: PF10528.8 210s Description: GLEYA domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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 210s 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 210s 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- 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 65.9 1.8 7.1e-22 1.7e-20 2 89 .. 256 345 .. 255 347 .. 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: 65.9 bits; conditional E-value: 7.1e-22 210s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEE CS 210s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyangggagslnfsv 89 210s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang g+++f + 210s CUFF.31.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANGAYIGGFDFAF 345 210s 789***********************************************9666899999999************************987 PP 210s 210s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -3.6 0.0 3.6 85 70 84 .. 13 27 .. 3 33 .. 0.60 210s 2 ! 65.2 2.1 1.2e-21 2.9e-20 2 90 .. 157 253 .. 156 254 .. 0.92 210s 210s Alignments for each domain: 210s == domain 1 score: -3.6 bits; conditional E-value: 3.6 210s EEEEEEEEE-S-.EE CS 210s GLEYA 70 yPiRivyangggags 84 210s +P+ +a++ g+ s 210s CUFF.11.1.p1 13 LPFTTTLAQASGTVS 27 210s 577777777766555 PP 210s 210s == domain 2 score: 65.2 bits; conditional E-value: 1.2e-21 210s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.......TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEEE CS 210s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.......sgssesktvt.vtltaGtyyPiRivyangggagslnfsvt 90 210s +++++ +++ p+t tYt+ ++n+Dd+++ w+GdkA+s+w+++n d+++ + g+ + +++t + +G+++P+R+v+ang g+++f +t 210s CUFF.11.1.p1 157 VIVYQFFLRIPETDTYTLVVNNVDDVFFGWFGDKAISGWSNNNFDAYSYWhespnmgLGTVGMGNFTvGNYPEGYFLPVRFVVANGAYIGGFDFYFT 253 210s 689***********************************************9999888444677777757899**********************998 PP 210s 210s >> CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 59.6 0.7 6.9e-20 1.6e-18 2 79 .. 256 335 .] 255 335 .] 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: 59.6 bits; conditional E-value: 6.9e-20 210s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 210s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 210s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 210s CUFF.30.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 335 210s 789***********************************************9666899999999***************96 PP 210s 210s >> CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -3.0 0.0 2.3 55 59 86 .. 20 45 .. 14 50 .. 0.50 210s 2 ? -2.0 0.1 1.1 26 75 75 .. 66 66 .. 31 96 .. 0.59 210s 3 ! 60.3 0.7 4e-20 9.4e-19 2 79 .. 170 249 .] 169 249 .] 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: -3.0 bits; conditional E-value: 2.3 210s EEEEEE-TT-BEEEEEEEEE-S-.EEEE CS 210s GLEYA 59 tvtvtltaGtyyPiRivyangggagsln 86 210s + +v+++ G+ + +y g ++++ 210s CUFF.30.2.p1 20 SSSVSVETGSCVRYTTIYSSGS--SEFT 45 210s 4455666666554444444433..3444 PP 210s 210s == domain 2 score: -2.0 bits; conditional E-value: 1.1 210s E CS 210s GLEYA 75 v 75 210s 210s CUFF.30.2.p1 66 H 66 210s 1 PP 210s 210s == domain 3 score: 60.3 bits; conditional E-value: 4e-20 210s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 210s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 210s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 210s CUFF.30.2.p1 170 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 249 210s 789***********************************************9666899999999***************96 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (91 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 210s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 4 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1033.13 210s // 210s Query: Glyco_hydro_cc [M=239] 210s Accession: PF11790.7 210s Description: Glycosyl hydrolase catalytic core 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 199.1 0.0 4.5e-63 4.3e-61 1 239 [] 298 528 .. 298 528 .. 0.92 210s 210s Alignments for each domain: 210s == domain 1 score: 199.1 bits; conditional E-value: 4.5e-63 210s Glyco_hydro_cc 1 GlaynadasddkllsaksskisWyYnwsskpsselssaalefvPmlwgaksadtdalanvksaakenskylLgFNePDlks.qsnmspeeAaklw 94 210s Gla++ +++ ++ + ++ i+WyYnw+s++s+ +ss e+v ++a+s + +++s+ ++ +++gFNePDl+ + +++++Aa+++ 210s CUFF.59.1.p1 298 GLAWIPGTDLGYSDNFVNKGINWYYNWGSYSSGLSSSF--EYVLNQHDANSLS-----SASSV-FTGGATVIGFNEPDLSAaGNPIDAATAASYY 384 210s 78999888888888999**************9988885..********99865.....44444.55579**********8889************ PP 210s 210s Glyco_hydro_cc 95 kqliqplre..kgvklvsPavaatnseegleWldeFleacskdckvdflavHwYkgdfeelkehieelheaynkpiWvTEfalqs..esgdasqe 185 210s q+++plre +l+sPa+++ g +Wl+eF++acs dck+df+a+HwY+ df++l+++i++l ++y++piW+TEfa+++ +s+ s + 210s CUFF.59.1.p1 385 LQYLTPLREsgAIGYLGSPAISN--V--GEDWLSEFMSACS-DCKIDFIACHWYGIDFSNLQDYINSL-ANYGLPIWLTEFACTNwdDSNLPSLD 473 210s ********6355669******33..3..669**********.************999***********.9***************999999**** PP 210s 210s Glyco_hydro_cc 186 etkeflnevlawldsqeyVeryawfg.frsevsnvgannaLldenGeltelgsaY 239 210s e+k++++++l +ld + +Very+wf+ +++ ++vg+nnaL++++G+l+e+g++Y 210s CUFF.59.1.p1 474 EVKTLMTSALGFLDGHGSVERYSWFApATELGAGVGNNNALISSSGGLSEVGEIY 528 210s *****************************************************99 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (239 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1807.94 210s // 210s Query: Glyco_tranf_2_3 [M=230] 210s Accession: PF13641.5 210s Description: Glycosyltransferase like family 2 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 210s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 210s 210s Alignments for each domain: 210s == domain 1 score: -1.4 bits; conditional E-value: 0.19 210s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 210s + ++ D+ t ++P+tl++l++ 210s CUFF.60.1.p1 237 VCIISDGRTKIHPRTLAYLAA 257 210s 45688999*******999876 PP 210s 210s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 210s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 210s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 210s CUFF.60.1.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 210s 5667889999********************9999999999999888766666666668888********************8566779****** PP 210s 210s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 210s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 210s CUFF.60.1.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 210s ******999****************9984466699************9988899*****************************86 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 210s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 210s 210s Alignments for each domain: 210s == domain 1 score: -1.4 bits; conditional E-value: 0.19 210s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 210s + ++ D+ t ++P+tl++l++ 210s CUFF.60.2.p1 237 VCIISDGRTKIHPRTLAYLAA 257 210s 45688999*******999876 PP 210s 210s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 210s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 210s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 210s CUFF.60.2.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 210s 5667889999********************9999999999999888766666666668888********************8566779****** PP 210s 210s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 210s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 210s CUFF.60.2.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 210s ******999****************9984466699************9988899*****************************86 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (230 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 737.95 210s // 210s Query: Glyco_transf_34 [M=239] 210s Accession: PF05637.11 210s Description: galactosyl transferase GMA12/MNN10 family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 283.8 0.3 1.4e-88 6.5e-87 2 238 .. 98 334 .. 97 335 .. 0.97 210s 210s Alignments for each domain: 210s == domain 1 score: 283.8 bits; conditional E-value: 1.4e-88 210s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 210s +++ivlllvs+ ++++ ++ +++++++i+NrvdY++k++y+++y++v+ l ++vW+k+pa+ ++mkkyP+aewiW+lDqdA+i+n++ls 210s CUFF.51.1.p2 98 SQNIVLLLVSDGHTSY--NNGANTFEEAIQNRVDYSTKQNYNFEYVNVTGLPI---PAVWSKMPAVLQTMKKYPKAEWIWLLDQDAIITNTHLS 186 210s 789***********97..455559***************************99...************************************** PP 210s 210s Glyco_transf_34 96 leehvlkperLeelllkntpv........vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesd 181 210s l++++lkpe+L+++l++nt + +lr+++++++ +d+e+ +viisqd+nglnags+l+rns +++l+lD+w+dp+++e++ka ++ 210s CUFF.51.1.p2 187 LQDSFLKPENLQKTLITNTILtkrpinanGDLRYTPSNYSLKDIENLMVIISQDHNGLNAGSILFRNSPATALFLDIWTDPVVAECAKA---NN 277 210s *******************999*****9999**********************************************************...** PP 210s 210s Glyco_transf_34 182 eqsaleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankc 238 210s eq++l+yl++kh++++s vgl++q+ in+++eg++++++++gdlv+hfagC+v+n+c 210s CUFF.51.1.p2 278 EQDMLGYLISKHSQLASLVGLIPQRKINAFHEGPENMEWQKGDLVIHFAGCWVENRC 334 210s ********************************************************9 PP 210s 210s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 281.4 0.0 7.1e-88 3.4e-86 2 239 .] 84 318 .. 83 318 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 281.4 bits; conditional E-value: 7.1e-88 210s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 210s ++eiv+ll+s+ + s +++ll++++kNr++Ya++++y++++++vs+l + vW k+pai ++m+kyP+a+wiWwlDqdAlimn++ls 210s CUFF.52.1.p2 84 SHEIVMLLASDGNVG---SFESNLLDDCFKNRIEYAKLQNYNFEFVNVSSLVV---PPVWGKMPAILQTMRKYPSAKWIWWLDQDALIMNKNLS 171 210s 79**********997...58999***************************999...************************************** PP 210s 210s Glyco_transf_34 96 leehvlkperLeelllkntpv......vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesdeq 183 210s l+e +l+p +L+++ll+++p+ ++ r ++ +++e++e+++++isqd+nglnagsfl+rns+ +ll+Dl++dp+l++++++ ++eq 210s CUFF.52.1.p2 172 LQELFLSPAMLQKSLLREQPIinsfgeDNFRITPAAYSKEMIEQIQFLISQDHNGLNAGSFLVRNSRSIALLMDLLTDPSLADAGVV---RHEQ 262 210s **************************999**********************************************************...**** PP 210s 210s Glyco_transf_34 184 saleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankca 239 210s ++++y+++kh++v+s+vg+++q++in+++eg+++++++egdl++hfagC+v+nkca 210s CUFF.52.1.p2 263 DLIGYFIQKHSQVASMVGILPQRFINAFHEGPPTMQWQEGDLALHFAGCWVENKCA 318 210s ******************************************************96 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (239 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2478.54 210s // 210s Query: Glyco_transf_8 [M=256] 210s Accession: PF01501.19 210s Description: Glycosyl transferase family 8 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 37.5 1.6 1.1e-13 1e-11 9 221 .. 84 321 .. 77 336 .. 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 37.5 bits; conditional E-value: 1.1e-13 210s Glyco_transf_8 9 nYllgasvviksllknakepawfalnfhiltaeievenleklnklassykevlellesdkksledfesklklrspkylsllnylRlylpelfpkl 103 210s Y ++ v+i+ l + +++ +++ + ++++ ++e+++k + s++ ++++ sd+ ++++++++ ++ + ++ +l+++e ++ 210s CUFF.51.1.p1 84 YYFNATRVLIHRLKYHPTTKSKYPIHIL-ALRGVDEWKIERFRKDGASVIVIDPIASSDIVY----DTSSFSQEISARYEQMFSKLRIFEQ-IQF 172 210s 5677778888888888886556666666.7899*******************9999998843....3578899999999999*********.9** PP 210s 210s Glyco_transf_8 104 dkilylDaDvvvqgdlseLwdldlk.gkvlaaved............................krfkkylnksepliaenfkp..eacyFnaGvl 167 210s dki +D+D+++ +++++++d++ ++++ + + + + l + + +++p + yFnaG++ 210s CUFF.51.1.p1 173 DKICVIDSDILIMKNIDDIFDTPYMyQQINTLNYTrlpsytkpdddtvyhfnedfkeygasrsEFYPYLLAAVSDRGEHHSIPpeDTPYFNAGLM 267 210s **********************9997888888888*************************8863333333444444444444411567******* PP 210s 210s Glyco_transf_8 168 lfdldewrkenitetlikwlnlnekrtllklgdqdilnivfk....gkvkeldkkynv 221 210s l+ + e + + i + + ++e+ k ++q +ln++f + +ld++yn 210s CUFF.51.1.p1 268 LIRPSELHFNRILKI-GRFPYMYEN---AKMMEQSLLNLAFSldgwFPWTRLDPYYNG 321 210s *******99988764.455566666...89***********86655789999999995 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (256 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1310.02 210s // 210s Query: Glyco_trans_2_3 [M=197] 210s Accession: PF13632.5 210s Description: Glycosyl transferase family group 2 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 210s 210s Alignments for each domain: 210s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 210s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 210s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 210s CUFF.60.1.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 210s 799**************999*988************97765333347788888888**********************************8888 PP 210s 210s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 210s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 210s CUFF.60.1.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 210s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 210s 210s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 210s +r++ +++++s ++ +++++f+++ + ++++l 210s CUFF.60.1.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 210s 3333313445555555555555566665544333321....22222 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 210s 210s Alignments for each domain: 210s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 210s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 210s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 210s CUFF.60.2.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 210s 799**************999*988************97765333347788888888**********************************8888 PP 210s 210s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 210s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 210s CUFF.60.2.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 210s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 210s 210s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 210s +r++ +++++s ++ +++++f+++ + ++++l 210s CUFF.60.2.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 210s 3333313445555555555555566665544333321....22222 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (197 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 210s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 210s # Mc/sec: 404.29 210s // 210s Query: GNAT_acetyltr_2 [M=227] 210s Accession: PF13718.5 210s Description: GNAT acetyltransferase 2 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.4 0.0 8.6e-06 0.00041 94 131 .. 72 109 .. 67 128 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 12.4 bits; conditional E-value: 8.6e-06 210s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 210s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 210s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 210s 679******************98766666666665554 PP 210s 210s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.3 0.0 9e-06 0.00043 94 131 .. 72 109 .. 67 130 .. 0.79 210s 210s Alignments for each domain: 210s == domain 1 score: 12.3 bits; conditional E-value: 9e-06 210s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 210s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 210s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 210s 679******************98766666666665554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (227 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3322.69 210s // 210s Query: His_Phos_1 [M=194] 210s Accession: PF00300.21 210s Description: Histidine phosphatase superfamily (branch 1) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 77.3 0.0 7e-26 6.6e-24 1 181 [. 9 203 .. 9 215 .. 0.86 210s 210s Alignments for each domain: 210s == domain 1 score: 77.3 bits; conditional E-value: 7e-26 210s EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT.......--EEE-GGGS----GGGT. CS 210s His_Phos_1 1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg.......lpveldegLrEidfGdwe. 86 210s +yL+RHG+ ++n+ d+ Lt eG+eq eala+ l++ +pid i++Sp++R+ qT+e+++++ +pv + + ++E+ + ++ 210s CUFF.48.1.p2 9 VYLIRHGQAQHNVGPDeDHNIRDPVLTSEGIEQCEALAKELESkqIPIDGIVCSPMRRTLQTMEIALKKYLaeggpdkVPVYISPFFQEVGHLPCDi 105 210s 69*********99877778889999****************9988999999***************99876788999************99999999 PP 210s 210s T-B.HHHHHH..HSHHHHHHHHH-GGG-B....S-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH.T--GGGGG.GB---TT-EE CS 210s His_Phos_1 87 glttaeiaeeypeeleawlrdpadvrppg....gEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll.glpleelr.rleldnaslt 177 210s gl+ +++++ yp++ + +d p++ + a R ++ale laa +++ ++v++H ++ir ll++++ ++++l+ +l ++n++ 210s CUFF.48.1.p2 106 GLELDKLNKLYPKYNFQSCQDGIY--PEKrdiyASDVTISAIRSKEALEYLAALPQQQ-IAVITHSAFIRFLLKKMVkAADIDFLPpQLSFKNCEFR 199 210s **********99987777666653..3334587888888899***********99987.*****************966777766546777999887 PP 210s 210s EEEE CS 210s His_Phos_1 178 vley 181 210s + ++ 210s CUFF.48.1.p2 200 IYDL 203 210s 7765 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (194 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4427.87 210s // 210s Query: Hpt [M=85] 210s Accession: PF01627.22 210s Description: Hpt domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.9 0.3 1.1e-05 0.0011 32 64 .. 217 248 .. 205 267 .. 0.74 210s 210s Alignments for each domain: 210s == domain 1 score: 11.9 bits; conditional E-value: 1.1e-05 210s HHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTS CS 210s Hpt 32 aaHtLKGsagmlGltelaelahelEdlldrage 64 210s ++H+++Gsa+ lGl+ l ++a+ ++++d a 210s CUFF.19.1.p1 217 LVHKIAGSAAALGLD-LHQVAQVAQSVIDNAAT 248 210s 79***********64.66666666666654444 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (85 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2822.95 210s // 210s Query: HTH_29 [M=63] 210s Accession: PF13551.5 210s Description: Winged helix-turn helix 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 5.3 0.0 0.0011 0.1 16 35 .. 122 141 .. 111 145 .. 0.88 210s 2 ! 4.0 0.0 0.0027 0.26 10 30 .. 278 298 .. 271 301 .. 0.83 210s 210s Alignments for each domain: 210s == domain 1 score: 5.3 bits; conditional E-value: 0.0011 210s HTH_29 16 sqiAkllglsrrtvyrwlkr 35 210s ++A ++glsr+++++++++ 210s CUFF.17.1.p1 122 PELANQCGLSRKHIFDAVED 141 210s 589************99986 PP 210s 210s == domain 2 score: 4.0 bits; conditional E-value: 0.0027 210s HTH_29 10 eGvstvsqiAkllglsrrtvy 30 210s +s+v ++Ak +++s+ t 210s CUFF.17.1.p1 278 AILSRVEELAKKYNVSMATLA 298 210s 456799************986 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (63 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2523.11 210s // 210s Query: HTH_psq [M=45] 210s Accession: PF05225.15 210s Description: helix-turn-helix, Psq domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 3.8 0.0 0.0026 0.25 24 33 .. 81 90 .. 80 93 .. 0.91 210s 2 ? -1.9 0.0 0.16 16 7 16 .. 169 179 .. 165 180 .. 0.80 210s 3 ! 4.1 0.0 0.0021 0.2 21 33 .. 285 297 .. 281 304 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 3.8 bits; conditional E-value: 0.0026 210s HTH_psq 24 rkYgiPrsTL 33 210s rkY+iPrs++ 210s CUFF.17.1.p1 81 RKYEIPRSSI 90 210s 79******98 PP 210s 210s == domain 2 score: -1.9 bits; conditional E-value: 0.16 210s HTH_psq 7 aAleavv.nGk 16 210s +Al++vv +Gk 210s CUFF.17.1.p1 169 RALNDVVeSGK 179 210s 8******8887 PP 210s 210s == domain 3 score: 4.1 bits; conditional E-value: 0.0021 210s HTH_psq 21 kAArkYgiPrsTL 33 210s ++A+kY+++ TL 210s CUFF.17.1.p1 285 ELAKKYNVSMATL 297 210s 79********999 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (45 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2083.74 210s // 210s Query: Hydantoinase_A [M=291] 210s Accession: PF01968.17 210s Description: Hydantoinase/oxoprolinase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -3.5 0.2 0.54 26 82 95 .. 5 18 .. 4 22 .. 0.87 210s 2 ! 349.6 0.2 1.4e-108 6.5e-107 1 290 [. 239 540 .. 239 541 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: -3.5 bits; conditional E-value: 0.54 210s Hydantoinase_A 82 ItfDmGGTstDvsl 95 210s I +D GGT tD+++ 210s CUFF.44.1.p1 5 IHIDRGGTFTDAIA 18 210s 889********875 PP 210s 210s == domain 2 score: 349.6 bits; conditional E-value: 1.4e-108 210s Hydantoinase_A 1 rtetavvnAylspilreylesvekslekrgak......arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaat.sklagekkvItfDmGG 88 210s r+++a+ +Aylsp++r+yl ++++ + + ++ r+ +mqsdGglv+++++++ ++ilSGPa+Gvvg+a t ++++ + +vI+fDmGG 210s CUFF.44.1.p1 239 RATSATADAYLSPVVRRYLAGFQSGFLHGLKTkdnskgVRCEFMQSDGGLVDVNKFSGL--HAILSGPAGGVVGFALTsYDEDVKIPVIGFDMGG 331 210s 7889*********************9997776999999********************9..*****************77888888********* PP 210s 210s Hydantoinase_A 89 TstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls. 182 210s TstDvs++ g++e+++et++agv++++p+ldi+tv+agGgs+l ++++g + vgpesaga+pgp+cyrkGg ltvTDanl+LGrl pe+f++ 210s CUFF.44.1.p1 332 TSTDVSRYG-GSYEHVFETTTAGVTIQSPQLDINTVAAGGGSRL-FWKNGLFVVGPESAGAHPGPVCYRKGG-YLTVTDANLLLGRLLPESFPKi 423 210s *********.**********************************.***************************.********************** PP 210s 210s Hydantoinase_A 183 .gpdgdqkldvelarrafeelakelnlk........veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkv 268 210s gp++d++ldve +r++fe+l++e+n + ++evA g++++a+e+ma+++r l++++g+d++ + l++fGGaG+qh+aa+a++lg+++v 210s CUFF.44.1.p1 424 fGPNEDESLDVESTRKEFEKLTAEINSGlekerqmtADEVAFGFIKIANETMARPIRALTEAKGHDISIHRLTSFGGAGGQHCAAIAKSLGITQV 518 210s *********************************************************************************************** PP 210s 210s Hydantoinase_A 269 ivppyagvlsalGmalAdvree 290 210s +v++y+++lsa+GmalAdv +e 210s CUFF.44.1.p1 519 LVHKYSSILSAYGMALADVVSE 540 210s ******************9876 PP 210s 210s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 296.2 0.0 2.7e-92 1.3e-90 44 290 .. 1 252 [. 1 253 [. 0.97 210s 210s Alignments for each domain: 210s == domain 1 score: 296.2 bits; conditional E-value: 2.7e-92 210s Hydantoinase_A 44 lvsadearkkpvetilSGPaaGvvgaaat..sklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvde 136 210s lv++d+++ +i+SGPaaG vg+a+t + ++++++I+fDmGGTstDvs+++ g++e+ +e +i g+ +++p+ldi+tv+agGgs+l +++ 210s CUFF.42.1.p1 1 LVDIDNFTAI--SAIMSGPAAGTVGFAKTssLHADDKTPAIGFDMGGTSTDVSRYD-GKFEHIYEANIFGLYIQSPQLDIQTVAAGGGSRL-FWR 91 210s 6789999987..*****************5445567788*****************.**********************************.999 PP 210s 210s Hydantoinase_A 137 ggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvave 223 210s ++ ++vgpesaga pgpacy +Gg +ltvTDan++LGr+ p++f++ gp+++++++++++ ++f+el + +n + +ee+A+g+++va+e 210s CUFF.42.1.p1 92 NQLFSVGPESAGAFPGPACYLNGG-PLTVTDANVLLGRIIPDFFPKifGPKENESMNKDIVIEKFSELRDIINIDiekektIEEIAMGFIQVANE 185 210s ************************.********************************************************************** PP 210s 210s Hydantoinase_A 224 nmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290 210s +m++++rkl+++rgld + ++l+vfGGaG+qha+a+a l+++k+i+++y++vlsa+G+alA+v++e 210s CUFF.42.1.p1 186 TMCRPIRKLTESRGLDLSAHHLAVFGGAGGQHACAIASLLNIEKIIIHKYSSVLSAYGLALAHVTHE 252 210s ****************************************************************998 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (291 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1352.64 210s // 210s Query: Hydantoinase_B [M=516] 210s Accession: PF02538.13 210s Description: Hydantoinase B/oxoprolinase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 708.2 0.1 5.6e-217 2.7e-215 1 516 [] 749 1285 .. 749 1285 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 708.2 bits; conditional E-value: 5.6e-217 210s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyagg 93 210s Dpi l+vf +r+m++ae+mgr+lq+t++S+n+kerlD+scalfda+g+lva+aph+pvhlgsms++v+++++ +eg+lkpGDvl+tN+P +gg 210s CUFF.44.1.p1 749 DPIYLSVFGSRFMAVAEQMGRALQKTSVSTNVKERLDYSCALFDAKGNLVANAPHMPVHLGSMSTCVRTQAKIHEGKLKPGDVLVTNHPSYGG 841 210s 9**********************************************************************99999***************** PP 210s 210s Hydantoinase_B 94 tHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........Rtpednl 176 210s tHlpDit+itP f +e++f+va+raHhaDiGGi pGsmp++++e+ eEG+ i++ klv +g+ +ee++++ll +++ R+++dnl 210s CUFF.44.1.p1 842 THLPDITTITPHFEGDEIMFYVAARAHHADIGGILPGSMPSSSKELSEEGATIKSEKLVVDGVfQEERMIDLLYNEPakveggsgsRCLRDNL 934 210s *************9889*********************************************************999**************** PP 210s 210s Hydantoinase_B 177 gDlkAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgts 263 210s +DlkAq++anq+g+++++ li+eyG++ v ++m++i++nae avr++l +++ +++ aed++ddg++i++++tid+++ a++Dftgt 210s CUFF.44.1.p1 935 NDLKAQVSANQKGINLITSLIKEYGKNSVLRYMKAIQENAESAVRQLLLGVRErflgEDLYAEDHMDDGSKICLRITIDEENgdAIFDFTGTT 1027 210s ************************************************7777777778899*******************9999********* PP 210s 210s Hydantoinase_B 264 pqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtm 356 210s ++++gniNap+avt+sa+iy+lr+l++e+iplN+Gcl pi+v++p++++l+pse+aavvggnv+tsqr++d++lka++ ++Aasqg++ 210s CUFF.44.1.p1 1028 EEIYGNINAPEAVTYSAIIYCLRVLISENIPLNQGCLLPIKVIIPDNCFLKPSETAAVVGGNVLTSQRITDTILKAFQ------ACAASQGDT 1114 210s ******************************************************************************......********* PP 210s 210s Hydantoinase_B 357 nnltf..ggvderg...geffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreief 444 210s nnltf gg+d+++ + fgyyeti+gGsGA g dG+s+vh+hmtntr+td E+lErryPv++++f +r++sgGaGky+GGdGv+r+ief 210s CUFF.44.1.p1 1115 NNLTFgiGGKDPETgevKPGFGYYETICGGSGAIDGLDGTSGVHTHMTNTRITDLEVLERRYPVILRKFIIRENSGGAGKYKGGDGVIRDIEF 1207 210s ****94446677669998889************************************************************************ PP 210s 210s Hydantoinase_B 445 lepevtvsilserrvfapwGlaGGepGargrvvlnllvr..........greenlggkatvelkagdvlvietpGGGGyGdp 516 210s + p vt+silserr ++p+G++GG+++++g+ n+++r r++n+ggk+t++++agd +vi+tpGGGGyG p 210s CUFF.44.1.p1 1208 RIP-VTLSILSERRAYHPYGMKGGKDAECGK---NIWIRkdilpsgeqrVRQINVGGKNTCHMQAGDHIVIMTPGGGGYGPP 1285 210s **9.***************************...88888899999998899*****************************86 PP 210s 210s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 701.5 0.3 5.9e-215 2.8e-213 1 515 [. 459 986 .. 459 987 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 701.5 bits; conditional E-value: 5.9e-215 210s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyaggtH 95 210s 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 210s CUFF.42.1.p1 459 DPITMTIFANRFMSISEQMGQVLQKTAVSVNVKERLDYSCALFSPDGGLVANAPHVPAMLGSMQTAVKWQHNYWKGKLVPGDVLLSNHPIAGGVH 553 210s 9********************************************************************************************** PP 210s 210s Hydantoinase_B 96 lpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........RtpednlgDl 179 210s lpD+tv+tPvf +++ ++f++a+r+H++D+GGitpGsmp++++ i+eEG++i+++k+v++g+ +e+++++ll +++ Rt++dn++D+ 210s CUFF.42.1.p1 554 LPDLTVVTPVFDNNKdIIFYCAARGHMVDVGGITPGSMPSNSKAIYEEGAAIKTFKVVKAGTfDEKGLTQLLFDEPakypdcsgsRTLRDNISDV 648 210s ***********98879******************************************************************************* PP 210s 210s Hydantoinase_B 180 kAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgtspqvkg 268 210s kA+++a+++g++ +++l+ eyGl+ v++ m i++ ae+avr++l++++ + ++a dy+ddg+p++++v+id+++ a++Df+gt+p+v+g 210s CUFF.42.1.p1 649 KAMLSACHRGRSMVEKLVVEYGLDIVQRSMYGIQAAAEKAVRDVLKAFSVqnsqKPLKAIDYMDDGTPLQLEVKIDPETgdAVFDFEGTGPEVYG 743 210s *********************************************9877766777899********************99*************** PP 210s 210s Hydantoinase_B 269 niNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfgg 363 210s n+Nap a+t+s viy+lr+++++diplNeGcl+pie+++p+ ++lnpse+aavvggnv+tsqr++dv+lka++ ++Aasqg+mnnltfg 210s CUFF.42.1.p1 744 NWNAPIAITYSSVIYCLRSIINQDIPLNEGCLKPIEIRIPPSCFLNPSETAAVVGGNVLTSQRITDVILKAFS------ICAASQGCMNNLTFGY 832 210s *************************************************************************......***************7 PP 210s 210s Hydantoinase_B 364 vderggeffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserr 458 210s e+g+e f++yetiagG+GA+p+++G+s+vh+hmtntr+td+E++Err Pv+++rf lr++sgG+G+y+GGdGv+r++ef+++ +++silserr 210s CUFF.42.1.p1 833 DGENGEEGFAMYETIAGGAGAGPTWNGTSGVHTHMTNTRITDPEVVERRAPVILRRFCLRENSGGKGEYHGGDGVIRHFEFRRS-MHCSILSERR 926 210s 777779999**************************************************************************7.********** PP 210s 210s Hydantoinase_B 459 vfapwGlaGGepGargrvvlnllvr......greenlggkatvelkagdvlvietpGGGGyGd 515 210s + ap+G++GGe+Ga+g n+++ r +nlggk++v + +gd +vietpGGGGyG 210s CUFF.42.1.p1 927 SRAPYGMNGGEDGAMGV---NTWIDcsnpdfPRYVNLGGKNHVLMGKGDHIVIETPGGGGYGA 986 210s *****************...99999999999*******************************6 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (516 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 210s # Mc/sec: 1000.60 210s // 210s Query: Hydant_A_N [M=178] 210s Accession: PF05378.12 210s Description: Hydantoinase/oxoprolinase N-terminal region 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 210.0 0.0 1.1e-66 1.1e-64 1 178 [] 4 220 .. 4 220 .. 0.98 210s 2 ! 2.4 0.6 0.0062 0.59 2 14 .. 325 337 .. 324 355 .. 0.82 210s 210s Alignments for each domain: 210s == domain 1 score: 210.0 bits; conditional E-value: 1.1e-66 210s Hydant_A_N 1 rigIDvGGTfTDavaldeke.eevavlKllst.....pdavaegirealeevleesipr.....tskidvvrmGTTvatNallerkgervaLittkg 86 210s +i+ID+GGTfTDa+a+ ++e + +v+Klls+ +da +e++r++le v+++sipr ts+i+++r+GTTvatNallerkger+a+ittkg 210s CUFF.44.1.p1 4 KIHIDRGGTFTDAIATFADEsRPPIVIKLLSEdpsnyKDASIEAVRRILEIVQGKSIPRtekldTSCINHLRCGTTVATNALLERKGERCAFITTKG 100 210s 699************998777999************************************************************************* PP 210s 210s Hydant_A_N 87 frdlleigrqnrpdlfelrikkplvlyeevvevdervead............................gevlkpldeeevrealkalkaagvesiav 155 210s f+d l ig+q+rp++fel i++p+vly++v+evderv+++ ++++k++d++++r++l+al+++g++siav 210s CUFF.44.1.p1 101 FKDGLLIGNQSRPNIFELGIRRPEVLYSKVIEVDERVTLEdyvedpmkvkttidgsdpslvvgrsgevVRIMKKVDCDALRKDLQALYDEGFTSIAV 197 210s ***************************************99******************************************************** PP 210s 210s Hydant_A_N 156 vllhSylnpehElrvaeiareig 178 210s +l+hS+++p+hEl v++ia+e+g 210s CUFF.44.1.p1 198 CLAHSFTFPDHELLVGKIAEEVG 220 210s ********************975 PP 210s 210s == domain 2 score: 2.4 bits; conditional E-value: 0.0062 210s Hydant_A_N 2 igIDvGGTfTDav 14 210s ig D+GGT TD+ 210s CUFF.44.1.p1 325 IGFDMGGTSTDVS 337 210s 899********96 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (178 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1882.02 210s // 210s Query: IBR [M=62] 210s Accession: PF01485.20 210s Description: IBR domain, a half RING-finger domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.8 2.4 1.2e-05 0.0012 10 51 .. 569 611 .. 561 613 .. 0.71 210s 210s Alignments for each domain: 210s == domain 1 score: 11.8 bits; conditional E-value: 1.2e-05 210s IBR 10 kslesdpnlkwCprpdCeaiiekseg...cksvtCskCgfefCfn 51 210s ++ ++++++ C C i ++ e ++ +Cs+C +e+C++ 210s CUFF.12.1.p1 569 TTQNNNESFAVCL--ACAIIQRSLERkklSTPTQCSSCFQEYCWD 611 210s 33455777999*9..9997776555544445578**********6 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (62 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1918.65 210s // 210s Query: Lung_7-TM_R [M=295] 210s Accession: PF06814.12 210s Description: Lung seven transmembrane receptor 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 24.4 18.7 8.4e-10 8e-08 59 258 .. 80 270 .. 26 288 .. 0.83 210s 210s Alignments for each domain: 210s == domain 1 score: 24.4 bits; conditional E-value: 8.4e-10 210s Lung_7-TM_R 59 vllgilWlfilakykkdilkiqkliaavivlkmlelaf.vyieYatinskGssievlavlasilsalkktlsrlliliislGygivkpkLgdllkkvl 155 210s +l+ W++ ++ + k i++ qk+i + i+l +l++ + ie ++++s+ + ++ +++i+ l+ + rl ++ +lG+gi ++ + k l 210s CUFF.6.1.p1 80 LLFLSYWIWTCLHFSKIIFPAQKVICLYIFLFALNQTLqECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRT-----VPKYL 172 210s 466778*******************9999887776655167899999**************************************865.....66666 PP 210s 210s Lung_7-TM_R 156 llglllfvla.evlelvresseesessakllkvllfliplalldlffvvwifrsLqktlrdlklkrnlvklklYrkftvvlvisvvasviivlvekil 252 210s ++ ++ +v+a + + + ++ ++++ +i+ + ++ v+++ +L k + + n k++ +r+ +++ ++ + as + ++++i+ 210s CUFF.6.1.p1 173 MIKGISIVIAlCSVYWISLYKDVYVV-----SEIFDMIQYEVS-PAIWVYSICHLLKQCTSVTTYENASKARFFRRMLNAFIFIFCASPMLHYLSNII 264 210s 66555544441455555555444444.....689999999666.578888999********************************************9 PP 210s 210s Lung_7-TM_R 253 lktvds 258 210s + ++d+ 210s CUFF.6.1.p1 265 FGNFDY 270 210s 988775 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (295 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1468.89 210s // 210s Query: malic [M=182] 210s Accession: PF00390.18 210s Description: Malic enzyme, N-terminal domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 65.7 0.0 2.5e-22 2.4e-20 3 76 .. 32 108 .. 30 110 .. 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: 65.7 bits; conditional E-value: 2.5e-22 210s TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGET..CHHHHHTTSS..SS..EEEEE-SS CS 210s malic 3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdke..kikeilknlp.eedvkvivvtdge 76 210s +n+tlfy+l++++l e++pi+YtPt g+a++++s++yr+++g+yl+i++++ ik++l+++ +++v++i++td+e 210s CUFF.1.1.p1 32 TNQTLFYALISQHLIEMIPIIYTPTEGDAIKQFSDIYRYPEGCYLDIDHSDlsYIKQQLSEFGkSDSVEYIIITDSE 108 210s 799*******************************************99988779********97899********97 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (182 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 5153.36 210s // 210s Query: Mannosyl_trans3 [M=275] 210s Accession: PF11051.7 210s Description: Mannosyltransferase putative 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.4 1.2 4.1e-06 0.00039 92 143 .. 171 223 .. 85 298 .. 0.70 210s 210s Alignments for each domain: 210s == domain 1 score: 12.4 bits; conditional E-value: 4.1e-06 210s Mannosyl_trans3 92 sFeevllLDaDnvplknpdklFese.eYkktglllw.kdrdlwkrstspkfyei 143 210s F+++ ++D+D +++kn+d++F+++ Y++ ++l + + ++++k +++ y++ 210s CUFF.51.1.p1 171 QFDKICVIDSDILIMKNIDDIFDTPyMYQQINTLNYtRLPSYTKPD-DDTVYHF 223 210s 69*********************97358888888882224443333.4444444 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (275 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1616.74 210s // 210s Query: MatE [M=161] 210s Accession: PF01554.17 210s Description: MatE 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 210s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 210s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 210s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 210s CUFF.38.1.p3 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 210s 99****************************************************************************************.****** PP 210s 210s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 210s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 210s CUFF.38.1.p3 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 210s ***************************************************************86 PP 210s 210s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 210s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 210s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 210s CUFF.38.1.p3 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 210s 667789******************************************************************************************* PP 210s 210s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 210s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 210s CUFF.38.1.p3 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 210s *******************************************************99997 PP 210s 210s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 210s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 210s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 210s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 210s CUFF.39.1.p1 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 210s 99****************************************************************************************.****** PP 210s 210s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 210s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 210s CUFF.39.1.p1 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 210s ***************************************************************86 PP 210s 210s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 210s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 210s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 210s CUFF.39.1.p1 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 210s 667789******************************************************************************************* PP 210s 210s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 210s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 210s CUFF.39.1.p1 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 210s *******************************************************99997 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (161 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 22 (0.231579); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1893.74 210s // 210s Query: MDM31_MDM32 [M=525] 210s Accession: PF08118.10 210s Description: Yeast mitochondrial distribution and morphology (MDM) proteins 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 9.7 0.1 1.7e-05 0.0016 365 448 .. 134 218 .. 124 228 .. 0.68 210s 210s Alignments for each domain: 210s == domain 1 score: 9.7 bits; conditional E-value: 1.7e-05 210s MDM31_MDM32 365 eeevtskkaleeeekseelakeaks.aeeseeekeeeeekeeeeeekyvvvdlklklndvkAavPlftkdlsyvnnaliRpivay 448 210s e++++k+++ ++ +++++++a+s a++s + + + + + +++ k v ++klnd A++P ++ +s ++a Rp v++ 210s CUFF.20.1.p1 134 VEKISQKNQEARSRANSRVNSRANSrANSSVSLAGMDGSPNWKRKMKSAVFGSRVKLNDEEAQLPRNKSSVSIAEQAASRPKVSF 218 210s 33344443333333333444333330333444444555666678889999*********************************99 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (525 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4293.53 210s // 210s Query: MFS_1 [M=353] 210s Accession: PF07690.15 210s Description: Major Facilitator Superfamily 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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( 210s 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(+) 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 135.1 27.5 5.9e-43 1.4e-41 2 349 .. 113 492 .. 112 497 .. 0.82 210s 2 ? -1.5 0.1 0.2 4.8 230 256 .. 500 529 .. 493 543 .. 0.53 210s 210s Alignments for each domain: 210s == domain 1 score: 135.1 bits; conditional E-value: 5.9e-43 210s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGl 97 210s +++++++++a+s++++ + +a++l++s +++l ++ + +g++v+slp+++lsd +Gr +++++ll+f ++ + + a+++w+l+++r++qG+ 210s CUFF.37.1.p1 113 SVITIVVTFASSVYSSGII-DIASELHSSIP-VSTLGSCtFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGV 207 210s 56889999**********9.9******5555.56666664888********************************6666645*************** PP 210s 210s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeee..... 188 210s ++++ +++++ i+d+f++ +r+ ++ + ++ lG+i+gp++g +++ s+l Wr++f+i+ i ++ ++v++++++pe++ + + +++ + 210s CUFF.37.1.p1 208 FGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFITqSYLEWRWTFWINMIWAAAVIVFVFIFFPETHEDTILDYKAKYLrkttg 304 210s ************************************************99999*********************************999999***** PP 210s 210s MFS_1 189 ..........kgtgpaplvp....awkallkdpvlwillialllfffgfsglltllplylqevlgls.glllaglllallalvgail....allagr 266 210s +++ + ++++ a +++++ p + +++ l++ +++++ + ++ +g++ g +++ +++++ +++++ ++ + + 210s CUFF.37.1.p1 305 ntayytiherERDPKNAMIQaatqAVSLIFTEPIVV-CFTLYLTVVYIINYINFEGYPIVFAKYGFNkG-EQGLSFIGVGVGIVCAGlctpFIYWHY 399 210s ******9999777777777789999********554.44444444444444444444446888899984.555555555555544444444888888 PP 210s 210s MFS_1 267 ls.dr.....lgrrrrlllallllllaalglallavt...ssavllll..vlvliGf.glgfvfpsllalasdlappeeagtasglfntagslgg 349 210s l ++ + ++ rl+ +++++l+ ++++++a+t ++ ++++ +++++Gf l ++f+s++++++++ ++a +a+++++++++ ++ 210s CUFF.37.1.p1 400 LKvNKkrngvICPEDRLYPLFIGCFLLPISMFWFAWTcypHHIHWIVPiiASAFFGFsLLIVFFVSYNYIIDSYQ--HMAPSALAAATLVRYSAS 492 210s 8766666666555************************98855555544558888***888888899888888888..999999999998877443 PP 210s 210s == domain 2 score: -1.5 bits; conditional E-value: 0.2 210s MFS_1 230 lplylqevlgls....glllaglllallalv 256 210s p+yl+ +++ g +++++++++++++ 210s CUFF.37.1.p1 500 RPMYLNLGDHWAtsvlG-FISVAMVPIPFIF 529 210s 57777777777744443.3333333333333 PP 210s 210s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 128.6 21.0 5.6e-41 1.3e-39 2 352 .. 66 429 .. 65 430 .. 0.87 210s 2 ? -2.4 0.0 0.39 9.4 282 296 .. 450 464 .. 440 476 .. 0.44 210s 210s Alignments for each domain: 210s == domain 1 score: 128.6 bits; conditional E-value: 5.6e-41 210s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlg 98 210s +++++++l+rs++g a+ ++e+l + + ++ +++++++++++ p +l+ r+ + r+l + ++++ ++l+ f ss+ l++ r++ Gl 210s CUFF.45.1.p2 66 GFLYLMAFLDRSNIGNAAVAGMTEALSLYGERLNVAVSIFYVLYILVETPSVVLVKRIKASRMLAFISFAWSMTVLFSGFMSSYGGLIATRLILGLL 162 210s 6899******************************************************999988888888888834444536666************ PP 210s 210s MFS_1 99 agalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg....Wravfyilaivsllafvlfllllpeepperkrkspkeee.. 188 210s +g+lfpa + +++ ++++e+ + +++l a+++l+ ++g l++ +l ++g W++++++ ++vs++++ l l+ lp++ + + + +e+e 210s CUFF.45.1.p2 163 EGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEqVHAGnkegWQWIYIVEGLVSFIGVPLCLFALPDKMENAWFLTREEREva 259 210s ********************************************999666669******************776555555555555555555555** PP 210s 210s MFS_1 189 ..........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275 210s +g +++++++ ++ +kdp +++ ++ +++ ++++g++++lp++ + lg+ g l++ ++ ++++g+i++l++++lsdr++ 210s CUFF.45.1.p2 260 iirrdinaryHGEQHFEWSE-VRKAFKDPKVYVSATSQFCADMVLYGFSSFLPVI-IKGLGFVG-LQTNYMTIPVYIAGVISFLFVAWLSDRTQL-- 351 210s ********************.888888888878*********************7.*******8.888889999999999************776.. PP 210s 210s MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntagslggalg 352 210s r + +++ +++a+g++++ +++s+++ + + ++i +g + ++ l ++++++ + +++ta+g+ +t+ + +g+++ 210s CUFF.45.1.p2 352 RAVYLISASTVVAVGYIIMLASDSNAAKYTATYIIAIGCYIGPGLNLGWLNNNVaGHYKRATAIGIQQTLANSSGIVA 429 210s 88889999999999999999998999999988887775555566666666665546689*********9999999987 PP 210s 210s == domain 2 score: -2.4 bits; conditional E-value: 0.39 210s MFS_1 282 lllllaalglallav 296 210s ++++++ l+++++ + 210s CUFF.45.1.p2 450 GCVIVGGLAYVVMFF 464 210s 222222222222222 PP 210s 210s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 54.9 16.8 1.5e-18 3.5e-17 2 263 .. 92 349 .. 85 361 .. 0.77 210s 2 ! 26.7 12.4 5.4e-10 1.3e-08 212 353 .] 370 516 .. 357 516 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 54.9 bits; conditional E-value: 1.5e-18 210s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGl 97 210s l + + sa+++s++++ + + +++ s i++l + a+ ++v ++lG +sd +r ++ l ll++++g ++ + + s++ + +++ v+ ++ 210s CUFF.25.1.p1 92 LACSWASAIQSSTTYSYQV-YATASFN-RTSMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIG-FIVVASsSTISAYVIGSVFISI 185 210s 5677778888888777777.8999999.88889999999******************96666************.55552446677*********** PP 210s 210s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyilaivsllafv.lfllllpeepperkrkspkeee.... 188 210s g+++l + ++ d+++ + rg++++lls+ + + + g ++ g++ +Wr+ + ++ai++ ++ +++l++ e+ ++k ++ k+ 210s CUFF.25.1.p1 186 GSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVwFTGFIVQGIID--SNWRWGYGMFAIIMPAVMTpAVIILMYLERQANKDENIKKIInyqt 280 210s *************************************666677777777..45*****999999999955533444444444444444333335577 PP 210s 210s MFS_1 189 ...kgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailall 263 210s ++ +++++ ++wka+l l+ +ll+ +g+s+ l + l++y g+++ +++ +++++ v++i+ 210s CUFF.25.1.p1 281 eekNKNKQSKWQKLWKAVLEVD----LFGLILLG-VGWSIllLPFSLTSY--AKNGWKNPSMIA--MMVVGGVILIA--Y 349 210s 77788999999999*****999....44444444.366665588888887..777777335555..77777776666..4 PP 210s 210s == domain 2 score: 26.7 bits; conditional E-value: 5.4e-10 210s MFS_1 212 llialllfffgfsg....lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallll.llaalglallavt.ssavl 302 210s +i+++++ f++++ ++++++y+ +++s + +++ + ++ ++++++ag++++ + r ++l +++l++ ++++ +l+ +++ + +v 210s CUFF.25.1.p1 370 TFITAVIIDFFYYLagylQSMYFTTYTWILYDWS-YRDWTYFNNTMTIALCVFGVFAGAMHRVFHRYKYLQIIGLVIkIVGYGILIRPNFAaTGKVD 465 210s 3444444444444445558889999999******.55555556666666666689999999998887766655555505555555555555999999 PP 210s 210s MFS_1 303 lllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353 210s l+++l+liG+g++f ++ +++ ++ ++p + + as+l ++ ++gga+g+ 210s CUFF.25.1.p1 466 LAWSLILIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGA 516 210s 999**********************************************96 PP 210s 210s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 53.0 19.0 5.4e-18 1.3e-16 23 293 .. 47 347 .. 6 350 .. 0.71 210s 2 ! 26.7 11.5 5.6e-10 1.3e-08 3 201 .. 267 475 .. 266 507 .. 0.74 210s 210s Alignments for each domain: 210s == domain 1 score: 53.0 bits; conditional E-value: 5.4e-18 210s MFS_1 23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpke 117 210s +++++ +s+ + ll+++ +g+++++++ +++++r+G + +++ +++++ lll + a ++w +lv+ +l+G+g gal ++ + ++++p++ 210s CUFF.24.1.p1 47 ISNSYSYSAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAeLLLVT-AVPSWiQVLVGKILAGVGIGALSVLSPGYQSEVAPPQ 142 210s 24444466666888999999*********************************666666.567787******************************* PP 210s 210s MFS_1 118 ergraigllsagfslGailgpllgg...llasslgWravfyilaivsllafvlfllllpeepperkrkspkeee....................... 188 210s rg +++ +++++ +a++++ + l ++Wr +f i+ + ++l++v ++l+lpe+p+ k ee 210s CUFF.24.1.p1 143 IRGAVVATYQIFSTGAALVAACINMgthKLRKTASWRTSFGINMLWGILLMV-GVLFLPESPRYLIYKGRDEEAlrimcnmaelspeseiiqtnfnt 238 210s ***********999999999888772323335555***************88.558888888888887777776*******9888887777666666 PP 210s 210s MFS_1 189 ........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrl 277 210s g+a w +++ + + +++l++ f + + + y+ +v++ +g + l +l++++++ + a + +d lgrr++l 210s CUFF.24.1.p1 239 iksdieieMAGGKA----RWIEIFGKDIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGMTDIFLPAVILGAINFGTTFGALYTIDNLGRRNPL 331 210s 65555444344444....4444555553322333333333333334444444455555555533444446777777777676666667********* PP 210s 210s MFS_1 278 llallllllaalglal 293 210s +++ ++ +++++++a 210s CUFF.24.1.p1 332 IFGAAFQSICFFIYAA 347 210s ************9986 PP 210s 210s == domain 2 score: 26.7 bits; conditional E-value: 5.6e-10 210s MFS_1 3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrl..sdrfGrrrvlllglllfalglllll.fa............s 83 210s +++fl++l r ++g ++ + ++ + ++ + +l + + lga+ + +G+l +d++Grr l++g+++ ++++++ + ++ + 210s CUFF.24.1.p1 267 CLGFLVMLFRELIGNNYYFyYATQVFKGTGMTDIFLPA-VILGAINFGTTFGALytIDNLGRRNPLIFGAAFQSICFFIYAaVGdrkliykngtsdH 362 210s 67889999999999999987888888855555555444.556666666666655569*******************555552314444455555664 PP 210s 210s MFS_1 84 slw.lllvlrvlqGlgagalf.pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178 210s +++v+ +l + +++++ p+g +++ + fp + r++ +++++g+ lG + + +++ ++g+ + ++ ++i ++ +f+ +++++++++ 210s CUFF.24.1.p1 363 RAGsVMIVFSCLFLFSYCCSWgPMGWVIVGETFPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIGFKLGYIYACINLFSSFM---IFFLAKETK 456 210s 45556777777777777666537777999*****************************************998888888888877...677677766 PP 210s 210s MFS_1 179 rkrkspkeeekgtgpaplvpawk 201 210s + +++ ++ ++++p w+ 210s CUFF.24.1.p1 457 GLTLEEVNDL---YMSNIKP-WE 475 210s 6666666663...4444444.44 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (353 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 27 (0.284211); expected 1.9 (0.02) 210s Passed bias filter: 9 (0.0947368); expected 1.9 (0.02) 210s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 210s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 4 [number of targets reported over threshold] 210s # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 210s # Mc/sec: 308.26 210s // 210s Query: MFS_3 [M=522] 210s Accession: PF05977.12 210s Description: Transmembrane secretion effector 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 8.4 5.5 3.5e-05 0.0033 258 364 .. 60 168 .. 49 202 .. 0.73 210s 210s Alignments for each domain: 210s == domain 1 score: 8.4 bits; conditional E-value: 3.5e-05 210s MFS_3 258 illgalGvGAilgalllsrLRerlsser.lvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavql.avPrWvvgRalavYltvl 352 210s +l g++ +G ++ga+l+s er++++ + + v + + ll ++ ++s ++++ +l+G i als l q + P ++g ++a Y+ + 210s CUFF.24.1.p1 60 LLTGTINAGCLFGAMLSSPFTERIGKKYsICFFSGVYIIAELLLVTAVPSWIQVLVGKILAG-VGIGALSVLSPGYQSeVAPPQIRGAVVATYQIFS 155 210s 688999******************98861555666665555555555555555555555555.56********9999735699************** PP 210s 210s MFS_3 353 aGg.laaGsllWG 364 210s +G+ l a + G 210s CUFF.24.1.p1 156 TGAaLVAACINMG 168 210s 9972455555555 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (522 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 2964.22 210s // 210s Query: MFS_4 [M=363] 210s Accession: PF06779.13 210s Description: Uncharacterised MFS-type transporter YbfB 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.2 0.2 0.053 5.1 146 206 .. 101 156 .. 98 157 .. 0.65 210s 2 ! 16.9 0.5 1.7e-07 1.6e-05 38 175 .. 152 288 .. 132 311 .. 0.84 210s 3 ! 4.3 0.1 0.0012 0.11 119 144 .. 374 399 .. 365 405 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: -1.2 bits; conditional E-value: 0.053 210s MFS_4 146 sasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfG 206 210s s s W+++ +s++ +++ ++ + + ++++s+p+ l +l+GfG 210s CUFF.37.1.p1 101 SHSYKWWIVIQVSVITIVVTFASSV---YSSGIIDIA--SELHSSIPVSTLGSCTFLVGFG 156 210s 5566699999999998888877665...333333333..3677777777777777777776 PP 210s 210s == domain 2 score: 16.9 bits; conditional E-value: 1.7e-07 210s MFS_4 38 ylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavs 133 210s ++G+ vG+l + ls R + ll ++ + ++++++++++++Rf Gv + + l ++ ++ ++ +r v+ + + lG +++ 210s CUFF.37.1.p1 152 LVGFGVGSLPF-APLSDIYGRFIiYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGVFGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIG 247 210s 57999999988.677888888884567778888899999*********************************************99999******** PP 210s 210s MFS_4 134 gllvllllqlglsasslWlalavlsavllllvalllpraalr 175 210s ++ ++ q l++ ++ ++ + +a++++ v++ p + ++ 210s CUFF.37.1.p1 248 PIIGDFITQSYLEWRWTFWINMIWAAAVIVFVFIFFP-ETHE 288 210s ****************977777889999999999999.3333 PP 210s 210s == domain 3 score: 4.3 bits; conditional E-value: 0.0012 210s MFS_4 119 gallfaGvGlGiavsgllvllllqlg 144 210s ++l f GvG+Gi+ +gl+ +++ + 210s CUFF.37.1.p1 374 QGLSFIGVGVGIVCAGLCTPFIYWHY 399 210s 6899*************999887665 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (363 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 210s # Mc/sec: 1107.24 210s // 210s Query: MIP [M=227] 210s Accession: PF00230.19 210s Description: Major intrinsic protein 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 167.2 6.0 2.4e-53 2.3e-51 6 227 .] 308 548 .. 303 548 .. 0.91 210s 210s Alignments for each domain: 210s == domain 1 score: 167.2 bits; conditional E-value: 2.4e-53 210s HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS 210s MIP 6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllG 102 210s +f r+ +AEfl+tl+lv++gvgs+l+ +v++ + +++e+ ++a+g++ + +vy+a+giSG+H+NPavT++l+++rk++ ++++Yi Q+ G 210s CUFF.20.1.p1 308 HFFREGFAEFLGTLVLVVFGVGSNLQA--TVTN---GAGGSFESLSFAWGFGCMLGVYIAGGISGGHVNPAVTISLAIFRKFPWYKVPIYIFFQIWG 399 210s 6899******************99844..3433...34579******************************************************** PP 210s 210s HHHHHHHHHHHCHHH............HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHH CS 210s MIP 103 aivaaallklltkgl............esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgiplt 187 210s a+ + al ++ + + g + +kp+++ +a++ E+i t+vLv ++fa+ dd+++ + +++ +gll+a+i ++ +++t 210s CUFF.20.1.p1 400 AFFGGALAYGYHWSSitefeggkdirtPATGGCLYTNPKPYVTWRNAFFDEFIGTAVLVGCLFAILDDTNSPPTQGMTAFIVGLLIAAIGMALGYQT 496 210s *********99988889******9976556666678899*********************************99899******************** PP 210s 210s ST-SSHHHHHHHHHHHTH............STTTTHHHHHHHHHHHHHHHHH CS 210s MIP 188 GaamNpArslgpavvlnk............fedhwvylvGPliGailgalvY 227 210s +++NpAr+lgp+++++ + w + G + G+i+g+l+Y 210s CUFF.20.1.p1 497 SFTLNPARDLGPRMFAWWigygphsfhlyhWWWTWGAWGGTIGGGIAGGLIY 548 210s *************************98855555566788999999999**99 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (227 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 3224.87 210s // 210s Query: MVP_shoulder [M=118] 210s Accession: PF11978.7 210s Description: Shoulder domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 210s 210s Alignments for each domain: 210s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 210s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 210s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 210s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 210s CUFF.60.1.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 210s 57799999**************************************9.5555555554444 PP 210s 210s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 210s 210s Alignments for each domain: 210s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 210s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 210s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 210s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 210s CUFF.60.2.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 210s 57799999**************************************9.5555555554444 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (118 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1834.27 210s // 210s Query: Na_H_Exchanger [M=381] 210s Accession: PF00999.20 210s Description: Sodium/hydrogen exchanger family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 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 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 138.5 8.5 4.2e-44 1.3e-42 1 198 [. 83 291 .] 83 291 .] 0.97 210s 210s Alignments for each domain: 210s == domain 1 score: 138.5 bits; conditional E-value: 4.2e-44 210s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 210s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 210s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 210s CUFF.13.2.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 210s 6889999******997799999********************99999************************************************ PP 210s 210s HHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSX CS 210s Na_H_Exchanger 87 vlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeaggetslll 178 210s ++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++++ ++ 210s CUFF.13.2.p1 178 MAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRNAGRDW 271 210s **********9**8.69***************************988889**********************************99********* PP 210s 210s HHHHHHHHHHHHHHHHHHHH CS 210s Na_H_Exchanger 179 llliflvvavgglllglvig 198 210s +ll++l+++++g+++g+vig 210s CUFF.13.2.p1 272 VLLVVLYECAFGIFFGCVIG 291 210s ******************97 PP 210s 210s >> CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414-1770(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 87.5 2.1 1.3e-28 4.1e-27 82 198 .. 1 119 [] 1 119 [] 0.97 210s 210s Alignments for each domain: 210s == domain 1 score: 87.5 bits; conditional E-value: 1.3e-28 210s HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTS CS 210s Na_H_Exchanger 82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeagge 173 210s ++l++++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++ 210s CUFF.13.1.p2 1 MLLPVMAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRN 94 210s 67999*******9999998.79***************************988889**********************************99**** PP 210s 210s SSTSXHHHHHHHHHHHHHHHHHHHH CS 210s Na_H_Exchanger 174 tslllllliflvvavgglllglvig 198 210s ++ +++ll++l+++++g+++g+vig 210s CUFF.13.1.p2 95 AGRDWVLLVVLYECAFGIFFGCVIG 119 210s ***********************97 PP 210s 210s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 49.8 1.9 3.6e-17 1.1e-15 1 93 [. 83 184 .. 83 185 .. 0.96 210s 210s Alignments for each domain: 210s == domain 1 score: 49.8 bits; conditional E-value: 3.6e-17 210s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 210s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 210s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 210s CUFF.13.3.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 210s 6889999******997799999********************99999************************************************ PP 210s 210s HHHHHHH CS 210s Na_H_Exchanger 87 vlitvvl 93 210s ++ +++ 210s CUFF.13.3.p1 178 MAYGWIF 184 210s ****987 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (381 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 3 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2779.94 210s // 210s Query: NEMO [M=68] 210s Accession: PF11577.7 210s Description: NF-kappa-B essential modulator NEMO 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.3 0.0 1.5e-05 0.0014 22 55 .. 54 87 .. 50 98 .. 0.93 210s 210s Alignments for each domain: 210s == domain 1 score: 11.3 bits; conditional E-value: 1.5e-05 210s NEMO 22 lkqsNqalkeRlEeLsawqekqkeerefleeklr 55 210s lk N++lk+R+ e s ++ ee f + klr 210s CUFF.54.1.p1 54 LKNANDSLKGRILEVSLADLQKDEEHSFRKVKLR 87 210s 89**************************999998 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (68 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2207.71 210s // 210s Query: Nucleotid_trans [M=212] 210s Accession: PF03407.15 210s Description: Nucleotide-diphospho-sugar transferase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 15.0 0.0 1e-06 9.9e-05 106 189 .. 238 318 .. 210 333 .. 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 15.0 bits; conditional E-value: 1e-06 210s Nucleotid_trans 106 desknliNsGfffvrateatkallkkwaeelase.sglw.DqdvfnlllregaakesglkvrvLdtalfvngkgyfvq.vrdeeevk 189 210s ++++n +N G + +r+++at +l+ w + + +e +++ +qd++ +l + + + v++++++++ + f + ++ e+ k 210s CUFF.51.1.p2 238 SQDHNGLNAGSILFRNSPATALFLDIWTDPVVAEcAKANnEQDMLGYLISKHSQ--LASLVGLIPQRKI----NAFHEgPENMEWQK 318 210s 4567888************************999855556*********99664..8888999999999....77777655555554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (212 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4171.51 210s // 210s Query: Oleosin [M=113] 210s Accession: PF01277.16 210s Description: Oleosin 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s ------ inclusion threshold ------ 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -2.3 0.0 0.21 20 87 107 .. 57 77 .. 47 82 .. 0.60 210s 2 ? -0.2 0.1 0.045 4.3 35 46 .. 107 118 .. 104 127 .. 0.85 210s 3 ? 8.8 1.0 7.4e-05 0.007 41 63 .. 141 163 .. 140 167 .. 0.86 210s 210s Alignments for each domain: 210s == domain 1 score: -2.3 bits; conditional E-value: 0.21 210s Oleosin 87 gadqldqakrrlaekasevke 107 210s +++++ k++++ k++++ke 210s CUFF.5.1.p1 57 FTNTIKPQKDKMNIKTNKIKE 77 210s 455555666666666666655 PP 210s 210s == domain 2 score: -0.2 bits; conditional E-value: 0.045 210s Oleosin 35 tPllvlfSPvlv 46 210s Pll++ S ++v 210s CUFF.5.1.p1 107 WPLLIIWSIIIV 118 210s 69*****99998 PP 210s 210s == domain 3 score: 8.8 bits; conditional E-value: 7.4e-05 210s Oleosin 41 fSPvlvPaaivialavagflasg 63 210s +S ++vP+ai + l+v ++l+ 210s CUFF.5.1.p1 141 YSEIWVPIAIYVCLLVLMLLSLI 163 210s 688*************9999864 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (113 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3063.78 210s // 210s Query: Orthopox_A5L [M=271] 210s Accession: PF06193.10 210s Description: Orthopoxvirus A5L protein-like 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 8.2 4.9 8.4e-05 0.008 146 192 .. 3 49 .. 1 92 [. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 8.2 bits; conditional E-value: 8.4e-05 210s Orthopox_A5L 146 ttpstqpsqtlPtttcvrqsdasistttdivtppqppivatvctptP 192 210s t t s tlP tt q+ +++s t +iv+p + p t + 210s CUFF.11.1.p1 3 TVTETITSGTLPFTTTLAQASGTVSGTVEIVSPKNNPTTVYSGTVAT 49 210s 56678899*************************98886543322222 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (271 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 4814.61 210s // 210s Query: Oxidored_FMN [M=341] 210s Accession: PF00724.19 210s Description: NADH:flavin oxidoreductase / NADH oxidase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 453.0 0.0 1.1e-139 3.6e-138 1 341 [] 12 360 .. 12 360 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 453.0 bits; conditional E-value: 1.1e-139 210s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 210s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 210s 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++ 210s CUFF.52.1.p1 12 KLFQPIKVGNMQLQHRMVHAPATRLRCLDNGLVMTDLVKEYYKQRSSIPGTLLITESLFSGAKSGGFSNIPCLYNDEHVEAWKPIVQAIHDNDCFVF 108 210s 7************************************************************************************************ PP 210s 210s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 210s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 210s +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+ 210s CUFF.52.1.p1 109 IQFWNLPGELKVDYLEDQErlekvtqGECPMDPTGLPAALGsaysICGEELyvdKFMTKQDIQEHITTYTEAAKRAVFgCGADGVEVHQVNGFLLDK 205 210s *************************99************99999999999999******************************************** PP 210s 210s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 210s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 210s F+ +++++++D+++ Gs+enRarF+le++++v++a+g+ervgyR+Sp+++++k++d++e+ +++++k++++r++ +la++h++epr++++g+v+ 210s CUFF.52.1.p1 206 FVLNGYGDKCDPEYcGSLENRARFCLELLESVVNAIGQERVGYRISPFSDIWKDKDSFEA--HVFMIKKIKERFP---NLAYLHAIEPRQYWNGHVH 297 210s ************************************************************..*************...******************* PP 210s 210s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 210s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 210s ++q+ kn+ ++k++w +p+it+G++d+++ a+++a++e+tlvafgR+fl++pdl+++lk+++pln 210s CUFF.52.1.p1 298 ITQE-KNTLIYKNLWGDPFITAGGHDRDS--AIQMAEQENTLVAFGRYFLSNPDLPFRLKYNLPLN 360 210s **66.************************..********************************997 PP 210s 210s >> CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 210s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 210s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 210s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 210s CUFF.48.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 210s 69*****************************.9999************************************************************* PP 210s 210s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 210s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 210s +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+ 210s CUFF.48.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 210s *************************9***************9999888888999******************************************* PP 210s 210s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 210s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 210s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 210s CUFF.48.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 210s ************************************************************..*************...******************* PP 210s 210s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 210s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 210s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 210s CUFF.48.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 210s **66.9**********************9..********************************987 PP 210s 210s >> CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 210s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 210s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 210s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 210s CUFF.49.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 210s 69*****************************.9999************************************************************* PP 210s 210s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 210s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 210s +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+ 210s CUFF.49.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 210s *************************9***************9999888888999******************************************* PP 210s 210s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 210s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 210s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 210s CUFF.49.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 210s ************************************************************..*************...******************* PP 210s 210s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 210s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 210s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 210s CUFF.49.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 210s **66.9**********************9..********************************987 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (341 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 3 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 1465.37 210s // 210s Query: Pantoate_ligase [M=266] 210s Accession: PF02569.14 210s Description: Pantoate-beta-alanine ligase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 341.6 0.0 1.5e-106 1.4e-104 4 265 .. 5 278 .. 2 279 .. 0.91 210s 210s Alignments for each domain: 210s == domain 1 score: 341.6 bits; conditional E-value: 1.5e-106 210s -SHHHHHHHHHHHHHTT-EEEEEEE-SS--HHHHHHHHHHHHHSSEEEEEE---GGGSSTTSCTTTS---HHHHHHHHHHTT-SEEE---HHHH CS 210s Pantoate_ligase 4 ktvaelrellkelrkegkkvglVpTmGaLHeGHlsLvkaakeendvvvvSiFvNplqFgpkedlekYPrtleaDlelleeagvdlvFaPsveem 97 210s k+ ++++++++rk+g+++++VpTmG+LHeGH sLv++ak+++++vvvSiFvNp+qF++ +dl YPrt+++D+++l+++gvdlv+aP+vee+ 210s CUFF.50.1.p2 5 KEKLLIHQQVDNWRKDGNRIAFVPTMGNLHEGHFSLVREAKRHAEKVVVSIFVNPMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYAPTVEEL 98 210s 55566788999***9999**************************************************************************** PP 210s 210s ST......EEEEECSGGCSTHHHHSTTHHHHHHHHHHHHHHHH--SEEEEEGGGHHHHHHHHHHHHHTT-SSEEEEE-XXBXTTSXBXXGGGGG CS 210s Pantoate_ligase 98 yp......tevevkelsevlegasrpghFrGVatvvtkLfnivqpdrayfGqKDaqqlavirrlvkdlnlpveivavpivReedgLAlSSRNky 185 210s yp t v+v++ls++legasrpghFrGV+tvv+kLf+iv+pd+a+fG+KD+qq+a+i+++v+dln+ +ei++vpivR++dgLAlSSRN y 210s CUFF.50.1.p2 99 YPegsqdiTFVDVPKLSTMLEGASRPGHFRGVTTVVSKLFHIVNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQVPIVRADDGLALSSRNGY 192 210s ********99************************************************************************************ PP 210s 210s SXHHHHHHTTHHHHHHHHHH........BHHHHHHHHHHHHHTHTTEEEEEEEEEETTTSSX.BSSBXSEEEEEEEEEETTEEEEEEE CS 210s Pantoate_ligase 186 LseeerkaAlvlykaLkaak........eaealkeaakeeleeeelekadyveivdaetleeleleeekkavllvaakvgkvrLiDni 265 210s L++eerk A++lyk+Lk+++ + e+l +++++el++ ++ d +ei+d++tle+++ + +k++v+l+aa++gk+rLiDni 210s CUFF.50.1.p2 193 LTSEERKIAPNLYKILKKLAqelsngngDLEKLIAETNTELSRCRFI-PDQLEICDSTTLEPFT-AGTKNVVILAAAWLGKARLIDNI 278 210s *******************9555555444444445555555544433.5***********9964.55588*****************8 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (266 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3637.01 210s // 210s Query: Pantoate_transf [M=259] 210s Accession: PF02548.14 210s Description: Ketopantoate hydroxymethyltransferase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 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- 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 341.7 0.0 2.8e-106 1.3e-104 2 258 .. 6 261 .. 5 262 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 341.7 bits; conditional E-value: 2.8e-106 210s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 210s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 210s CUFF.50.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 210s 79*************************************************************************************.99**** PP 210s 210s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 210s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 210s CUFF.50.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 210s *********9.********99866********************************************************************** PP 210s 210s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPa 258 210s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ a +i++a+++Y+ ev++g +Pa 210s CUFF.50.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLSGAGDIRTAIQRYIYEVEQGLYPA 261 210s *********************************************************************8 PP 210s 210s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 319.5 0.0 1.7e-99 8.1e-98 2 235 .. 6 238 .. 5 240 .] 0.98 210s 210s Alignments for each domain: 210s == domain 1 score: 319.5 bits; conditional E-value: 1.7e-99 210s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 210s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 210s CUFF.52.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 210s 79*************************************************************************************.99**** PP 210s 210s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 210s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 210s CUFF.52.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 210s *********9.********99866********************************************************************** PP 210s 210s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyae 235 210s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ 210s CUFF.52.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLS 238 210s ********************************************986 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (259 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2878.89 210s // 210s Query: Phosphodiest [M=357] 210s Accession: PF01663.21 210s Description: Type I phosphodiesterase / nucleotide pyrophosphatase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 13.6 0.3 2e-06 0.00019 1 59 [. 48 108 .. 48 116 .. 0.87 210s 2 ! 40.3 0.1 1.6e-14 1.5e-12 143 237 .. 166 261 .. 117 275 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 13.6 bits; conditional E-value: 2e-06 210s EEEEEETT-BCCHHHHCGGTSHHHHHHHHHSEEESE..EE-SSS-SHHHHHHHHHHSS-HH CS 210s Phosphodiest 1 vlvislDGlradlldrlaellpnlaaLakegvsapn..lrpvfPtlTfpnhaslvTGlyPg 59 210s v+++ +D lrad ++ ++ +p+ ++L+ +++++ + Pt+T+p + +l TG+ Pg 210s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGfsAFARSPTVTMPRLKALTTGTIPG 108 210s 7999***********9448*********977666643488889***************997 PP 210s 210s == domain 2 score: 40.3 bits; conditional E-value: 1.6e-14 210s THHHHHHHHHHCHHHHCHTHCHHHHHTT.TSECEEEEEEEHHHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEE....EEEEES--- CS 210s Phosphodiest 143 pledkvdkavlqtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetn....iilvSDHGm 234 210s ++ ++v + ++++f +++l+ +l +d l++++ ++D++gH +Gp sp ++ +l ++D i +++++l+e +++tn i+l +DHGm 210s CUFF.53.1.p1 166 SFFVSDYTEVD-NNVTRNF-DHALPSSLsHSWDALILHYLGVDHIGHLYGPSSPLLNIKLLEIDTIISRIYKYLQEY--DEKTNthslIVLCGDHGM 258 210s 33332223344.4478888.568888889**********************************************98..444444466********* PP 210s 210s EE- CS 210s Phosphodiest 235 adv 237 210s ++v 210s CUFF.53.1.p1 259 NEV 261 210s 998 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (357 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1403.87 210s // 210s Query: PLA2_B [M=491] 210s Accession: PF01735.17 210s Description: Lysophospholipase catalytic domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 677.6 1.8 4.4e-208 4.2e-206 1 490 [. 132 614 .. 132 615 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 677.6 bits; conditional E-value: 4.4e-208 210s PLA2_B 1 iaiavSGGGyramltgaGvlkAldsRtdnatglgGlLqsatYlaGlsGgsWlvgslavNnftsvqellkkkeedsvwdlensivnpeglnlvknikr 97 210s ++ia+SGGG+ram++g+G+ +A+dsR + + l+GlLqsa+Y++GlsGgsWlvgs+a+Nnft+++ l++ +vw+le+s+++p+g n+++n+++ 210s CUFF.12.1.p1 132 LGIAFSGGGLRAMVNGGGAFNAFDSRFESDSPLSGLLQSAMYISGLSGGSWLVGSVAINNFTNITYLRD-----NVWNLEHSVFAPHGDNVIENLNY 223 210s 69*******************************************************************.....8********************** PP 210s 210s PLA2_B 98 yeeivdevekKksagfnvsltDiwGralseklveleegganltlsslkdaekfqnaemplPiivadgrkpgesvinlNatvfEfsPyelgswdakln 194 210s y+++ +e+++Kk+agf+ sltD+wGrals+klv++e+gg+ +t+ss++++++fqna++p+Piivad+r ++e++i +N+++fEf+ ye+g+wd++++ 210s CUFF.12.1.p1 224 YNDLRKEIDQKKHAGFDCSLTDLWGRALSRKLVDAERGGPGITYSSMRNQSWFQNADYPYPIIVADSRLEEETAIPANTSIFEFTAYEFGTWDNGIK 320 210s ************************************************************************************************* PP 210s 210s PLA2_B 195 sFvdvkylGtklsnGtvvkkgkcvagfdnaGflmgtsstlFnevlleinstsmlesllkellkkllkdlsedsediaqyapnpfkdaeeenqnatqs 291 210s +F++++y+Gt+l +G+++ +++c++++dnaGf+mgts+tlFn++ll++n++ +++ +++l+ +l+dls+ ++dia y+ np++++++ n+ + ++ 210s CUFF.12.1.p1 321 AFIPMEYVGTHLLDGVPP-DKSCIHNYDNAGFVMGTSATLFNSFLLDWNENVKKNDTYYDILHAILEDLSKHQDDIAPYP-NPYQNYTTSNTSVVNA 415 210s ******************.*********************************9**************************9.**************** PP 210s 210s PLA2_B 292 ivesktLdlvdggedgqniplvpllqkerkvdvifaldssadteeswpdgsslvktyeRvle...ssqvkgkkfpyvpdqntfvnlgLnkrptffGc 385 210s ++ +t+dlvdgged +nipl+pll+++r vdv+fa+ds+++ + wp gss+v+tyeRv++ +++v++++fpy+pd+nt+++lgLn+rptffGc 210s CUFF.12.1.p1 416 FEPYDTIDLVDGGEDRENIPLWPLLHPQRFVDVVFAIDSTYNDPYGWPLGSSIVATYERVVTfnaNKSVDVRGFPYIPDENTIISLGLNTRPTFFGC 512 210s ************************************************************999889999**************************** PP 210s 210s PLA2_B 386 DarnltdlsatvdestpPlvvylpnekytylsnlstfklsykdseregliengfeaatqdnekdddefaacvacaiirRklerknittpseckkcFe 482 210s 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+ 210s CUFF.12.1.p1 513 DGKNTTAGNHDVDNNTPPLLVYFPNYPWTYYSNISTFTMSMDDKMANGILENAFMSTTQNN---NESFAVCLACAIIQRSLERKKLSTPTQCSSCFQ 606 210s ************************************************************9...9******************************** PP 210s 210s PLA2_B 483 nycwngtv 490 210s +ycw+gt+ 210s CUFF.12.1.p1 607 EYCWDGTL 614 210s ******97 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (491 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 2255.15 210s // 210s Query: Polysacc_synt_C [M=142] 210s Accession: PF14667.5 210s Description: Polysaccharide biosynthesis C-terminal domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 210s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 210s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 210s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: -1.8 bits; conditional E-value: 0.34 210s Polysacc_synt_C 13 slstvlssiLqglg 26 210s +++ ++++ L++lg 210s CUFF.38.1.p3 51 YMFAMSTGWLIALG 64 210s 33333333333332 PP 210s 210s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 210s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 210s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 210s CUFF.38.1.p3 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 210s 7899999999999999*********************************8883357******************99999999999889955555 PP 210s 210s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 210s l p++ ++giv++ ++ +++ 210s CUFF.38.1.p3 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 210s 4444666666666666555555555543 PP 210s 210s == domain 3 score: -0.6 bits; conditional E-value: 0.14 210s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 210s +l gl+ +a +a +++v+vg ++ + + 210s CUFF.38.1.p3 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 210s 33333333331111335555555555555544 PP 210s 210s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 210s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 210s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 210s CUFF.38.1.p3 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 210s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 210s 210s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 210s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 210s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 210s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: -1.8 bits; conditional E-value: 0.34 210s Polysacc_synt_C 13 slstvlssiLqglg 26 210s +++ ++++ L++lg 210s CUFF.39.1.p1 51 YMFAMSTGWLIALG 64 210s 33333333333332 PP 210s 210s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 210s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 210s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 210s CUFF.39.1.p1 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 210s 7899999999999999*********************************8883357******************99999999999889955555 PP 210s 210s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 210s l p++ ++giv++ ++ +++ 210s CUFF.39.1.p1 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 210s 4444666666666666555555555543 PP 210s 210s == domain 3 score: -0.6 bits; conditional E-value: 0.14 210s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 210s +l gl+ +a +a +++v+vg ++ + + 210s CUFF.39.1.p1 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 210s 33333333331111335555555555555544 PP 210s 210s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 210s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 210s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 210s CUFF.39.1.p1 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 210s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (142 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 18 (0.189474); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 210s # Mc/sec: 389.66 210s // 210s Query: Pombe_5TM [M=256] 210s Accession: PF09437.9 210s Description: Pombe specific 5TM protein 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 516.1 19.2 9.6e-160 9.1e-158 15 256 .] 1 242 [. 1 242 [. 1.00 210s 210s Alignments for each domain: 210s == domain 1 score: 516.1 bits; conditional E-value: 9.6e-160 210s Pombe_5TM 15 sfaysgnsesvlvgenitsirktllinetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 112 210s sfaysgnsesv++genitsi+kt+linetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 210s CUFF.6.1.p1 1 SFAYSGNSESVWTGENITSIWKTILINETGSYCVAARPMTMDGAEFNLDLMGYSVSEDQINNDEIGIWNYISVAEMGGVLLFLSYWIWTCLHFSKIIF 98 210s 8************************************************************************************************* PP 210s 210s Pombe_5TM 113 paqkviclyiflfalnqtlqekieeyvfssevikyrkfysvyeiidflrtnfyrlfviycalgigiirtvskylvikgisivialesvyrislkkdvy 210 210s paqkviclyiflfalnqtlqe+ieeyvfsse+ikyr+fysvyeiidflrtnfyrlfviycalg+gi+rtv+kyl+ikgisivial+svy+isl+kdvy 210s CUFF.6.1.p1 99 PAQKVICLYIFLFALNQTLQECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRTVPKYLMIKGISIVIALCSVYWISLYKDVY 196 210s ************************************************************************************************** PP 210s 210s Pombe_5TM 211 vvseifdliqyevfpaiwvysichllkqctsvttyenaskarfirr 256 210s vvseifd+iqyev paiwvysichllkqctsvttyenaskarf+rr 210s CUFF.6.1.p1 197 VVSEIFDMIQYEVSPAIWVYSICHLLKQCTSVTTYENASKARFFRR 242 210s *********************************************8 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (256 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3171.80 210s // 210s Query: PsbN [M=43] 210s Accession: PF02468.14 210s Description: Photosystem II reaction centre N protein (psbN) 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.8 0.0 9e-06 0.00043 27 43 .] 118 136 .. 106 136 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: 12.8 bits; conditional E-value: 9e-06 210s PsbN 27 FGPPskeLaDPF..edHED 43 210s FGP +++L DPF dH D 210s CUFF.13.3.p1 118 FGPHAAKLVDPFswGDHGD 136 210s ***********84469988 PP 210s 210s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.0 0.0 1.6e-05 0.00075 27 43 .] 118 136 .. 107 136 .. 0.84 210s 210s Alignments for each domain: 210s == domain 1 score: 12.0 bits; conditional E-value: 1.6e-05 210s PsbN 27 FGPPskeLaDPF..edHED 43 210s FGP +++L DPF dH D 210s CUFF.13.2.p1 118 FGPHAAKLVDPFswGDHGD 136 210s ***********84469988 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (43 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1767.49 210s // 210s Query: REPA_OB_2 [M=98] 210s Accession: PF16900.4 210s Description: Replication protein A OB domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 210s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 210s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 210s CUFF.40.1.p3 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 210s 689999****555554444444367789**********************9875 PP 210s 210s >> CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 210s 210s Alignments for each domain: 210s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 210s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 210s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 210s CUFF.41.1.p2 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 210s 689999****555554444444367789**********************9875 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (98 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2776.49 210s // 210s Query: Ribosomal_S3Ae [M=205] 210s Accession: PF01015.17 210s Description: Ribosomal S3Ae family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 303.1 3.9 5e-95 4.7e-93 2 205 .] 16 221 .. 15 221 .. 0.99 210s 210s Alignments for each domain: 210s == domain 1 score: 303.1 bits; conditional E-value: 5e-95 210s S----S-TTSSEEEEEEE--TTSSSSEECEEEEE--BTTC-SCCCHCC-EEEEESHCCCTTCCCSS-EEEEEEEEEETT.EEEEEEEEE--HHHH CS 210s Ribosomal_S3Ae 2 kkkkvvDkfkkKeWydvkaPalfgkreiGktlvtrtqgtkiaseglkgrvvevslaDLtndeeqafrklklkiedvqgk.altnFhgmeltrDkl 95 210s kk+vvD+f++K+Wyd+kaPa+f+ +++Gktlv+rt+g k+a+++lkgr++evslaDL++dee++frk+kl++ed+qgk +lt+F+g ++t+Dkl 210s CUFF.54.1.p1 16 IKKRVVDPFSRKDWYDIKAPAFFEVKNVGKTLVNRTAGLKNANDSLKGRILEVSLADLQKDEEHSFRKVKLRVEDIQGKsCLTSFNGFDMTSDKL 110 210s 599***********************************************************99******************************* PP 210s 210s HHC--CTB-EEEEEEEEEETTTEEEEEEEEEEE--TGCGS.S-B---HHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHCTTHHHHHHHHHHTTTS CS 210s Ribosomal_S3Ae 96 rslvrkwsslIeaivdvkttDgyllrvfvvafTkkrenqk.ktsyakssqvkaIrkkmveilteeaseldlkelvkklipesigkeiekeakkIy 189 210s rslvrkw+s+Iea+ ++kttDgyl r+fv++fT +r nq+ kt+ya+ssq++aI++km+++++++a+ +++kelv+klipe ig+ iek++++Iy 210s CUFF.54.1.p1 111 RSLVRKWQSTIEANQTIKTTDGYLCRIFVIGFTSRRVNQVkKTTYAQSSQIRAIHQKMFQVIQNQANGCSMKELVQKLIPEVIGRAIEKATNNIY 205 210s *********************************************************************************************** PP 210s 210s -EEEEEEEEEEEEE-- CS 210s Ribosomal_S3Ae 190 plrnveirKvkvlkkP 205 210s pl+nv++rKvk+lk+P 210s CUFF.54.1.p1 206 PLQNVFVRKVKILKAP 221 210s **************98 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (205 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3918.18 210s // 210s Query: Ribosomal_S6e [M=126] 210s Accession: PF01092.18 210s Description: Ribosomal protein S6e 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 199.8 0.0 6.5e-64 6.2e-62 1 126 [] 11 136 .. 11 136 .. 1.00 210s 210s Alignments for each domain: 210s == domain 1 score: 199.8 bits; conditional E-value: 6.5e-64 210s -EEEEEETTTTEEEEEE---HHHHTTCTT-BSSEEEESTTT-SSS-S-EEEEEEEEESCC-BB-TT--SSSEEEEEE-TTSSS---SSSS--EEEE CS 210s Ribosomal_S6e 1 mklnisdpatgkqklievddekklrtfiekrigeevdgdalgeelkgyvlkitggsdkqGfpmkqgvlthgrvrlLlskggsgyrprrkGerkrks 96 210s mklnis+pa+g+qklie+dd+++lr f+ekr+g+ev gd++g+e++gyv+kitgg+dkqGfpm qgvl ++rvrlLl+ g+++yrprr+Gerkrks 210s CUFF.58.1.p1 11 MKLNISYPANGTQKLIEIDDDRRLRVFMEKRMGQEVPGDSVGPEFAGYVFKITGGNDKQGFPMFQGVLLPHRVRLLLRAGHPCYRPRRDGERKRKS 106 210s 9*********************************************************************************************** PP 210s 210s EE-SB--SSEEEEEEEEEE--SS--TTSSS CS 210s Ribosomal_S6e 97 vrgcivsadlsvlnlvivkkgekdiegLtd 126 210s vrgciv +dl+vl l i+k+ge+di+gLtd 210s CUFF.58.1.p1 107 VRGCIVGQDLAVLALAIIKQGEQDIPGLTD 136 210s *****************************8 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (126 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 3910.18 210s // 210s Query: RNA_POL_M_15KD [M=36] 210s Accession: PF02150.15 210s Description: RNA polymerases M/15 Kd subunit 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 9.6 0.0 4.5e-05 0.0043 19 33 .. 56 70 .. 53 72 .. 0.78 210s 2 ! 4.0 0.0 0.0026 0.24 8 24 .. 112 128 .. 109 130 .. 0.87 210s 210s Alignments for each domain: 210s == domain 1 score: 9.6 bits; conditional E-value: 4.5e-05 210s STEEEETTSS-EEES CS 210s RNA_POL_M_15KD 19 gknfeCrqCgYeepa 33 210s +k++ C+qC+ +epa 210s CUFF.7.1.p1 56 NKVLRCSQCDWHEPA 70 210s 33466*********8 PP 210s 210s == domain 2 score: 4.0 bits; conditional E-value: 0.0026 210s TSBEEEEECSSSTEEEE CS 210s RNA_POL_M_15KD 8 gNlLlpkedkegknfeC 24 210s Nl l+k+++eg++f C 210s CUFF.7.1.p1 112 QNLFLSKSKEEGVIFLC 128 210s 59**********99988 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (36 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1611.99 210s // 210s Query: SAUGI [M=111] 210s Accession: PF06106.10 210s Description: S. aureus uracil DNA glycosylase inhibitor 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(-) 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 210s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 210s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 210s y ++ n ++i g +nhf ++++ 210s CUFF.26.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 210s 4666788999***********998754 PP 210s 210s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 210s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 210s +n + + i+ lm+an l s+ +l h+ + + 210s CUFF.26.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 210s 555566667764269**************997654 PP 210s 210s >> CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 210s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 210s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 210s y ++ n ++i g +nhf ++++ 210s CUFF.27.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 210s 4666788999***********998754 PP 210s 210s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 210s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 210s +n + + i+ lm+an l s+ +l h+ + + 210s CUFF.27.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 210s 555566667764269**************997654 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (111 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 781.41 210s // 210s Query: Smim3 [M=60] 210s Accession: PF17307.1 210s Description: Small integral membrane protein 3 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 3.5 0.0 0.0027 0.26 12 33 .. 11 32 .. 2 35 .. 0.70 210s 2 ! 5.4 0.1 0.00072 0.068 42 56 .. 88 102 .. 85 106 .. 0.89 210s 210s Alignments for each domain: 210s == domain 1 score: 3.5 bits; conditional E-value: 0.0027 210s Smim3 12 vLPkhiLDiWvivLiiLativi 33 210s LP++ ++ +vLii+ t ++ 210s CUFF.51.1.p1 11 SLPRYKFLLFSVVLIIVMTTLV 32 210s 5677777777788877766555 PP 210s 210s == domain 2 score: 5.4 bits; conditional E-value: 0.00072 210s Smim3 42 ataviiYRvrthPvl 56 210s at v+i+R++ hP+ 210s CUFF.51.1.p1 88 ATRVLIHRLKYHPTT 102 210s 9************85 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (60 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2402.23 210s // 210s Query: SnoaL [M=126] 210s Accession: PF07366.11 210s Description: SnoaL-like polyketide cyclase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 5.8 0.0 0.00065 0.062 45 64 .. 7 26 .. 3 28 .. 0.89 210s 2 ! 22.5 0.1 4.3e-09 4.1e-07 5 110 .. 14 107 .. 9 114 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 5.8 bits; conditional E-value: 0.00065 210s HHHHHHHHHCTTCEEEEEEE CS 210s SnoaL 45 afveelfkafPDlkvevedl 64 210s f+++lfkaf D++++ve+l 210s CUFF.36.1.p1 7 SFIRQLFKAFTDFSTDVESL 26 210s 5889*************986 PP 210s 210s == domain 2 score: 22.5 bits; conditional E-value: 4.3e-09 210s HHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE-TT-EEEEEEEE CS 210s SnoaL 5 rfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGipptGkkvkfeeit 101 210s ++++++ s d++ l+ ++++d+ + ++++ l++f ++++l++ + l ++v+++v++g k+a+ + + i +G + +++ i 210s CUFF.36.1.p1 14 KAFTDF--STDVESLRGFLTPDYRQL--VDGRELTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIA--------HAIRSSGESSRIKVIA 98 210s 556666..779***********9988..559**********************************99998885........56999*********** PP 210s 210s EEEEETTEE CS 210s SnoaL 102 llrvedGkI 110 210s ++ ++dG+I 210s CUFF.36.1.p1 99 FYSFKDGRI 107 210s ********9 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (126 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1316.33 210s // 210s Query: SnoaL_2 [M=102] 210s Accession: PF12680.6 210s Description: SnoaL-like domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 38.4 0.0 8.5e-14 8.1e-12 2 100 .. 10 108 .. 9 110 .. 0.92 210s 210s Alignments for each domain: 210s == domain 1 score: 38.4 bits; conditional E-value: 8.5e-14 210s HHHHHHHH..TTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEET CS 210s SnoaL_2 2 rrflaaln..agdldalaalfapdvvwedpggelrGreairaffraafaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrved 96 210s r+++ a++ + d++ l+ +++pd+++ g e ++++ + +a++ ++ l++ ++++v++g+++a+ +++ i+ +g+ ++++++++ ++d 210s CUFF.36.1.p1 10 RQLFKAFTdfSTDVESLRGFLTPDYRQLVDGRE-LTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIAHA-IRSSGESSRIKVIAFYSFKD 104 210s 789999998899***************999865.5889999999999999*******************9888877.9******************* PP 210s 210s TEEE CS 210s SnoaL_2 97 GkIv 100 210s G+I 210s CUFF.36.1.p1 105 GRIS 108 210s ***6 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (102 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3920.15 210s // 210s Query: Sugar_tr [M=452] 210s Accession: PF00083.23 210s Description: Sugar (and other) transporter 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 370.4 24.1 1.4e-114 6.7e-113 2 451 .. 10 466 .. 9 467 .. 0.95 210s 210s Alignments for each domain: 210s == domain 1 score: 370.4 bits; conditional E-value: 1.4e-114 210s HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTST.T--SHHHHHH....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-T CS 210s Sugar_tr 2 alvaalggllfgYdtgvigafltllkfaknfg.lsksksskee.ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaa 96 210s +++++++g l+g dtg i+++l + +f+++f ++ s+ ++ s+ ++ l+++ ++G+++G+++++++++r+G+k+s+ +++ +++i+ +l ++a 210s CUFF.24.1.p1 10 VVFISMSGWLQGADTGSISGILGMRDFQSRFAdRYNPISNSYSySAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAELLLVTA 106 210s 67899**********************99987534433333334899************************************************** PP 210s 210s TTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS 210s Sugar_tr 97 kgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193 210s s+ +++vg++l+G+g+G+ svl+P y+sE+Ap+++Rga+v yq + t lvaa++++g+ k +++ wr +g+++++ +ll++++lflPE 210s CUFF.24.1.p1 107 V--PSWIQVLVGKILAGVGIGALSVLSPGYQSEVAPPQIRGAVVATYQIFSTGAALVAACINMGTHKLRKTASWRTSFGINMLWGILLMVGVLFLPE 201 210s *..89******************************************************************************************** PP 210s 210s -HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS- CS 210s Sugar_tr 194 SPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeee....kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgl 286 210s SPryl+ kg++eea +++ ++ + +++++ ++ +++++ e e ka w e++++ ++r+r+ +g+++++f l G+n+ +yy++++f+ +g+ 210s CUFF.24.1.p1 202 SPRYLIYKGRDEEALRIMCNMAELSPESEIIQTNFNTIKSDIEIEmaggKARWIEIFGK-DIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGM 297 210s ********************99999999988888888888888888888*********9.99*********************************** PP 210s 210s THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH.....HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH CS 210s Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg...ivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsEl 378 210s ++ +l +i+g++nf +tf a++++d +GRR+ l++Gaa+++icf+i++ l++++++ a+ v+ivf +lf++ + ++wgp+ wv+v E+ 210s CUFF.24.1.p1 298 TDIFLPAVILGAINFGTTFGALYTIDNLGRRNPLIFGAAFQSICFFIYAavgDRKLIYKNGTsdHRAGSVMIVFSCLFLFSYCCSWGPMGWVIVGET 394 210s *************************************************87655667777768899******************************* PP 210s 210s SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS 210s Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieel 451 210s fp + Rsk++++a+ nwl nf is+++p+i +aig ++ ++++a++++++ +++ff etkg+tlee++ l 210s CUFF.24.1.p1 395 FPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIG-FKLGYIYACINLFSSFMIFFLAKETKGLTLEEVNDL 466 210s ************************************.********************************9976 PP 210s 210s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 30.0 30.1 2.7e-11 1.3e-09 25 437 .. 121 530 .. 105 534 .. 0.75 210s 210s Alignments for each domain: 210s == domain 1 score: 30.0 bits; conditional E-value: 2.7e-11 210s HHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS 210s Sugar_tr 25 llkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121 210s + + ++ g s+ +s s+l + flvG +Gsl + +l+d++GR ++ ++ ++f i +v ++a+ +v+ l++ R++ G++ + + 210s CUFF.37.1.p1 121 FASSVYSSGIIDIASELHSSIPVSTLGSCTFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAH---NVWTLAIVRFFQGVFGSTPLA 214 210s 5555555555555555555677899999*********************************************...********************* PP 210s 210s HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS---HHHHHHTT-HHHHHHHHHHHHH CS 210s Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill.lflPESPrylvekgkeeeakevlaklrg 216 210s + +is + ++ R ++ + ++ +G +++ i+g ++ + + + wr+++++++++a ++++++ +f+PE+ e + + + l+k g 210s CUFF.37.1.p1 215 NAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFItQSYLE---WRWTFWINMIWAAAVIVFVfIFFPET----HEDTILDYKAKYLRKTTG 304 210s *********999999999999999999********99888455555...**************99998689****....333333333334444333 PP 210s 210s C....HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHT.TTHHHHSS-THH.....HHHHHHHHHH.HHH CS 210s Sugar_tr 217 e....edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyys.ptifenlglsks.....llvtiivgvv.nfv 302 210s + + +re + + ++++a+ ++ ++ ++++ ++++ + ++ + in+i + + p +f + g++k + + ++vg+v + 210s CUFF.37.1.p1 305 NtayyTIHERERDPKNAMIQAA----TQAVSLIFTE------PIVVCFTLYLTVVYIINYINFEGyPIVFAKYGFNKGeqglsF-IGVGVGIVcAGL 390 210s 3123333333333333333333....3344444444......455555666666777787777654889********9988844.444444440445 PP 210s 210s HHHHHHHHHHHS-SHHHHHHH........HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH..SHTTTHHHHHH CS 210s Sugar_tr 303 atfvaiflvdrfGRRtllllG........aagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsEl..fpqsvRskala 389 210s t + + ++ +++ +++ ++g++++ + + ++++ i iv ++ a+f++++ v++v + + q++ ++ala 210s CUFF.37.1.p1 391 CTPFIYWHYLKVNKKRNGVICpedrlyplFIGCFLLPISMF--WFAWTCYP--HHIHWIVP-IIASAFFGFSLLIVFFVSYNYIidSYQHMAPSALA 482 210s 56666688999999999****9***7765555555555554..44444443..23444444.455699999******999999844469******** PP 210s 210s HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS CS 210s Sugar_tr 390 iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffv 437 210s a+ v a+ is++ + ++g + v +++ v+++ + f+f+ 210s CUFF.37.1.p1 483 AATLVRYSASGGISMVARPMYLNLGDHWATSVLGFISVAMVPIPFIFY 530 210s *************************99999999999999999998886 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (452 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 210s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 2 [number of targets reported over threshold] 210s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 210s # Mc/sec: 734.97 210s // 210s Query: SUI1 [M=76] 210s Accession: PF01253.21 210s Description: Translation initiation factor SUI1 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+ 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 16.5 0.2 5e-07 4.8e-05 3 52 .. 82 132 .. 80 177 .. 0.88 210s 2 ? -1.8 0.0 0.26 25 16 38 .. 167 188 .. 158 189 .. 0.69 210s 210s Alignments for each domain: 210s == domain 1 score: 16.5 bits; conditional E-value: 5e-07 210s SUI1 3 pkihirveqrggrKkvTtvsglepfgidlkklakelkkkfacsgsvvk.dg 52 210s +k+++rve +g+ ++T +g+++ +l +l+++++++ ++ ++ dg 210s CUFF.54.1.p1 82 RKVKLRVEDIQGKSCLTSFNGFDMTSDKLRSLVRKWQSTIEANQTIKTtDG 132 210s 69*******************************************944444 PP 210s 210s == domain 2 score: -1.8 bits; conditional E-value: 0.26 210s SUI1 16 KkvTtvsglepfgidlkklakel 38 210s K ++++ ++g +k+l+++l 210s CUFF.54.1.p1 167 KMFQVIQNQ-ANGCSMKELVQKL 188 210s 444455555.8888888888876 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (76 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 1017.57 210s // 210s Query: Sulfatase [M=309] 210s Accession: PF00884.22 210s Description: Sulfatase 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 11.6 0.1 7.3e-06 0.00069 3 61 .. 48 106 .. 46 125 .. 0.91 210s 2 ! 11.6 0.0 7.7e-06 0.00073 218 309 .] 223 321 .. 221 321 .. 0.71 210s 210s Alignments for each domain: 210s == domain 1 score: 11.6 bits; conditional E-value: 7.3e-06 210s EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS- CS 210s Sulfatase 3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgry 61 210s vv++++d l+a+ + + ++ ++ t+ l + ++g+ f+ f + +++ p + al tg 210s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGFSAFARSPTVTMPRLKALTTGTI 106 210s 9***********9999999999999999999**********999************975 PP 210s 210s == domain 2 score: 11.6 bits; conditional E-value: 7.7e-06 210s HHHHHHHHHHHHHHHHHTTTGGGE..EEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC......EEECSEEE......GGGHH CS 210s Sulfatase 218 veyvDdligrvlaaLeenglldnt..lvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap......rvseelvs......hiDlf 300 210s + ++D i+r++++L+e ++ nt l+v +Dhg + +gg + + + t l+ ++e+++ ++++++s ++D++ 210s CUFF.53.1.p1 223 LLEIDTIISRIYKYLQEYDEKTNThsLIVLCGDHGMNEVG----NHGGSS---SGETTAALSLLFPSNELSHinkpilNMDDNPYSilerveQVDVV 312 210s 6799************999999987789999****94322....222222...33444444455555555556666776888888888888899999 PP 210s 210s HHHHHHTTE CS 210s Sulfatase 301 ptildlagi 309 210s pti l+gi 210s CUFF.53.1.p1 313 PTICLLLGI 321 210s 999888875 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (309 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3397.80 210s // 210s Query: ThiJ_like [M=196] 210s Accession: PF17124.4 210s Description: ThiJ/PfpI family-like 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(-) 210s 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( 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 29.3 0.3 1.1e-10 3.3e-09 3 155 .. 47 185 .. 46 198 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 29.3 bits; conditional E-value: 1.1e-10 210s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 210s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 210s CUFF.47.1.p1 47 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 134 210s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 210s 210s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlw 155 210s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + 210s CUFF.47.1.p1 135 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYH 185 210s 99.9999999999988888.......4568*****************999998887655 PP 210s 210s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 29.1 0.2 1.2e-10 3.9e-09 3 160 .. 26 169 .. 25 185 .. 0.78 210s 210s Alignments for each domain: 210s == domain 1 score: 29.1 bits; conditional E-value: 1.2e-10 210s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 210s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 210s CUFF.46.1.p1 26 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 113 210s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 210s 210s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmerts 160 210s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + t+ 210s CUFF.46.1.p1 114 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYHKHVTA 169 210s 99.9999999999988888.......4568*****************99999998866655555 PP 210s 210s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 10.9 0.2 4.5e-05 0.0014 77 169 .. 77 164 .. 16 190 .. 0.77 210s 210s Alignments for each domain: 210s == domain 1 score: 10.9 bits; conditional E-value: 4.5e-05 210s ThiJ_like 77 sesFsleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpe...ldlktttlPlwmertsillgstaek 169 210s ++ ++ +y++ + GG++ ++ lh+ ++ + v++a+c+g + l + k+ +k t+ ++ e + ++ +++ 210s CUFF.42.1.p2 77 ASDINFSDYSIFFAAGGHGTLF-DFPSATNLHKGAAKIY-------SMGGVIAAVCHGPVILPCIKDStgfSIVKGKTVTAFNEIAEQQMNLMPTF 164 210s 3345889************999.9999999999988877.......5568********99998887775554456666666666555555555555 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (196 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 210s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 210s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 3 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 210s # Mc/sec: 587.34 210s // 210s Query: TPP_enzyme_C [M=153] 210s Accession: PF02775.20 210s Description: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 2.2 0.0 0.0076 0.72 115 153 .] 132 172 .. 107 172 .. 0.80 210s 2 ? -3.6 0.1 0.47 45 112 124 .. 234 246 .. 227 252 .. 0.76 210s 3 ! 81.8 0.0 2.3e-27 2.2e-25 24 153 .] 415 539 .. 395 539 .. 0.85 210s 210s Alignments for each domain: 210s == domain 1 score: 2.2 bits; conditional E-value: 0.0076 210s HHHHHTTSE.EE..EESSH.HHHHHHHHHHHHCSSSEEEEEE CS 210s TPP_enzyme_C 115 klaealGak.ga..rvekadveeleealkealekkgpaliev 153 210s ++a+ l + +a r e+a + ++ a+++a+ +++p++ie+ 210s CUFF.32.1.p1 132 EIAKKLTCAaVAikRAEDA-PVMIDHAIRQAILQHKPVYIEI 172 210s 6788887775667665555.78899*******999****996 PP 210s 210s == domain 2 score: -3.6 bits; conditional E-value: 0.47 210s -HHHHHHHTTSEE CS 210s TPP_enzyme_C 112 dfaklaealGakg 124 210s f+klaeal + + 210s CUFF.32.1.p1 234 AFVKLAEALNCAA 246 210s 6999999998874 PP 210s 210s == domain 3 score: 81.8 bits; conditional E-value: 2.3e-27 210s ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHT CS 210s TPP_enzyme_C 24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaeal 120 210s + +g++G+++p A+G ++a+p+r+ +++vGDG+f+ ++qe+++++r++lp+++++lnN+gy + ++ ++ r ++ dfa+++e+l 210s CUFF.32.1.p1 415 EMQWGHIGWSVPSAMGYAVAAPERRTIVMVGDGSFQLTGQEISQMIRHKLPVLIFLLNNRGYTIEIQIHDGPYN-R--------IQNWDFAAFCESL 502 210s 56789*********************************************************766666666664.2........6799********* PP 210s 210s TSE.EE....EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS 210s TPP_enzyme_C 121 Gak.ga....rvekadveeleealkeal.ekkgpaliev 153 210s + g ++ eel a+k al +k+gp+lie+ 210s CUFF.32.1.p1 503 NGEtGKakglHAKTG--EELTSAIKVALqNKEGPTLIEC 539 210s 666555674455555..***********99*******97 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (153 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 2975.89 210s // 210s Query: TPP_enzyme_M [M=137] 210s Accession: PF00205.21 210s Description: Thiamine pyrophosphate enzyme, central domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 76.8 0.0 7.2e-26 6.9e-24 3 113 .. 207 316 .. 205 325 .. 0.90 210s 210s Alignments for each domain: 210s == domain 1 score: 76.8 bits; conditional E-value: 7.2e-26 210s HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHH.HH-SEEEEES-SSSTCCCTTTT CS 210s TPP_enzyme_M 3 raaellkkakrpvilvGggvsrsgaskelrelaeklgiPvvttlmgkgaipedhplylG.mlgllgspaaneal.eeaDlvlllGarlsdirttgss 97 210s aael++k+++p++l+G + + +ga+ ++++lae+l++ + ++++kg+++e+h++y+G ++g ++s++ +a+ e++Dlv+ G+ ++d++t g 210s CUFF.32.1.p1 207 IAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMPAAKGFYSEEHKNYAGvYWGEVSSSETTKAVyESSDLVIGAGVLFNDYSTVGWR 303 210s 599***************************************************************99999999899****************9966 PP 210s 210s TTTTTT-EEEEEESSC CS 210s TPP_enzyme_M 98 pefapeakiihididp 113 210s + +p+ i +++d 210s CUFF.32.1.p1 304 AAPNPN---ILLNSDY 316 210s 666666...5555554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (137 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3005.79 210s // 210s Query: TPP_enzyme_N [M=172] 210s Accession: PF02776.17 210s Description: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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( 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 121.7 0.1 1.3e-39 1.3e-37 1 170 [. 9 183 .. 9 185 .. 0.94 210s 2 ! 2.6 0.0 0.005 0.48 136 161 .. 516 541 .. 428 545 .. 0.91 210s 210s Alignments for each domain: 210s == domain 1 score: 121.7 bits; conditional E-value: 1.3e-39 210s EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEE CS 210s TPP_enzyme_N 1 ltvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvls 97 210s +tv+++l+++L + g++ f vpG+ +l lld l+ +g++ + + +E ++afaA+gyar+ g +++++vt+ +Ga+ a+ ++ +A+ +++P++++s 210s CUFF.32.1.p1 9 MTVGTYLAQRLVEIGIKNHFVVPGDYNLRLLDFLEYYPGLSEIGCCNELNCAFAAEGYARSNG-IACAVVTYSVGALTAFDGIGGAYAENLPVILVS 104 210s 89**********************************************************976.********************************* PP 210s 210s EE--CCCHH.....S--TC.-T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EEEH CS 210s TPP_enzyme_N 98 gdrptslrg.....qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleevde 170 210s g+++t + + +++l q+++++++t +a+ ++++e++p++++ Air+a ++ Pvy+e+p ++ +++++ 210s CUFF.32.1.p1 105 GSPNTNDLSsghllHHTLGTHDfeYQMEIAKKLTCAAVAIKRAEDAPVMIDHAIRQA-ILQHKPVYIEIPTNMANQPCPV 183 210s *********9888755555333657********************************.99****************9986 PP 210s 210s == domain 2 score: 2.6 bits; conditional E-value: 0.005 210s HHHHHHHHHHHHHSSS--EEEEEEEH CS 210s TPP_enzyme_N 136 lpealrrAirtalsgrpgPvylelpk 161 210s + e+l Ai++al+++ gP ++e + 210s CUFF.32.1.p1 516 TGEELTSAIKVALQNKEGPTLIECAI 541 210s 568999***************99665 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (172 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 210s # Mc/sec: 3014.93 210s // 210s Query: Transferase [M=434] 210s Accession: PF02458.14 210s Description: Transferase family 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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(+) 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 12.1 0.0 3.1e-06 0.0003 348 403 .. 49 107 .. 37 111 .. 0.76 210s 210s Alignments for each domain: 210s == domain 1 score: 12.1 bits; conditional E-value: 3.1e-06 210s Transferase 348 nstlkaelv..skgkkdgeevtvsswlklplyevdFGwgkP..vyvvpvvsskkdnkill 403 210s n tl+a+++ ++g ++ + +v +wlk++l v FG g P v++ +++s+ + ++i++ 210s CUFF.2.1.p1 49 N-TLMAHCFetYNGVEKSGTQCVADWLKVGLLAVTFGAGGPrlVNTLGGSSPTTKRVIYI 107 210s 4.5666664226777777*********************995566777888888877554 PP 210s 210s 210s 210s Internal pipeline statistics summary: 210s ------------------------------------- 210s Query model(s): 1 (434 nodes) 210s Target sequences: 95 (31269 residues searched) 210s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 210s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 210s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 210s Initial search space (Z): 95 [actual number of targets] 210s Domain search space (domZ): 1 [number of targets reported over threshold] 210s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 210s # Mc/sec: 7210.66 210s // 210s Query: TRAPP [M=146] 210s Accession: PF04051.15 210s Description: Transport protein particle (TRAPP) component 210s Scores for complete sequences (score includes all domains): 210s --- full sequence --- --- best 1 domain --- -#dom- 210s E-value score bias E-value score bias exp N Sequence Description 210s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 210s 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 210s 210s 210s Domain annotation for each sequence (and alignments): 210s >> CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-505(+) 210s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 210s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 210s 1 ! 83.1 0.2 8.5e-28 8e-26 1 99 [. 34 142 .. 34 163 .. 0.88 210s 210s Alignments for each domain: 210s == domain 1 score: 83.1 bits; conditional E-value: 8.5e-28 210s TRAPP 1 fefllgelvsylirdskdveeve..........krLekmGyrvGlrllelllarerpretdilevlkfickdlWkalfgkqidnlktnhrgeyvltd 87 210s ++fll+elv+++ r ++d ++ + + Le++G++vG +++e +l+ +r+r t++ +v+ f+c++lW ++f+k+ dnlktn+rg +vltd 210s CUFF.55.1.p1 34 LDFLLIELVHTAKRLAEDRKKKSsseksiesdfQMLESIGFQVGRKITE-RLLLNRNRITETTDVMRFLCRELWPIVFRKPLDNLKTNRRGIFVLTD 129 210s 58************9999888889999**********************.888888***************************************** PP 210s 210s TRAPP 88 nef.pltrfvelp 99 210s + f ++t+++ + 210s CUFF.55.1.p1 130 TYFyWFTKMTAMT 142 210s *********6433 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (146 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 211s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 3797.94 211s // 211s Query: TRI12 [M=599] 211s Accession: PF06609.12 211s Description: Fungal trichothecene efflux pump (TRI12) 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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(+) 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 29.7 27.0 1.3e-11 1.2e-09 31 494 .. 69 553 .. 49 575 .. 0.69 211s 211s Alignments for each domain: 211s == domain 1 score: 29.7 bits; conditional E-value: 1.3e-11 211s TRI12 31 elpegyyrsprvvasfaafslnvvatyfvlqasasa.lpnilqdvgqsensslfstlwttgqavsil...vmgrltdrfgrrpfvilthilglvgai 123 211s + + y+ r + af + ++a + +s+ + + +s++stl +s + ++g+++d r l ++ ++g i 211s CUFF.25.1.p1 69 AVRDSIYQNKRGMYLAYAFGIAILACSWASAIQSSTtYSYQVYATASFNRTSMISTLEIATAIISSVckpILGKFSDITSRPMTYTLVLLFYVIGFI 165 211s 4567777777777666778877777766543333330333334445556679999998776665544233899999987765555666677788889 PP 211s 211s TRI12 124 vgctatkfntllaamtllgv.aagpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiy.iitsaiav.llivvwy 217 211s v ++++ + + + ++ + ++g l+vg+l s k + + ++s p ++t + ++ q + i+ +wrw + ++ ii+ a+ +i++ y 211s CUFF.25.1.p1 166 VVASSSTISAYVIGSVFISIgSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVWFTGFIVQGI-IDSNWRWGYGMFaIIMPAVMTpAVIILMY 261 211s 888888888877777776662457777899*********9987777889********9999999986.9******9987646777765514555555 PP 211s 211s TRI12 218 ypps......fa.....qlhgk...kvrkreelak....ldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkp 296 211s ++ q k k +k ++l k +d g+il+ vg s++ll s ++ w+ +i ++ g l+ ++ ye++ p 211s CUFF.25.1.p1 262 LERQankdenIKkiinyQTEEKnknKQSKWQKLWKavleVDLFGLILLGVGWSILLLPFSLTSYAKNGWKNPSMIAMMVVGGVILIAYSGYEMFIAP 358 211s 4332111111221111122223111444555554444448*******************************************************99 PP 211s 211s TRI12 297 vrpivppalfkdtrgfvcillissimgamnlslviiypqq.vvnifgsslknwee..tawmsatasfgtgagvvvlgslfhlvrhirwqilvgalwl 390 211s p p +++ r f+ ++i + l +y ++ s ++w + a + fg +ag + +fh ++++ lv + 211s CUFF.25.1.p1 359 Y-PSCPRRVMN--RTFITAVIIDFFYY-LAGYLQSMYFTTyTWILYDWSYRDWTYfnNTMTIALCVFGVFAGAM--HRVFHRYKYLQIIGLVIKI-- 447 211s 6.888998875..77999888876554.44455556655504556889*****8521334457789******87..6899977776544444333.. PP 211s 211s TRI12 391 taflgamssvnrd.nknaaialsv.lsgfvvawaqditmllvqfittdedlgvafavvaaarpfagsiftaafislysnrypkelashlssalrgtd 485 211s g + n + +a s+ l g+ +++ + + q +dl +a +++ + g+i +a ++sn+ pk l +l s++ t+ 211s CUFF.25.1.p1 448 -VGYGILIRPNFAaTGKVDLAWSLiLIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGAAIASPIFSNKVPKYLREYLPSSINDTQ 543 211s .33344433332202233344443144555555555566778999999***************999999999999*******************999 PP 211s 211s TRI12 486 ipq.asfssl 494 211s + + s ssl 211s CUFF.25.1.p1 544 VYNfYSDSSL 553 211s 7651455555 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (599 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 211s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 211s # Mc/sec: 1013.73 211s // 211s Query: UPF0489 [M=178] 211s Accession: PF12640.6 211s Description: UPF0489 domain 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 12.0 0.0 1e-05 0.00099 7 43 .. 186 229 .. 183 270 .. 0.67 211s 211s Alignments for each domain: 211s == domain 1 score: 12.0 bits; conditional E-value: 1e-05 211s UPF0489 7 HheaLeaiyraigskklpsdlslvHlDaHpDllipk..........k 43 211s H+ +L+ i r +++ + ++s++H+D+H D pk 211s CUFF.38.1.p4 186 HTIVLP-ILRSVSRAY--GPVSIIHFDSHLDSWKPKvfgggkssvgS 229 211s 444444.555566666..99***********8777666555554440 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (178 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 211s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 4378.72 211s // 211s Query: Usher [M=551] 211s Accession: PF00577.19 211s Description: Outer membrane usher protein 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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- 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 11.1 0.0 7.2e-06 0.00069 35 132 .. 17 114 .. 2 116 .. 0.77 211s 211s Alignments for each domain: 211s == domain 1 score: 11.1 bits; conditional E-value: 7.2e-06 211s EEEEEEEEEETTTTEEEEEEEEE--SSSS---EEEEEEEEE-GGGS-CCCCCEEEEEEEEESSSEEEEEECTTEEEEEEEE-SEEEEE-S---TTTT CS 211s Usher 35 ssrtylqraipqlkskLtlGesytssdiFdsvsfrGvsLasddnmlPdslrgyaPevrGiArtnAkVtirqnGyviYqtlVppGpFeiqdlnptsss 131 211s +s + r + +l+++ G s+++++i + + + +L+ + + + ++ +P G Ar+n +t+ + +viY+t+ +pG + + s++ 211s CUFF.20.1.p2 17 WSARRVCRIFANLRTHRARGSSNVKNEIKKQEGNVSFQLKMSVKQFVSDGHIVRPYLLGLARSNPGLTVIEHDRVIYRTASAPGSGDLPKVTLVSGG 113 211s 5555566667777777777777777777777777777777776666667777889999**************************9888888777766 PP 211s 211s C CS 211s Usher 132 g 132 211s g 211s CUFF.20.1.p2 114 G 114 211s 5 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (551 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 211s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 211s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 3266.95 211s // 211s Query: zf-C2H2 [M=23] 211s Accession: PF00096.25 211s Description: Zinc finger, C2H2 type 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 16.2 1.0 5.9e-07 5.6e-05 1 20 [. 31 50 .. 31 51 .. 0.95 211s 2 ! 19.7 1.9 4.7e-08 4.4e-06 2 23 .] 60 82 .. 59 82 .. 0.96 211s 211s Alignments for each domain: 211s == domain 1 score: 16.2 bits; conditional E-value: 5.9e-07 211s EEETTTTEEESSHHHHHHHH CS 211s zf-C2H2 1 ykCpdCgksFkrksnLkrHi 20 211s ++C+ C k+F+r +nL+rH 211s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 211s 89*****************5 PP 211s 211s == domain 2 score: 19.7 bits; conditional E-value: 4.7e-08 211s EETTTTEEESSHHHHHHHHHC.C CS 211s zf-C2H2 2 kCpdCgksFkrksnLkrHirt.H 23 211s +Cp+C ++krk++LkrHi++ H 211s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRfH 82 211s 6********************99 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (23 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 211s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1214.43 211s // 211s Query: zf-C2H2_4 [M=24] 211s Accession: PF13894.5 211s Description: C2H2-type zinc finger 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 10.0 4.0 7.8e-05 0.0074 1 20 [. 31 50 .. 31 53 .. 0.89 211s 2 ! 12.9 1.6 8.8e-06 0.00084 2 24 .] 60 82 .. 59 82 .. 0.93 211s 211s Alignments for each domain: 211s == domain 1 score: 10.0 bits; conditional E-value: 7.8e-05 211s zf-C2H2_4 1 fkCpiCgksFsskkaLlrHl 20 211s f+C++C k+F+++++L rH 211s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 211s 89********99999****4 PP 211s 211s == domain 2 score: 12.9 bits; conditional E-value: 8.8e-06 211s zf-C2H2_4 2 kCpiCgksFsskkaLlrHlkthH 24 211s +Cp+C +++k+ L+rH+++ H 211s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRFH 82 211s 7********99999*****9988 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (24 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 211s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1276.11 211s // 211s Query: zf-C2H2_6 [M=27] 211s Accession: PF13912.5 211s Description: C2H2-type zinc finger 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 20.0 3.1 2.7e-08 2.6e-06 1 26 [. 30 55 .. 30 56 .. 0.96 211s 2 ? -3.5 0.6 0.62 59 4 7 .. 61 64 .. 60 65 .. 0.86 211s 211s Alignments for each domain: 211s == domain 1 score: 20.0 bits; conditional E-value: 2.7e-08 211s zf-C2H2_6 1 vfeCdeCsksFpslqaLggHkksHrk 26 211s vf Cd+C k+F + +L+ Hk++H k 211s CUFF.45.1.p1 30 VFPCDQCAKRFTRHENLTRHKACHSK 55 211s 79**********************97 PP 211s 211s == domain 2 score: -3.5 bits; conditional E-value: 0.62 211s zf-C2H2_6 4 CdeC 7 211s C++C 211s CUFF.45.1.p1 61 CPYC 64 211s **** PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (27 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 211s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1093.04 211s // 211s Query: zf-C2H2_jaz [M=27] 211s Accession: PF12171.7 211s Description: Zinc-finger double-stranded RNA-binding 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 8.2 0.2 0.00018 0.017 2 21 .. 31 50 .. 30 51 .. 0.92 211s 2 ! 5.3 0.1 0.0014 0.13 4 21 .. 61 78 .. 58 79 .. 0.93 211s 3 ? -3.8 0.1 1 95 10 16 .. 166 172 .. 165 172 .. 0.83 211s 211s Alignments for each domain: 211s == domain 1 score: 8.2 bits; conditional E-value: 0.00018 211s CBBTTTTBBBSSHHHHHCCT CS 211s zf-C2H2_jaz 2 fYCvlCdKyFksenaldnHl 21 211s f C C+K F +++l H+ 211s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 211s 77*****************6 PP 211s 211s == domain 2 score: 5.3 bits; conditional E-value: 0.0014 211s BTTTTBBBSSHHHHHCCT CS 211s zf-C2H2_jaz 4 CvlCdKyFksenaldnHl 21 211s C++C+ +k l+ H+ 211s CUFF.45.1.p1 61 CPYCEIKCKRKDLLKRHI 78 211s *****************8 PP 211s 211s == domain 3 score: -3.8 bits; conditional E-value: 1 211s BBSSHHH CS 211s zf-C2H2_jaz 10 yFksena 16 211s F+sen+ 211s CUFF.45.1.p1 166 SFNSENV 172 211s 59***96 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (27 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 211s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1427.86 211s // 211s Query: zf-Di19 [M=54] 211s Accession: PF05605.11 211s Description: Drought induced 19 protein (Di19), zinc-binding 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s ------ inclusion threshold ------ 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ? 11.2 1.0 2e-05 0.0019 3 28 .. 59 85 .. 57 88 .. 0.79 211s 211s Alignments for each domain: 211s == domain 1 score: 11.2 bits; conditional E-value: 2e-05 211s zf-Di19 3 ftCPyCgkeltvkeLv.eHvedeHrve 28 211s ++CPyC+ + + k L+ +H++ H ++ 211s CUFF.45.1.p1 59 IPCPYCEIKCKRKDLLkRHIQRFHNDK 85 211s 68*****99877776527***999876 PP 211s 211s eval $cmd 211s ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (54 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 211s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 211s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 888.40 211s // 211s Query: zf-H2C2_2 [M=26] 211s Accession: PF13465.5 211s Description: Zinc-finger double domain 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 7.6 0.4 0.0003 0.028 12 26 .] 28 42 .. 26 42 .. 0.83 211s 2 ! 10.1 4.9 4.9e-05 0.0047 1 21 [. 45 65 .. 45 70 .. 0.90 211s 3 ? 0.9 0.1 0.042 4 2 10 .. 74 83 .. 74 89 .. 0.70 211s 211s Alignments for each domain: 211s == domain 1 score: 7.6 bits; conditional E-value: 0.0003 211s zf-H2C2_2 12 ekpyeCplCdkaFkt 26 211s ++ + C+ C+k+F++ 211s CUFF.45.1.p1 28 KRVFPCDQCAKRFTR 42 211s 4559*********85 PP 211s 211s == domain 2 score: 10.1 bits; conditional E-value: 4.9e-05 211s zf-H2C2_2 1 nLrrHlrkHtgekpyeCplCd 21 211s nL+rH + H + p Cp+C 211s CUFF.45.1.p1 45 NLTRHKACHSKAEPIPCPYCE 65 211s 8*******************7 PP 211s 211s == domain 3 score: 0.9 bits; conditional E-value: 0.042 211s zf-H2C2_2 2 LrrHlr.kHt 10 211s L+rH+ +H 211s CUFF.45.1.p1 74 LKRHIQrFHN 83 211s 89**962586 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (26 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 211s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1181.33 211s // 211s Query: zf-TRAF [M=60] 211s Accession: PF02176.17 211s Description: TRAF-type zinc finger 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s ------ inclusion threshold ------ 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ? 7.3 8.4 0.00042 0.04 9 56 .. 30 72 .. 27 80 .. 0.77 211s 2 ? -2.0 0.0 0.33 31 26 43 .. 276 293 .. 274 294 .. 0.77 211s 211s Alignments for each domain: 211s == domain 1 score: 7.3 bits; conditional E-value: 0.00042 211s EEE-TT--S-BEEETTTCCCCCCTTSTTS--XXSSXXXXSXXXXXHHH CS 211s zf-TRAF 9 pvpCpnecckkkilRkdlkdHlekdCkkaevkCkfkevGCkekvkrea 56 211s pC ++c+k ++l H + k +++C++ C+ k+kr++ 211s CUFF.45.1.p1 30 VFPC-DQCAKRFTRHENLTRHKACHSKAEPIPCPY----CEIKCKRKD 72 211s 5689.88**9999999*****997777889*****....555555554 PP 211s 211s == domain 2 score: -2.0 bits; conditional E-value: 0.33 211s CCCCCCTTSTTS--XXSS CS 211s zf-TRAF 26 lkdHlekdCkkaevkCkf 43 211s + + ++ +C + v C + 211s CUFF.45.1.p1 276 ISNLIDLECIRRSVFCLY 293 211s 666678889999999988 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (60 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 211s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 211s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1881.56 211s // 211s Query: Zn_clus [M=40] 211s Accession: PF00172.17 211s Description: Fungal Zn(2)-Cys(6) binuclear cluster domain 211s Scores for complete sequences (score includes all domains): 211s --- full sequence --- --- best 1 domain --- -#dom- 211s E-value score bias E-value score bias exp N Sequence Description 211s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 211s 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( 211s 211s 211s Domain annotation for each sequence (and alignments): 211s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 211s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 211s 1 ! 30.8 13.0 1.3e-11 1.2e-09 1 39 [. 5 42 .. 5 44 .. 0.91 211s 211s Alignments for each domain: 211s == domain 1 score: 30.8 bits; conditional E-value: 1.3e-11 211s -S-HHHHHCT---STSSSS-HHHHHCT---ECCCTCCCE CS 211s Zn_clus 1 haCdnCrkkKvKCdakkPaCsnCkklnleCtfysesskr 39 211s +aCd Cr kK+KC++++P C+ C +++C ys++ +r 211s CUFF.38.1.p1 5 KACDLCRLKKIKCSRGQPRCQTCTLFQADCH-YSNRARR 42 211s 59*****************************.7777665 PP 211s 211s 211s 211s Internal pipeline statistics summary: 211s ------------------------------------- 211s Query model(s): 1 (40 nodes) 211s Target sequences: 95 (31269 residues searched) 211s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 211s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 211s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 211s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 211s Initial search space (Z): 95 [actual number of targets] 211s Domain search space (domZ): 1 [number of targets reported over threshold] 211s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 211s # Mc/sec: 1773.12 211s // 211s [ok] 211s * [Mon Mar 11 04:10:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 211s * [Mon Mar 11 04:10:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 211s -skipping training candidate: CUFF.60.1.p1, not unique enough 211s -skipping training candidate: CUFF.26.1.p1, not unique enough 211s -skipping training candidate: CUFF.38.1.p3, not unique enough 211s -skipping training candidate: CUFF.48.1.p1, not unique enough 211s -skipping training candidate: CUFF.60.1.p2, not unique enough 211s -skipping training candidate: CUFF.30.1.p1, not unique enough 211s -skipping training candidate: CUFF.41.1.p1, not unique enough 211s -skipping training candidate: CUFF.41.1.p2, not unique enough 211s -skipping training candidate: CUFF.30.2.p1, not unique enough 211s -skipping training candidate: CUFF.52.1.p3, not unique enough 211s -skipping training candidate: CUFF.20.1.p2, not unique enough 211s -skipping training candidate: CUFF.47.1.p1, not unique enough 211s -skipping training candidate: CUFF.48.1.p3, not unique enough 211s -skipping training candidate: CUFF.13.3.p1, not unique enough 211s -skipping training candidate: CUFF.28.1.p1, not unique enough 211s -skipping training candidate: CUFF.34.1.p2, not unique enough 211s -skipping training candidate: CUFF.13.1.p1, not unique enough 211s -skipping training candidate: CUFF.38.1.p5, not unique enough 211s -skipping training candidate: CUFF.27.1.p2, not unique enough 211s -skipping training candidate: CUFF.41.1.p3, not unique enough 211s -skipping training candidate: CUFF.13.1.p2, not unique enough 211s -skipping training candidate: CUFF.27.1.p3, not unique enough 211s -skipping training candidate: CUFF.41.1.p4, not unique enough 211s 211s -redundancy-minimized set includes 72 / 95 = 75.79% 211s 211s * [Mon Mar 11 04:10:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 211s PCT_GC: 37 211s * [Mon Mar 11 04:10:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores 211s * [Mon Mar 11 04:10:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 212s * [Mon Mar 11 04:10:46 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 212s Selecting best orfsblastp output found (blastp.outfmt6) and processing... 212s PFAM output found (pfam.domtblout) and processing... 212s 212s * [Mon Mar 11 04:10:46 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement 212s Training start codon pattern recognition* [Mon Mar 11 04:10:46 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 212s * [Mon Mar 11 04:10:46 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 212s -round: 1 215s -round: 2 218s -round: 3 222s -round: 4 225s -round: 5 228s * [Mon Mar 11 04:11:02 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 228s -parsing scores 232s * [Mon Mar 11 04:11:06 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 233s Error in library(ggplot2) : there is no package called ‘ggplot2’ 233s Execution halted 233s * [Mon Mar 11 04:11:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 233s Error in library(ggplot2) : there is no package called ‘ggplot2’ 233s Execution halted 233s * [Mon Mar 11 04:11:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 233s Error in library(seqLogo) : there is no package called ‘seqLogo’ 233s Execution halted 233s * [Mon Mar 11 04:11:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 233s Error in library(seqLogo) : there is no package called ‘seqLogo’ 233s Execution halted 233s * [Mon Mar 11 04:11:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 233s num features: 62 num_incorporate: 18 233s -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 233s -feature swap of score: 1.94858034627835 instead of -0.884029553505083 233s -feature swap of score: 2.12188175995298 instead of -0.685343860113718 233s -feature swap of score: 2.31823471239686 instead of 1.3320086516586 233s -feature swap of score: 3.37895288616016 instead of 1.93080159572592 233s -feature swap of score: 3.63482432490867 instead of 3.22946119764082 233s -feature swap of score: 5.41689919345157 instead of 3.20580366781557 233s -num feature swaps: 7 233s * [Mon Mar 11 04:11:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 233s -round: 1 237s -round: 2 240s -round: 3 243s -round: 4 247s -round: 5 250s * [Mon Mar 11 04:11:24 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 250s -parsing scores 255s * [Mon Mar 11 04:11:29 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 256s Error in library(ggplot2) : there is no package called ‘ggplot2’ 256s Execution halted 256s * [Mon Mar 11 04:11:30 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 257s Error in library(ggplot2) : there is no package called ‘ggplot2’ 257s Execution halted 257s * [Mon Mar 11 04:11:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 257s Error in library(seqLogo) : there is no package called ‘seqLogo’ 257s Execution halted 257s * [Mon Mar 11 04:11:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 257s Refining start codon selections. 257s -number of revised start positions: 1 257s * [Mon Mar 11 04:11:31 2024] Running CMD: cp /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 257s copying output to final output file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Mon Mar 11 04:11:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 257s Making bed file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 257s * [Mon Mar 11 04:11:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 257s Making pep file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 257s * [Mon Mar 11 04:11:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 257s Making cds file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 257s transdecoder is finished. See output files /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* 257s 257s 258s 258s 258s ## convert to genome coordinates 258s ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3 258s 258s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1, 612 258s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [3], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1471, 2862 258s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CUFF.30.2.p1. 258s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1164, 2072 258s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 3, 440 258s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1899, 2783 258s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 2759, 3736 258s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1142, 4111 258s -Warning [16], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 3280, 4776 258s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 1, 534 258s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 4115, 4705 258s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 258s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 258s CDS coords: 3, 722 258s 258s 258s Done. 81 / 82 transcript orfs could be propagated to the genome 258s 258s 258s 258s ## make bed files for viewing with GenomeView 258s 258s # covert cufflinks gtf to bed 258s ../../util/gtf_to_bed.pl transcripts.gtf > transcripts.bed 258s 258s # convert the genome-based gene-gff3 file to bed 258s ../../util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.genome.gff3 > transcripts.fasta.transdecoder.genome.bed 258s 258s 258s 258s # ensure no fatal problems w/ pep file 258s ../../util/fasta_prot_checker.pl transcripts.fasta.transdecoder.pep 258s 258s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 258s 258s 258s exit 0 258s make[1]: Leaving directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 258s Running example in $... 258s make[1]: Entering directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 258s ./runMe.sh 258s #!/bin/bash -ve 258s 258s if [ ! -e genome.fasta ]; then 258s gunzip -c genome.fasta.gz > genome.fasta 258s fi 258s 258s if [ ! -e pasa_assemblies.fasta ]; then 258s gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta 258s fi 258s 258s if [ ! -e pasa_assemblies.gff3 ]; then 258s gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3 258s fi 258s 258s if [ ! -e pasa_assemblies_described.txt ]; then 258s gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt 258s fi 258s 258s 258s # get the gene-to-transcript relationships 258s cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt 258s 258s ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir 258s CMD: mkdir -p /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir 258s * [Mon Mar 11 04:11:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat 258s 258s 258s -first extracting base frequencies, we'll need them later. 258s 258s 258s - extracting ORFs from transcripts. 258s -total transcripts to examine: 858 260s [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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 260s 260s 260s ################################# 260s ### Done preparing long ORFs. ### 260s ################################## 260s 260s Use file: /tmp/autopkgtest.B13zNQ/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. 260s 260s Then, run TransDecoder.Predict for your final coding region predictions. 260s 260s 260s 260s 260s 260s ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir 260s * [Mon Mar 11 04:11:34 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 260s * [Mon Mar 11 04:11:34 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 260s -skipping training candidate: asmbl_804.p1, not unique enough 260s -skipping training candidate: asmbl_395.p1, not unique enough 260s -skipping training candidate: asmbl_805.p1, not unique enough 260s -skipping training candidate: asmbl_446.p1, not unique enough 260s -skipping training candidate: asmbl_745.p1, not unique enough 260s -skipping training candidate: asmbl_692.p1, not unique enough 260s -skipping training candidate: asmbl_570.p1, not unique enough 260s -skipping training candidate: asmbl_558.p1, not unique enough 260s -skipping training candidate: asmbl_694.p1, not unique enough 260s -skipping training candidate: asmbl_434.p1, not unique enough 260s -skipping training candidate: asmbl_688.p1, not unique enough 260s -skipping training candidate: asmbl_725.p1, not unique enough 260s -skipping training candidate: asmbl_507.p1, not unique enough 260s -skipping training candidate: asmbl_814.p1, not unique enough 260s -skipping training candidate: asmbl_632.p1, not unique enough 260s -skipping training candidate: asmbl_654.p1, not unique enough 260s -skipping training candidate: asmbl_777.p1, not unique enough 260s -skipping training candidate: asmbl_290.p1, not unique enough 260s -skipping training candidate: asmbl_745.p2, not unique enough 260s -skipping training candidate: asmbl_746.p1, not unique enough 260s -skipping training candidate: asmbl_290.p2, not unique enough 260s -skipping training candidate: asmbl_746.p2, not unique enough 260s -skipping training candidate: asmbl_115.p1, not unique enough 260s -skipping training candidate: asmbl_560.p1, not unique enough 260s -skipping training candidate: asmbl_561.p1, not unique enough 260s -skipping training candidate: asmbl_784.p1, not unique enough 260s -skipping training candidate: asmbl_778.p1, not unique enough 260s -skipping training candidate: asmbl_508.p1, not unique enough 260s -skipping training candidate: asmbl_21.p1, not unique enough 260s -skipping training candidate: asmbl_22.p1, not unique enough 260s -skipping training candidate: asmbl_450.p1, not unique enough 260s -skipping training candidate: asmbl_448.p1, not unique enough 260s -skipping training candidate: asmbl_449.p1, not unique enough 260s -skipping training candidate: asmbl_772.p1, not unique enough 260s -skipping training candidate: asmbl_556.p1, not unique enough 260s -skipping training candidate: asmbl_68.p1, not unique enough 260s -skipping training candidate: asmbl_363.p1, not unique enough 260s -skipping training candidate: asmbl_470.p1, not unique enough 260s -skipping training candidate: asmbl_471.p1, not unique enough 260s -skipping training candidate: asmbl_773.p1, not unique enough 260s -skipping training candidate: asmbl_667.p1, not unique enough 260s -skipping training candidate: asmbl_576.p1, not unique enough 260s -skipping training candidate: asmbl_774.p1, not unique enough 260s -skipping training candidate: asmbl_234.p1, not unique enough 260s -skipping training candidate: asmbl_639.p1, not unique enough 260s -skipping training candidate: asmbl_640.p1, not unique enough 260s -skipping training candidate: asmbl_727.p1, not unique enough 260s -skipping training candidate: asmbl_672.p1, not unique enough 260s -skipping training candidate: asmbl_852.p1, not unique enough 260s -skipping training candidate: asmbl_565.p1, not unique enough 260s -skipping training candidate: asmbl_813.p1, not unique enough 260s -skipping training candidate: asmbl_786.p1, not unique enough 260s -skipping training candidate: asmbl_726.p1, not unique enough 260s -skipping training candidate: asmbl_635.p1, not unique enough 260s -skipping training candidate: asmbl_501.p1, not unique enough 260s -skipping training candidate: asmbl_559.p1, not unique enough 260s -skipping training candidate: asmbl_624.p1, not unique enough 260s -skipping training candidate: asmbl_599.p1, not unique enough 260s -skipping training candidate: asmbl_768.p1, not unique enough 260s -skipping training candidate: asmbl_537.p1, not unique enough 260s -skipping training candidate: asmbl_787.p1, not unique enough 260s -skipping training candidate: asmbl_585.p1, not unique 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candidate: asmbl_628.p1, not unique enough 260s -skipping training candidate: asmbl_824.p1, not unique enough 260s -skipping training candidate: asmbl_597.p1, not unique enough 260s -skipping training candidate: asmbl_753.p1, not unique enough 260s -skipping training candidate: asmbl_614.p1, not unique enough 260s -skipping training candidate: asmbl_310.p1, not unique enough 260s -skipping training candidate: asmbl_724.p1, not unique enough 260s -skipping training candidate: asmbl_382.p1, not unique enough 260s -skipping training candidate: asmbl_819.p1, not unique enough 260s -skipping training candidate: asmbl_699.p1, not unique enough 260s -skipping training candidate: asmbl_700.p1, not unique enough 260s -skipping training candidate: asmbl_643.p1, not unique enough 260s -skipping training candidate: asmbl_571.p1, not unique enough 260s -skipping training candidate: asmbl_259.p1, not unique enough 260s -skipping training candidate: asmbl_521.p1, not unique enough 260s -skipping 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training candidate: asmbl_543.p1, not unique enough 261s -skipping training candidate: asmbl_664.p1, not unique enough 261s -skipping training candidate: asmbl_677.p1, not unique enough 261s -skipping training candidate: asmbl_748.p1, not unique enough 261s -skipping training candidate: asmbl_802.p1, not unique enough 261s -skipping training candidate: asmbl_117.p2, not unique enough 261s -skipping training candidate: asmbl_559.p2, not unique enough 261s -skipping training candidate: asmbl_825.p1, not unique enough 261s -skipping training candidate: asmbl_596.p1, not unique enough 261s -skipping training candidate: asmbl_703.p1, not unique enough 261s -skipping training candidate: asmbl_838.p1, not unique enough 261s -skipping training candidate: asmbl_469.p1, not unique enough 261s -skipping training candidate: asmbl_698.p1, not unique enough 261s -skipping training candidate: asmbl_798.p1, not unique enough 261s -skipping training candidate: asmbl_290.p3, not unique enough 261s -skipping training candidate: asmbl_409.p2, not unique enough 261s -skipping training candidate: asmbl_746.p3, not unique enough 261s -skipping training candidate: asmbl_780.p2, not unique enough 261s -skipping training candidate: asmbl_838.p2, not unique enough 261s -skipping training candidate: asmbl_295.p1, not unique enough 261s -skipping training candidate: asmbl_741.p1, not unique enough 261s -skipping training candidate: asmbl_232.p1, not unique enough 261s -skipping training candidate: asmbl_645.p1, not unique enough 261s -skipping training candidate: asmbl_589.p1, not unique enough 261s -skipping training candidate: asmbl_657.p1, not unique enough 261s -skipping training candidate: asmbl_218.p1, not unique enough 261s -skipping training candidate: asmbl_658.p1, not unique enough 261s -skipping training candidate: asmbl_656.p1, not unique enough 261s -skipping training candidate: asmbl_675.p1, not unique enough 261s -skipping training candidate: asmbl_697.p1, not unique enough 261s -skipping training candidate: asmbl_808.p1, not unique enough 261s -skipping training candidate: asmbl_674.p1, not unique enough 261s -skipping training candidate: asmbl_465.p1, not unique enough 261s -skipping training candidate: asmbl_443.p2, not unique enough 261s -skipping training candidate: asmbl_673.p1, not unique enough 261s -skipping training candidate: asmbl_788.p2, not unique enough 261s -skipping training candidate: asmbl_4.p1, not unique enough 261s -skipping training candidate: asmbl_278.p3, not unique enough 261s -skipping training candidate: asmbl_408.p2, not unique enough 261s -skipping training candidate: asmbl_464.p1, not unique enough 261s -skipping training candidate: asmbl_693.p3, not unique enough 261s -skipping training candidate: asmbl_837.p2, not unique enough 261s -skipping training candidate: asmbl_463.p2, not unique enough 261s -skipping training candidate: asmbl_13.p2, not unique enough 261s -skipping training candidate: asmbl_457.p2, not unique enough 261s -skipping training candidate: asmbl_458.p2, not unique enough 261s -skipping training candidate: asmbl_637.p1, not unique enough 261s -skipping training candidate: asmbl_750.p1, not unique enough 261s -skipping training candidate: asmbl_485.p1, not unique enough 261s -skipping training candidate: asmbl_562.p1, not unique enough 261s -skipping training candidate: asmbl_636.p2, not unique enough 261s -skipping training candidate: asmbl_748.p2, not unique enough 261s -skipping training candidate: asmbl_310.p4, not unique enough 261s -skipping training candidate: asmbl_724.p4, not unique enough 261s -skipping training candidate: asmbl_723.p1, not unique enough 261s -skipping training candidate: asmbl_305.p1, not unique enough 261s -skipping training candidate: asmbl_733.p1, not unique enough 261s -skipping training candidate: asmbl_644.p2, not unique enough 261s -skipping training candidate: asmbl_498.p2, not unique enough 261s -skipping training candidate: asmbl_704.p1, not unique enough 261s -skipping training candidate: asmbl_725.p3, not unique enough 261s -skipping training candidate: asmbl_230.p2, not unique enough 261s -skipping training candidate: asmbl_221.p1, not unique enough 261s -skipping training candidate: asmbl_622.p1, not unique enough 261s -skipping training candidate: asmbl_655.p1, not unique enough 261s -skipping training candidate: asmbl_643.p2, not unique enough 261s -skipping training candidate: asmbl_716.p1, not unique enough 261s -skipping training candidate: asmbl_726.p2, not unique enough 261s -skipping training candidate: asmbl_516.p1, not unique enough 261s -skipping training candidate: asmbl_587.p1, not unique enough 261s -skipping training candidate: asmbl_813.p2, not unique enough 261s -skipping training candidate: asmbl_310.p5, not unique enough 261s -skipping training candidate: asmbl_537.p2, not unique enough 261s -skipping training candidate: asmbl_578.p1, not unique enough 261s -skipping training candidate: asmbl_724.p5, not unique enough 261s -skipping training candidate: asmbl_751.p1, not unique enough 261s -skipping training candidate: asmbl_815.p2, not unique enough 261s -skipping training candidate: asmbl_151.p1, not unique enough 261s -skipping training candidate: asmbl_410.p1, not unique enough 261s -skipping training candidate: asmbl_582.p1, not unique enough 261s -skipping training candidate: asmbl_580.p1, not unique enough 261s -skipping training candidate: asmbl_839.p1, not unique enough 261s -skipping training candidate: asmbl_290.p4, not unique enough 261s -skipping training candidate: asmbl_557.p1, not unique enough 261s -skipping training candidate: asmbl_660.p2, not unique enough 261s -skipping training candidate: asmbl_700.p2, not unique enough 261s -skipping training candidate: asmbl_745.p4, not unique enough 261s -skipping training candidate: asmbl_746.p4, not unique enough 261s -skipping training candidate: asmbl_779.p2, not unique enough 261s -skipping training candidate: asmbl_696.p1, not unique enough 261s -skipping training candidate: asmbl_452.p2, not unique enough 261s -skipping training candidate: asmbl_763.p1, not unique enough 261s -skipping training candidate: asmbl_814.p2, not unique enough 261s -skipping training candidate: asmbl_523.p1, not unique enough 261s -skipping training candidate: asmbl_752.p1, not unique enough 261s -skipping training candidate: asmbl_797.p1, not unique enough 261s -skipping training candidate: asmbl_607.p2, not unique enough 261s -skipping training candidate: asmbl_780.p3, not unique enough 261s -skipping training candidate: asmbl_127.p1, not unique enough 261s -skipping training candidate: asmbl_550.p1, not unique enough 261s -skipping training candidate: asmbl_646.p2, not unique enough 261s -skipping training candidate: asmbl_782.p1, not unique enough 261s -skipping training candidate: asmbl_362.p2, not unique enough 261s -skipping training candidate: asmbl_507.p2, not unique enough 261s -skipping training candidate: asmbl_530.p1, not unique enough 261s -skipping training candidate: asmbl_784.p2, not unique enough 261s -skipping training candidate: asmbl_772.p2, not unique enough 261s -skipping training candidate: asmbl_786.p2, not unique enough 261s -skipping training candidate: asmbl_773.p2, not unique enough 261s -skipping training candidate: asmbl_826.p1, not unique enough 261s -skipping training candidate: asmbl_15.p1, not unique enough 261s -skipping training candidate: asmbl_456.p1, not unique enough 261s -skipping training candidate: asmbl_530.p2, not unique enough 261s -skipping training candidate: asmbl_601.p2, not unique enough 261s -skipping training candidate: asmbl_641.p1, not unique enough 261s -skipping training candidate: asmbl_290.p5, not unique enough 261s -skipping training candidate: asmbl_519.p2, not unique enough 261s -skipping training candidate: asmbl_691.p1, not unique enough 261s -skipping training candidate: asmbl_745.p5, not unique enough 261s -skipping training candidate: asmbl_746.p5, not unique enough 261s -skipping training candidate: asmbl_288.p2, not unique enough 261s -skipping training candidate: asmbl_431.p2, not unique enough 261s -skipping training candidate: asmbl_687.p2, not unique enough 261s -skipping training candidate: asmbl_689.p1, not unique enough 261s -skipping training candidate: asmbl_685.p2, not unique enough 261s -skipping training candidate: asmbl_742.p1, not unique enough 261s -skipping training candidate: asmbl_765.p3, not unique enough 261s -skipping training candidate: asmbl_21.p2, not unique enough 261s -skipping training candidate: asmbl_22.p2, not unique enough 261s -skipping training candidate: asmbl_228.p2, not unique enough 261s -skipping training candidate: asmbl_378.p2, not unique enough 261s -skipping training candidate: asmbl_379.p2, not unique enough 261s -skipping training candidate: asmbl_450.p2, not unique enough 261s -skipping training candidate: asmbl_448.p2, not unique enough 261s -skipping training candidate: asmbl_449.p2, not unique enough 261s -skipping training candidate: asmbl_642.p1, not unique enough 261s -skipping training candidate: asmbl_647.p2, not unique enough 261s -skipping training candidate: asmbl_648.p2, not unique enough 261s -skipping training candidate: asmbl_821.p2, not unique enough 261s -skipping training candidate: asmbl_822.p2, not unique enough 261s -skipping training candidate: asmbl_335.p2, not unique enough 261s -skipping training candidate: asmbl_331.p2, not unique enough 261s -skipping training candidate: asmbl_328.p2, not unique enough 261s -skipping training candidate: asmbl_330.p1, not unique enough 261s -skipping training candidate: asmbl_528.p2, not unique enough 261s -skipping training candidate: asmbl_628.p2, not unique enough 261s -skipping training candidate: asmbl_736.p1, not unique enough 261s -skipping training candidate: asmbl_751.p2, not unique enough 261s -skipping training candidate: asmbl_756.p1, not unique enough 261s -skipping training candidate: asmbl_757.p2, not unique enough 261s -skipping training candidate: asmbl_754.p2, not unique enough 261s -skipping training candidate: asmbl_592.p2, not unique enough 261s -skipping training candidate: asmbl_670.p1, not unique enough 261s -skipping training candidate: asmbl_834.p1, not unique enough 261s -skipping training candidate: asmbl_90.p2, not unique enough 261s -skipping training candidate: asmbl_512.p2, not unique enough 261s -skipping training candidate: asmbl_513.p2, not unique enough 261s -skipping training candidate: asmbl_635.p2, not unique enough 261s -skipping training candidate: asmbl_764.p1, not unique enough 261s -skipping training candidate: asmbl_835.p1, not unique enough 261s -skipping training candidate: asmbl_303.p2, not unique enough 261s -skipping training candidate: asmbl_414.p1, not unique enough 261s -skipping training candidate: asmbl_479.p2, not unique enough 261s -skipping training candidate: asmbl_693.p4, not unique enough 261s -skipping training candidate: asmbl_716.p2, not unique enough 261s -skipping training candidate: asmbl_742.p2, not unique enough 261s -skipping training candidate: asmbl_731.p2, not unique enough 261s -skipping training candidate: asmbl_794.p2, not unique enough 261s -skipping training candidate: asmbl_799.p1, not unique enough 261s -skipping training candidate: asmbl_833.p1, not unique enough 261s -skipping training candidate: asmbl_433.p1, not unique enough 261s -skipping training candidate: asmbl_677.p2, not unique enough 261s -skipping training candidate: asmbl_847.p2, not unique enough 261s -skipping training candidate: asmbl_570.p2, not unique enough 261s -skipping training candidate: asmbl_535.p1, not unique enough 261s -skipping training candidate: asmbl_627.p2, not unique enough 261s -skipping training candidate: asmbl_719.p2, not unique enough 261s -skipping training candidate: asmbl_722.p1, not unique enough 261s -skipping training candidate: asmbl_150.p1, not unique enough 261s -skipping training candidate: asmbl_579.p1, not unique enough 261s -skipping training candidate: asmbl_584.p2, not unique enough 261s -skipping training candidate: asmbl_682.p3, not unique enough 261s -skipping training candidate: asmbl_712.p2, not unique enough 261s -skipping training candidate: asmbl_815.p3, not unique enough 261s -skipping training candidate: asmbl_49.p2, not unique enough 261s -skipping training candidate: asmbl_50.p2, not unique enough 261s -skipping training candidate: asmbl_51.p2, not unique enough 261s -skipping training candidate: asmbl_343.p1, not unique enough 261s -skipping training candidate: asmbl_491.p2, not unique enough 261s -skipping training candidate: asmbl_492.p2, not unique enough 261s -skipping training candidate: asmbl_489.p2, not unique enough 261s -skipping training candidate: asmbl_490.p2, not unique enough 261s -skipping training candidate: asmbl_793.p1, not unique enough 261s -skipping training candidate: asmbl_198.p3, not unique enough 261s -skipping training candidate: asmbl_199.p3, not unique enough 261s -skipping training candidate: asmbl_200.p3, not unique enough 261s -skipping training candidate: asmbl_507.p3, not unique enough 261s -skipping training candidate: asmbl_592.p3, not unique enough 261s -skipping training candidate: asmbl_606.p2, not unique enough 261s -skipping training candidate: asmbl_593.p3, not unique enough 261s -skipping training candidate: asmbl_594.p3, not unique enough 261s -skipping training candidate: asmbl_839.p2, not unique enough 261s -skipping training candidate: asmbl_6.p1, not unique enough 261s -skipping training candidate: asmbl_146.p3, not unique enough 261s -skipping training candidate: asmbl_446.p2, not unique enough 261s -skipping training candidate: asmbl_466.p1, not unique enough 261s -skipping training candidate: asmbl_531.p2, not unique enough 261s -skipping training candidate: asmbl_585.p2, not unique enough 261s -skipping training candidate: asmbl_586.p3, not unique enough 261s -skipping training candidate: asmbl_606.p3, not unique enough 261s -skipping training candidate: asmbl_635.p3, not unique enough 261s -skipping training candidate: asmbl_726.p3, not unique enough 261s -skipping training candidate: asmbl_8.p2, not unique enough 261s -skipping training candidate: asmbl_9.p2, not unique enough 261s -skipping training candidate: asmbl_57.p2, not unique enough 261s -skipping training candidate: asmbl_365.p2, not unique enough 261s -skipping training candidate: asmbl_459.p2, not unique enough 261s -skipping training candidate: asmbl_460.p2, not unique enough 261s -skipping training candidate: asmbl_461.p2, not unique enough 261s -skipping training candidate: asmbl_462.p2, not unique enough 261s -skipping training candidate: asmbl_484.p2, not unique enough 261s -skipping training candidate: asmbl_770.p2, not unique enough 261s -skipping training candidate: asmbl_771.p2, not unique enough 261s -skipping training candidate: asmbl_820.p1, not unique enough 261s -skipping training candidate: asmbl_259.p2, not unique enough 261s -skipping training candidate: asmbl_349.p2, not unique enough 261s -skipping training candidate: asmbl_692.p2, not unique enough 261s -skipping training candidate: asmbl_713.p2, not unique enough 261s -skipping training candidate: asmbl_765.p4, not unique enough 261s -skipping training candidate: asmbl_787.p2, not unique enough 261s -skipping training candidate: asmbl_85.p2, not unique enough 261s -skipping training candidate: asmbl_518.p2, not unique enough 261s -skipping training candidate: asmbl_517.p2, not unique enough 261s -skipping training candidate: asmbl_709.p2, not unique enough 261s -skipping training candidate: asmbl_778.p3, not unique enough 261s -skipping training candidate: asmbl_830.p1, not unique enough 261s -skipping training candidate: asmbl_847.p3, not unique enough 261s -skipping training candidate: asmbl_530.p3, not unique enough 261s -skipping training candidate: asmbl_722.p2, not unique enough 261s -skipping training candidate: asmbl_817.p2, not unique enough 261s -skipping training candidate: asmbl_799.p2, not unique enough 261s -skipping training candidate: asmbl_813.p3, not unique enough 261s -skipping training candidate: asmbl_290.p6, not unique enough 261s -skipping training candidate: asmbl_746.p6, not unique enough 261s -skipping training candidate: asmbl_536.p2, not unique enough 261s -skipping training candidate: asmbl_534.p1, not unique enough 261s -skipping training candidate: asmbl_692.p3, not unique enough 261s -skipping training candidate: asmbl_115.p2, not unique enough 261s -skipping training candidate: asmbl_278.p5, not unique enough 261s -skipping training candidate: asmbl_320.p1, not unique enough 261s -skipping training candidate: asmbl_452.p3, not unique enough 261s -skipping training candidate: asmbl_569.p2, not unique enough 261s -skipping training candidate: asmbl_560.p2, not unique enough 261s -skipping training candidate: asmbl_561.p2, not unique enough 261s -skipping training candidate: asmbl_693.p5, not unique enough 261s -skipping training candidate: asmbl_695.p1, not unique enough 261s -skipping training candidate: asmbl_734.p2, not unique enough 261s -skipping training candidate: asmbl_721.p1, not unique enough 261s -skipping training candidate: asmbl_765.p5, not unique enough 261s -skipping training candidate: asmbl_766.p1, not unique enough 261s -skipping training candidate: asmbl_807.p2, not unique enough 261s -skipping training candidate: asmbl_800.p1, not unique enough 261s -skipping training candidate: asmbl_164.p2, not unique enough 261s -skipping training candidate: asmbl_531.p3, not unique enough 261s -skipping training candidate: asmbl_558.p2, not unique enough 261s -skipping training candidate: asmbl_626.p2, not unique enough 261s -skipping training candidate: asmbl_831.p1, not unique enough 261s 261s -redundancy-minimized set includes 396 / 1067 = 37.11% 261s 261s * [Mon Mar 11 04:11:35 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 261s PCT_GC: 42 261s * [Mon Mar 11 04:11:35 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores 262s * [Mon Mar 11 04:11:36 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores 268s * [Mon Mar 11 04:11:42 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 268s Selecting best orfs 268s * [Mon Mar 11 04:11:42 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement 268s Training start codon pattern recognition* [Mon Mar 11 04:11:42 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 269s * [Mon Mar 11 04:11:43 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores 269s -round: 1 274s -round: 2 279s -round: 3 284s -round: 4 289s -round: 5 294s * [Mon Mar 11 04:12:08 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 294s -parsing scores 300s * [Mon Mar 11 04:12:14 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 300s Error in library(ggplot2) : there is no package called ‘ggplot2’ 300s Execution halted 300s * [Mon Mar 11 04:12:14 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 300s Error in library(ggplot2) : there is no package called ‘ggplot2’ 300s Execution halted 300s * [Mon Mar 11 04:12:14 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : 301s Error in library(seqLogo) : there is no package called ‘seqLogo’ 301s Execution halted 301s * [Mon Mar 11 04:12:15 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : 301s Error in library(seqLogo) : there is no package called ‘seqLogo’ 301s Execution halted 301s * [Mon Mar 11 04:12:15 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced 301s num features: 238 num_incorporate: 71 301s -feature swap of score: 0.52233068358735 instead of -2.4838353992418 301s -feature swap of score: 3.4925122435335 instead of -2.69571560364119 301s -feature swap of score: -0.479799656028566 instead of -2.28706103601398 301s -feature swap of score: -0.0881342990948846 instead of -2.01923571762916 301s -feature swap of score: 3.70320425069563 instead of -2.540266312821 301s -feature swap of score: -1.18001089627022 instead of -2.19874275195072 301s -feature swap of score: 0.890711131288117 instead of -1.48110814799594 301s -feature swap of score: -1.05010135127967 instead of -1.29405271062499 301s -feature swap of score: -0.0660971314530546 instead of -1.10945144224631 301s -feature swap of score: 4.44453897240347 instead of -0.978468124148539 301s -feature swap of score: -0.464399759591707 instead of -0.841794961146521 301s -feature swap of score: 0.255068847557726 instead of -0.83142113951215 301s -feature swap of score: 1.95582633064074 instead of -0.76896518568472 301s -feature swap of score: -0.0332453222172366 instead of -0.682979129272786 301s -feature swap of score: 1.8228745697833 instead of -0.653744437026382 301s -feature swap of score: 1.00115669145456 instead of -0.336891026477184 301s -feature swap of score: 0.672803798904712 instead of -0.578246064931 301s -feature swap of score: 1.8162642359003 instead of -0.452564095078051 301s -feature swap of score: 0.280846761877589 instead of -0.647264557316993 301s -feature swap of score: 0.366355095526699 instead of -0.615212412314209 301s -feature swap of score: 2.52986097726451 instead of -0.758989032460075 301s -feature swap of score: -0.0952627696553691 instead of -0.817191160815284 301s -feature swap of score: 0.996754631653053 instead of -0.80551837636419 301s -feature swap of score: 0.354999699462731 instead of -0.274911636492182 301s -feature swap of score: 1.28605443964402 instead of 0.0980797372313064 301s -feature swap of score: 0.32578718956916 instead of -0.042861330285221 301s -feature swap of score: 2.48770150611293 instead of -0.0868957590364158 301s -feature swap of score: 2.64754362015744 instead of 0.2916904256282 301s -feature swap of score: 1.01988302433125 instead of 0.036666467034015 301s -feature swap of score: 0.702376236311601 instead of -0.128287580103504 301s -feature swap of score: 2.99676647453095 instead of 0.320673377955444 301s -feature swap of score: 4.3305495710187 instead of 0.295875888654129 301s -feature swap of score: 1.17421891679809 instead of 0.254710288367653 301s -feature swap of score: 0.401521517315352 instead of 0.370606147577384 301s -feature swap of score: 3.89634731515857 instead of 0.389772413567672 301s -feature swap of score: 2.74749373854816 instead of 0.451140083480975 301s -feature swap of score: 4.14790539102617 instead of 0.173512045799991 301s -feature swap of score: 2.68928352460324 instead of 0.0987413441847772 301s -feature swap of score: 0.570947526770153 instead of -0.152678189275884 301s -feature swap of score: 2.87693452246047 instead of 0.175971771120871 301s -feature swap of score: 0.345761582949679 instead of 0.189210540579853 301s -feature swap of score: 1.75381703871986 instead of -0.176138170873724 301s -feature swap of score: 6.3225755214291 instead of 0.182318752228176 301s -feature swap of score: -0.00356336589610784 instead of -0.074332288426649 301s -feature swap of score: 1.25652300984573 instead of 0.440440454930295 301s -feature swap of score: 4.35627103288236 instead of 0.601792868596411 301s -feature swap of score: 3.34305077634812 instead of 0.646355594435306 301s -feature swap of score: 0.89148415481126 instead of 0.847522010634187 301s -feature swap of score: 3.6953445371134 instead of 0.751030612474935 301s -feature swap of score: 5.78699079524925 instead of 0.699840066363169 301s -feature swap of score: 2.15409587173251 instead of 0.715035855107118 301s -feature swap of score: 1.47994164306661 instead of 0.417255934795064 301s -feature swap of score: 4.91570803685393 instead of 0.612782191206777 301s -feature swap of score: 0.527551455366298 instead of 0.495108302468003 301s -feature swap of score: 3.40423853426828 instead of 0.883665117310717 301s -feature swap of score: 0.802539851871931 instead of 0.787642557429234 301s -num feature swaps: 56 301s * [Mon Mar 11 04:12:15 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 301s -round: 1 306s -round: 2 310s -round: 3 315s -round: 4 320s -round: 5 325s * [Mon Mar 11 04:12:39 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 325s -parsing scores 330s * [Mon Mar 11 04:12:44 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 331s Error in library(ggplot2) : there is no package called ‘ggplot2’ 331s Execution halted 331s * [Mon Mar 11 04:12:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 331s Error in library(ggplot2) : there is no package called ‘ggplot2’ 331s Execution halted 331s * [Mon Mar 11 04:12:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 331s Error in library(seqLogo) : there is no package called ‘seqLogo’ 331s Execution halted 331s * [Mon Mar 11 04:12:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 331s Refining start codon selections. 331s -number of revised start positions: 83 331s * [Mon Mar 11 04:12:45 2024] Running CMD: cp /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 331s copying output to final output file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Mon Mar 11 04:12:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 331s Making bed file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 331s * [Mon Mar 11 04:12:45 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 332s Making pep file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 332s * [Mon Mar 11 04:12:46 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 332s Making cds file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 332s transdecoder is finished. See output files /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* 332s 332s 332s 332s ../../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 332s 332s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 205, 828 332s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_117.p2. 332s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_127.p1. 332s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 142, 1281 332s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_177.p1. 332s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_198.p3. 332s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_199.p3. 332s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_200.p3. 332s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. 332s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. 332s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. 332s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. 332s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. 332s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 107, 466 332s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_289.p2. 332s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_290.p1. 332s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [21], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [22], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [23], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_420.p1. 332s -Warning [25], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 140, 700 332s -Warning [26], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 340, 816 332s -Warning [27], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 93, 1106 332s -Warning [28], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [29], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [30], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 312, 1253 332s -Warning [31], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_550.p1. 332s -Warning [32], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_559.p2. 332s -Warning [33], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [34], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_592.p3. 332s -Warning [35], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_593.p3. 332s -Warning [36], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_594.p3. 332s -Warning [37], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [38], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_615.p1. 332s -Warning [39], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 80, 427 332s -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. 332s -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. 332s -Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. 332s -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. 332s -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 112, 447 332s -Warning [46], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_745.p2. 332s -Warning [47], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_746.p1. 332s -Warning [48], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 108, 452 332s -Warning [49], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 2, 562 332s -Warning [50], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 332s -Warning [51], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 141, 545 332s -Warning [52], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 332s CDS coords: 178, 1623 332s -Warning [53], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_855.p1. 332s 332s 332s Done. 765 / 792 transcript orfs could be propagated to the genome 332s 332s 332s 332s ../../util/fasta_prot_checker.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 332s Done. See pasa_assemblies.fasta.transdecoder.\* 332s 332s 332s echo "Done. See pasa_assemblies.fasta.transdecoder.\*" 332s 332s 332s exit 0 332s make[1]: Leaving directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 332s Running example in $... 332s make[1]: Entering directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 332s ./runMe.sh 333s CMD: mkdir -p /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir 333s * [Mon Mar 11 04:12:47 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl Trinity.fasta 0 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat 333s 333s 333s -first extracting base frequencies, we'll need them later. 333s 333s 333s - extracting ORFs from transcripts. 333s -total transcripts to examine: 921 335s [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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 335s 335s 335s ################################# 335s ### Done preparing long ORFs. ### 335s ################################## 335s 335s Use file: /tmp/autopkgtest.B13zNQ/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. 335s 335s Then, run TransDecoder.Predict for your final coding region predictions. 335s 335s 335s * [Mon Mar 11 04:12:49 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 335s * [Mon Mar 11 04:12:49 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 335s -skipping training candidate: comp847_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp992_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp718_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1177_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp999_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp989_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp836_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp621_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp844_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp594_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp956_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1044_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp835_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp1029_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1016_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1207_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp862_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp703_c0_seq1.p2, not unique enough 335s -skipping training candidate: comp1191_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp867_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp1207_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp905_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp784_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp674_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp924_c0_seq1.p2, not unique enough 335s -skipping training candidate: comp1174_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1046_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp1191_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp1044_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp873_c0_seq1.p1, not unique enough 335s -skipping training candidate: comp1177_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp1196_c0_seq2.p1, not unique enough 335s -skipping training candidate: comp999_c0_seq2.p2, not unique enough 335s -skipping training candidate: comp985_c0_seq2.p1, not unique enough 335s 335s -redundancy-minimized set includes 810 / 844 = 95.97% 335s 335s * [Mon Mar 11 04:12:49 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 336s PCT_GC: 38 336s * [Mon Mar 11 04:12:50 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores 337s * [Mon Mar 11 04:12:51 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores 343s * [Mon Mar 11 04:12:57 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 344s Selecting best orfs 344s * [Mon Mar 11 04:12:58 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement 344s Training start codon pattern recognition* [Mon Mar 11 04:12:58 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 344s * [Mon Mar 11 04:12:58 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores 344s -round: 1 349s -round: 2 355s -round: 3 360s -round: 4 365s -round: 5 370s * [Mon Mar 11 04:13:24 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 370s -parsing scores 376s * [Mon Mar 11 04:13:30 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 376s Error in library(ggplot2) : there is no package called ‘ggplot2’ 376s Execution halted 376s * [Mon Mar 11 04:13:30 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 376s Error in library(ggplot2) : there is no package called ‘ggplot2’ 376s Execution halted 376s * [Mon Mar 11 04:13:30 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : 377s Error in library(seqLogo) : there is no package called ‘seqLogo’ 377s Execution halted 377s * [Mon Mar 11 04:13:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : 377s Error in library(seqLogo) : there is no package called ‘seqLogo’ 377s Execution halted 377s * [Mon Mar 11 04:13:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced 377s num features: 358 num_incorporate: 107 377s -feature swap of score: 2.01860755745774 instead of -2.43253294753209 377s -feature swap of score: 2.34732451463516 instead of -2.03515280104856 377s -feature swap of score: 2.42600756963178 instead of -1.88586714183678 377s -feature swap of score: 4.04692570560011 instead of -2.07838396233827 377s -feature swap of score: -2.10349049055208 instead of -2.14357898216183 377s -feature swap of score: 3.34270681682176 instead of -1.68919591401722 377s -feature swap of score: 0.785638027271692 instead of -1.75537844488172 377s -feature swap of score: 0.124937617546208 instead of -1.42423447927029 377s -feature swap of score: 3.80360939610757 instead of -1.25581956645478 377s -feature swap of score: 2.22972790847055 instead of -1.43724022198391 377s -feature swap of score: 1.87223224767761 instead of -1.39134963935408 377s -feature swap of score: -0.869196741065359 instead of -1.45437592553593 377s -feature swap of score: 2.61126122082178 instead of -1.4644389491732 377s -feature swap of score: 0.041614898233897 instead of -1.38236698907653 377s -feature swap of score: 5.23702512832804 instead of -1.06647647854364 377s -feature swap of score: 0.489018424262898 instead of -0.95713076184448 377s -feature swap of score: 1.06810458576389 instead of -0.894284983683669 377s -feature swap of score: -0.226298629660561 instead of -0.948994050642804 377s -feature swap of score: 0.450699974271914 instead of -0.959497695240219 377s -feature swap of score: 4.28695919068754 instead of -0.978907600609435 377s -feature swap of score: 2.14133448495559 instead of -0.753180766675387 377s -feature swap of score: 4.12202729113471 instead of -0.76828282708309 377s -feature swap of score: -0.104946382094106 instead of -0.628776084467911 377s -feature swap of score: 0.000572807808514326 instead of -0.53263942949094 377s -feature swap of score: 0.198006134044188 instead of -0.34106805075173 377s -feature swap of score: 3.6047163749624 instead of -0.51212082035361 377s -feature swap of score: 0.814286538900709 instead of -0.339061555243772 377s -feature swap of score: 4.97523538835402 instead of -0.219644205392414 377s -feature swap of score: 1.97045125499639 instead of -0.113036838336636 377s -feature swap of score: 4.13053733045551 instead of -0.170052581383971 377s -feature swap of score: 0.00206436128981199 instead of -0.181062974960661 377s -feature swap of score: 1.604245252388 instead of 0.0517161275151237 377s -feature swap of score: 4.3932806981529 instead of 0.0860431565952234 377s -feature swap of score: 1.72957229182765 instead of 0.221968210457067 377s -feature swap of score: 1.57263236697426 instead of 0.288968311790631 377s -feature swap of score: 0.203166281459456 instead of 0.10534662338876 377s -feature swap of score: 4.38190400149154 instead of 0.196370432457334 377s -feature swap of score: 5.04613038233112 instead of 0.150614918926321 377s -feature swap of score: 2.26071953474249 instead of 0.230526386115092 377s -feature swap of score: 5.13639850152629 instead of 0.252892697647447 377s -feature swap of score: 1.17098382473728 instead of 0.282995900530861 377s -feature swap of score: 4.34776268138483 instead of 0.41430990147474 377s -feature swap of score: 2.15329616437699 instead of 0.429451771590664 377s -feature swap of score: 5.09229418476461 instead of 0.297828956020416 377s -feature swap of score: 1.13675328930652 instead of 0.171694593520241 377s -feature swap of score: 2.02231900226323 instead of 0.206703978994726 377s -feature swap of score: 2.66734827613583 instead of 0.443525927859022 377s -feature swap of score: 3.77684820014943 instead of 0.599510264128007 377s -feature swap of score: 1.29789971226826 instead of 0.51658385615187 377s -feature swap of score: 3.74256664801257 instead of 0.445260647950643 377s -feature swap of score: 4.32680419305246 instead of 0.596611075477652 377s -feature swap of score: 1.77920876164079 instead of 0.52605377488021 377s -feature swap of score: 1.61583261588263 instead of 0.65317830698915 377s -feature swap of score: 4.10400531839299 instead of 0.789843632233928 377s -feature swap of score: 1.83659343125585 instead of 0.716731928502843 377s -feature swap of score: 1.6438027810344 instead of 0.767790779444299 377s -feature swap of score: 2.51637019194037 instead of 0.699527206449989 377s -feature swap of score: 1.60560873858958 instead of 1.07464412670026 377s -feature swap of score: 2.89883210321421 instead of 1.07157389032513 377s -feature swap of score: 2.93101514977772 instead of 0.988616846801185 377s -feature swap of score: 3.72069918320373 instead of 0.868454192870146 377s -feature swap of score: 1.03519107357972 instead of 0.753010048444791 377s -feature swap of score: 4.01020820806659 instead of 0.886358064075704 377s -feature swap of score: 0.879618323769624 instead of 0.61109819149034 377s -feature swap of score: 7.15234940921215 instead of 1.03360771341683 377s -feature swap of score: 1.83921458905268 instead of 1.02334035960285 377s -feature swap of score: 2.23998772164463 instead of 0.834483027752134 377s -feature swap of score: 2.16522830829353 instead of 1.1968190751818 377s -feature swap of score: 3.565902255058 instead of 1.04816444694555 377s -feature swap of score: 1.1156878707122 instead of 0.972785593550388 377s -feature swap of score: 1.63015648897591 instead of 1.12916093095551 377s -feature swap of score: 3.15623525707792 instead of 1.19443129843577 377s -feature swap of score: 1.75064193312005 instead of 1.22439213990375 377s -feature swap of score: 2.22558017270471 instead of 1.41095670579146 377s -feature swap of score: 1.69472767650654 instead of 1.47090708539632 377s -feature swap of score: 5.71675848798316 instead of 1.54417528485585 377s -feature swap of score: 2.36834513989863 instead of 1.56065511814006 377s -feature swap of score: 4.72132107671951 instead of 1.39108914413569 377s -feature swap of score: 2.98996061269645 instead of 1.4726797291019 377s -feature swap of score: 2.30202014931778 instead of 1.35942459345001 377s -feature swap of score: 6.94448025054924 instead of 1.53071141968655 377s -feature swap of score: 2.02147832129674 instead of 1.39293685217156 377s -feature swap of score: 3.0540382236436 instead of 1.47682791921283 377s -feature swap of score: 8.35170655675059 instead of 1.54271367706925 377s -feature swap of score: 2.3591087448739 instead of 1.62983627612991 377s -feature swap of score: 3.33896220987853 instead of 1.74551832680512 377s -feature swap of score: 4.47931807129169 instead of 1.65656837994906 377s -feature swap of score: 6.43889512650897 instead of 1.63523856658065 377s -feature swap of score: 4.44139726355316 instead of 1.62413947257281 377s -feature swap of score: 4.3934217091148 instead of 1.5563895897064 377s -feature swap of score: 2.4178749161712 instead of 1.53540854291086 377s -feature swap of score: 4.50084537762944 instead of 1.99813615680005 377s -feature swap of score: 4.36085158331683 instead of 1.81509165074822 377s -feature swap of score: 3.50540200807125 instead of 1.84763588301182 377s -feature swap of score: 2.14307301177581 instead of 1.58943578807425 377s -feature swap of score: 2.80249705432441 instead of 2.03323063135445 377s -feature swap of score: 2.51995823874979 instead of 1.80649830131556 377s -feature swap of score: 2.18546699630314 instead of 2.01678734343503 377s -feature swap of score: 6.02870360838808 instead of 2.11230538713769 377s -feature swap of score: 4.79559537621424 instead of 1.93041915648434 377s -feature swap of score: 8.43445355562363 instead of 2.187388349484 377s -feature swap of score: 3.43057432858564 instead of 2.04524276099259 377s -feature swap of score: 2.64567534439595 instead of 1.91708045098195 377s -num feature swaps: 103 377s * [Mon Mar 11 04:13:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 377s -round: 1 382s -round: 2 388s -round: 3 392s -round: 4 397s -round: 5 402s * [Mon Mar 11 04:13:56 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 402s -parsing scores 408s * [Mon Mar 11 04:14:02 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 408s Error in library(ggplot2) : there is no package called ‘ggplot2’ 408s Execution halted 408s * [Mon Mar 11 04:14:02 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 409s Error in library(ggplot2) : there is no package called ‘ggplot2’ 409s Execution halted 409s * [Mon Mar 11 04:14:02 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 409s Error in library(seqLogo) : there is no package called ‘seqLogo’ 409s Execution halted 409s * [Mon Mar 11 04:14:03 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 409s Refining start codon selections. 409s -number of revised start positions: 43 409s * [Mon Mar 11 04:14:03 2024] Running CMD: cp /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 409s copying output to final output file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Mon Mar 11 04:14:03 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 409s Making bed file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 409s * [Mon Mar 11 04:14:03 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 409s Making pep file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 409s * [Mon Mar 11 04:14:03 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 410s Making cds file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 410s transdecoder is finished. See output files /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* 410s 410s 410s 410s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 266, 796 410s -WARNING, comp1008_c0_seq1 has no genome representation... skipping 410s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 410s -WARNING, comp1021_c0_seq1 has no genome representation... skipping 410s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1026_c0_seq1.p1. 410s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1037_c0_seq1.p2. 410s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 561, 1325 410s Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'asmbl' => 'comp1051_c1_seq1', 410s 'coords' => [ 410s [ 410s '1642973', 410s '1644586' 410s ] 410s ], 410s 'contig' => 'III', 410s 'gene_id' => '', 410s 'orient' => '-', 410s 'trans_id' => '' 410s }; 410s TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 410s asmbl_id: comp1051_c1_seq1 410s strand: + 410s is_pseudogene: 0 410s gene_length: 1616 410s source: transdecoder 410s mid_pt: 808 410s gene_type: protein-coding 410s num_exons: 1 410s is_5prime_partial: 0 410s com_name: ORF type:5prime_partial (+),score=83.26 410s Model_feat_name: comp1051_c1_seq1.p1 410s is_3prime_partial: 0 410s classification: annotated_genes 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1616 CDS-exon: 2, 820 410s gene_span: 1-1616 410s model_span: 2-820 410s 410s Error, couldn't localize pt [1615] within coordsets: $VAR1 = [ 410s [ 410s '1642973', 410s '1644586' 410s ] 410s ]; 410s -WARNING, comp1053_c0_seq1 has no genome representation... skipping 410s Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'gene_id' => '', 410s 'orient' => '-', 410s 'trans_id' => '', 410s 'asmbl' => 'comp1058_c0_seq1', 410s 'coords' => [ 410s [ 410s 5095548, 410s '5095878' 410s ], 410s [ 410s 5095142, 410s '5095301' 410s ] 410s ], 410s 'contig' => 'I' 410s }; 410s is_pseudogene: 0 410s gene_length: 496 410s TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 410s asmbl_id: comp1058_c0_seq1 410s strand: + 410s mid_pt: 248 410s source: transdecoder 410s is_5prime_partial: 0 410s com_name: ORF type:5prime_partial (+),score=32.57 410s num_exons: 1 410s gene_type: protein-coding 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp1058_c0_seq1.p1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 496 CDS-exon: 3, 422 410s gene_span: 1-496 410s model_span: 3-422 410s 410s Error, couldn't localize pt [494] within coordsets: $VAR1 = [ 410s [ 410s 5095142, 410s '5095301' 410s ], 410s [ 410s 5095548, 410s '5095878' 410s ] 410s ]; 410s -Warning [6], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 3441, 3773 410s -WARNING, comp1075_c0_seq1 has no genome representation... skipping 410s Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'orient' => '-', 410s 'trans_id' => '', 410s 'gene_id' => '', 410s 'contig' => 'III', 410s 'asmbl' => 'comp1112_c0_seq1', 410s 'coords' => [ 410s [ 410s 2380416, 410s '2380466' 410s ], 410s [ 410s 2379717, 410s '2380336' 410s ] 410s ] 410s }; 410s TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 410s asmbl_id: comp1112_c0_seq1 410s strand: + 410s is_pseudogene: 0 410s gene_length: 2081 410s source: transdecoder 410s mid_pt: 1041 410s gene_type: protein-coding 410s num_exons: 1 410s is_5prime_partial: 0 410s com_name: ORF type:complete (+),score=155.28 410s Model_feat_name: comp1112_c0_seq1.p1 410s is_3prime_partial: 0 410s classification: annotated_genes 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 2081 CDS-exon: 365, 1903 410s gene_span: 1-2081 410s model_span: 365-1903 410s 410s Error, couldn't localize pt [1717] within coordsets: $VAR1 = [ 410s [ 410s 2379717, 410s '2380336' 410s ], 410s [ 410s 2380416, 410s '2380466' 410s ] 410s ]; 410s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 410s -WARNING, comp1124_c0_seq1 has no genome representation... skipping 410s Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'orient' => '-', 410s 'trans_id' => '', 410s 'gene_id' => '', 410s 'contig' => 'II', 410s 'asmbl' => 'comp1198_c0_seq1', 410s 'coords' => [ 410s [ 410s 402195, 410s '402246' 410s ], 410s [ 410s 402017, 410s '402141' 410s ], 410s [ 410s 401844, 410s '401910' 410s ], 410s [ 410s 401352, 410s '401683' 410s ] 410s ] 410s }; 410s strand: + 410s asmbl_id: comp1198_c0_seq1 410s TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 410s gene_length: 597 410s is_pseudogene: 0 410s source: transdecoder 410s mid_pt: 299 410s gene_type: protein-coding 410s num_exons: 1 410s com_name: ORF type:internal (+),score=37.56 410s is_5prime_partial: 0 410s Model_feat_name: comp1198_c0_seq1.p1 410s is_3prime_partial: 0 410s classification: annotated_genes 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 597 CDS-exon: 2, 595 410s gene_span: 1-597 410s model_span: 2-595 410s 410s Error, couldn't localize pt [596] within coordsets: $VAR1 = [ 410s [ 410s 401352, 410s '401683' 410s ], 410s [ 410s 401844, 410s '401910' 410s ], 410s [ 410s 402017, 410s '402141' 410s ], 410s [ 410s 402195, 410s '402246' 410s ] 410s ]; 410s Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'asmbl' => 'comp1210_c0_seq1', 410s 'coords' => [ 410s [ 410s 368840, 410s '369008' 410s ], 410s [ 410s 367430, 410s '368790' 410s ] 410s ], 410s 'contig' => 'III', 410s 'gene_id' => '', 410s 'orient' => '-', 410s 'trans_id' => '' 410s }; 410s com_name: ORF type:5prime_partial (+),score=12.16 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_type: protein-coding 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp1210_c0_seq1.p1 410s gene_length: 1554 410s is_pseudogene: 0 410s strand: + 410s asmbl_id: comp1210_c0_seq1 410s TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 410s mid_pt: 777 410s source: transdecoder 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1554 CDS-exon: 2, 781 410s gene_span: 1-1554 410s model_span: 2-781 410s 410s Error, couldn't localize pt [1553] within coordsets: $VAR1 = [ 410s [ 410s 367430, 410s '368790' 410s ], 410s [ 410s 368840, 410s '369008' 410s ] 410s ]; 410s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 410s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 410s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 3, 392 410s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 410s Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'gene_id' => '', 410s 'trans_id' => '', 410s 'orient' => '-', 410s 'coords' => [ 410s [ 410s '3840968', 410s '3841303' 410s ] 410s ], 410s 'asmbl' => 'comp366_c0_seq1', 410s 'contig' => 'II' 410s }; 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp366_c0_seq1.p1 410s is_5prime_partial: 0 410s com_name: ORF type:internal (-),score=12.83 410s num_exons: 1 410s gene_type: protein-coding 410s mid_pt: 170 410s source: transdecoder 410s gene_length: 340 410s is_pseudogene: 0 410s asmbl_id: comp366_c0_seq1 410s TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 410s strand: - 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 340, 1 CDS-exon: 339, 1 410s gene_span: 340-1 410s model_span: 339-1 410s 410s Error, couldn't localize pt [340] within coordsets: $VAR1 = [ 410s [ 410s '3840968', 410s '3841303' 410s ] 410s ]; 410s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 1, 384 410s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 3, 347 410s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 1, 492 410s -WARNING, comp504_c0_seq1 has no genome representation... skipping 410s -WARNING, comp576_c0_seq1 has no genome representation... skipping 410s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp583_c0_seq1.p1. 410s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. 410s Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'contig' => 'I', 410s 'coords' => [ 410s [ 410s '5471264', 410s '5472770' 410s ] 410s ], 410s 'asmbl' => 'comp610_c0_seq1', 410s 'trans_id' => '', 410s 'orient' => '-', 410s 'gene_id' => '' 410s }; 410s gene_length: 1509 410s is_pseudogene: 0 410s asmbl_id: comp610_c0_seq1 410s TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 410s strand: + 410s mid_pt: 755 410s source: transdecoder 410s is_5prime_partial: 0 410s com_name: ORF type:5prime_partial (+),score=50.55 410s num_exons: 1 410s gene_type: protein-coding 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp610_c0_seq1.p1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1509 CDS-exon: 2, 1210 410s gene_span: 1-1509 410s model_span: 2-1210 410s 410s Error, couldn't localize pt [1508] within coordsets: $VAR1 = [ 410s [ 410s '5471264', 410s '5472770' 410s ] 410s ]; 410s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 410s CDS coords: 1441, 1941 410s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. 410s Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'contig' => 'I', 410s 'asmbl' => 'comp645_c0_seq1', 410s 'coords' => [ 410s [ 410s '4333088', 410s '4336727' 410s ] 410s ], 410s 'orient' => '-', 410s 'trans_id' => '', 410s 'gene_id' => '' 410s }; 410s source: transdecoder 410s mid_pt: 1827 410s strand: + 410s asmbl_id: comp645_c0_seq1 410s TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 410s gene_length: 3653 410s is_pseudogene: 0 410s is_3prime_partial: 0 410s Model_feat_name: comp645_c0_seq1.p1 410s classification: annotated_genes 410s gene_type: protein-coding 410s com_name: ORF type:5prime_partial (+),score=273.35 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 3653 CDS-exon: 2, 3571 410s gene_span: 1-3653 410s model_span: 2-3571 410s 410s Error, couldn't localize pt [3652] within coordsets: $VAR1 = [ 410s [ 410s '4333088', 410s '4336727' 410s ] 410s ]; 410s Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'coords' => [ 410s [ 410s 380308, 410s '380560' 410s ], 410s [ 410s 380624, 410s '381243' 410s ] 410s ], 410s 'asmbl' => 'comp688_c0_seq1', 410s 'contig' => 'II', 410s 'gene_id' => '', 410s 'trans_id' => '', 410s 'orient' => '+' 410s }; 410s source: transdecoder 410s mid_pt: 1392 410s strand: + 410s asmbl_id: comp688_c0_seq1 410s TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 410s gene_length: 2784 410s is_pseudogene: 0 410s is_3prime_partial: 0 410s Model_feat_name: comp688_c0_seq1.p1 410s classification: annotated_genes 410s gene_type: protein-coding 410s com_name: ORF type:complete (+),score=172.54 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 2784 CDS-exon: 83, 2578 410s gene_span: 1-2784 410s model_span: 83-2578 410s 410s Error, couldn't localize pt [2578] within coordsets: $VAR1 = [ 410s [ 410s 380308, 410s '380560' 410s ], 410s [ 410s 380624, 410s '381243' 410s ] 410s ]; 410s -WARNING, comp701_c0_seq1 has no genome representation... skipping 410s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp703_c0_seq1.p2. 410s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp707_c0_seq1.p2. 410s -WARNING, comp831_c0_seq1 has no genome representation... skipping 410s Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'orient' => '+', 410s 'trans_id' => '', 410s 'gene_id' => '', 410s 'contig' => 'II', 410s 'asmbl' => 'comp856_c0_seq1', 410s 'coords' => [ 410s [ 410s 3753910, 410s '3754392' 410s ], 410s [ 410s 3754438, 410s '3755057' 410s ] 410s ] 410s }; 410s num_exons: 1 410s is_5prime_partial: 0 410s com_name: ORF type:complete (+),score=71.94 410s gene_type: protein-coding 410s classification: annotated_genes 410s Model_feat_name: comp856_c0_seq1.p1 410s is_3prime_partial: 0 410s is_pseudogene: 0 410s gene_length: 1569 410s TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 410s asmbl_id: comp856_c0_seq1 410s strand: + 410s mid_pt: 785 410s source: transdecoder 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1569 CDS-exon: 161, 1504 410s gene_span: 1-1569 410s model_span: 161-1504 410s 410s Error, couldn't localize pt [1504] within coordsets: $VAR1 = [ 410s [ 410s 3753910, 410s '3754392' 410s ], 410s [ 410s 3754438, 410s '3755057' 410s ] 410s ]; 410s Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'orient' => '-', 410s 'trans_id' => '', 410s 'gene_id' => '', 410s 'contig' => 'II', 410s 'asmbl' => 'comp873_c0_seq2', 410s 'coords' => [ 410s [ 410s 3727877, 410s '3728121' 410s ], 410s [ 410s 3727705, 410s '3727810' 410s ], 410s [ 410s 3726988, 410s '3727657' 410s ] 410s ] 410s }; 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp873_c0_seq2.p1 410s com_name: ORF type:5prime_partial (+),score=8.59 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_type: protein-coding 410s mid_pt: 513 410s source: transdecoder 410s gene_length: 1025 410s is_pseudogene: 0 410s strand: + 410s asmbl_id: comp873_c0_seq2 410s TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1025 CDS-exon: 3, 677 410s gene_span: 1-1025 410s model_span: 3-677 410s 410s Error, couldn't localize pt [1023] within coordsets: $VAR1 = [ 410s [ 410s 3726988, 410s '3727657' 410s ], 410s [ 410s 3727705, 410s '3727810' 410s ], 410s [ 410s 3727877, 410s '3728121' 410s ] 410s ]; 410s Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'gene_id' => '', 410s 'trans_id' => '', 410s 'orient' => '-', 410s 'coords' => [ 410s [ 410s 1268244, 410s '1268583' 410s ], 410s [ 410s 1267938, 410s '1268172' 410s ] 410s ], 410s 'asmbl' => 'comp888_c0_seq1', 410s 'contig' => 'III' 410s }; 410s classification: annotated_genes 410s is_3prime_partial: 0 410s Model_feat_name: comp888_c0_seq1.p1 410s com_name: ORF type:5prime_partial (+),score=23.94 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_type: protein-coding 410s mid_pt: 295 410s source: transdecoder 410s is_pseudogene: 0 410s gene_length: 589 410s strand: + 410s TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 410s asmbl_id: comp888_c0_seq1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 589 CDS-exon: 2, 355 410s gene_span: 1-589 410s model_span: 2-355 410s 410s Error, couldn't localize pt [588] within coordsets: $VAR1 = [ 410s [ 410s 1267938, 410s '1268172' 410s ], 410s [ 410s 1268244, 410s '1268583' 410s ] 410s ]; 410s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp924_c0_seq1.p2. 410s -WARNING, comp932_c0_seq1 has no genome representation... skipping 410s Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'gene_id' => '', 410s 'orient' => '+', 410s 'trans_id' => '', 410s 'asmbl' => 'comp940_c0_seq1', 410s 'coords' => [ 410s [ 410s 105641, 410s '105736' 410s ], 410s [ 410s 105785, 410s '106404' 410s ] 410s ], 410s 'contig' => 'III' 410s }; 410s source: transdecoder 410s mid_pt: 1065 410s strand: + 410s asmbl_id: comp940_c0_seq1 410s TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 410s gene_length: 2129 410s is_pseudogene: 0 410s is_3prime_partial: 0 410s Model_feat_name: comp940_c0_seq1.p1 410s classification: annotated_genes 410s gene_type: protein-coding 410s com_name: ORF type:complete (+),score=94.37 410s is_5prime_partial: 0 410s num_exons: 1 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 2129 CDS-exon: 40, 1731 410s gene_span: 1-2129 410s model_span: 40-1731 410s 410s Error, couldn't localize pt [1731] within coordsets: $VAR1 = [ 410s [ 410s 105641, 410s '105736' 410s ], 410s [ 410s 105785, 410s '106404' 410s ] 410s ]; 410s Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: 410s $VAR1 = { 410s 'contig' => 'I', 410s 'coords' => [ 410s [ 410s 4100066, 410s '4100163' 410s ], 410s [ 410s 4098246, 410s '4100014' 410s ] 410s ], 410s 'asmbl' => 'comp983_c0_seq1', 410s 'trans_id' => '', 410s 'orient' => '-', 410s 'gene_id' => '' 410s }; 410s gene_type: protein-coding 410s com_name: ORF type:5prime_partial (+),score=143.65 410s is_5prime_partial: 0 410s num_exons: 1 410s is_3prime_partial: 0 410s Model_feat_name: comp983_c0_seq1.p1 410s classification: annotated_genes 410s strand: + 410s asmbl_id: comp983_c0_seq1 410s TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 410s gene_length: 1870 410s is_pseudogene: 0 410s source: transdecoder 410s mid_pt: 935 410s gene_synonyms: 410s mRNA_coords 410s CDS_coords 410s RNA-exon: 1, 1870 CDS-exon: 2, 1810 410s gene_span: 1-1870 410s model_span: 2-1810 410s 410s Error, couldn't localize pt [1869] within coordsets: $VAR1 = [ 410s [ 410s 4098246, 410s '4100014' 410s ], 410s [ 410s 4100066, 410s '4100163' 410s ] 410s ]; 410s -WARNING, comp995_c0_seq1 has no genome representation... skipping 410s 410s 410s Done. 646 / 679 transcript orfs could be propagated to the genome 410s 410s make[1]: Leaving directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 410s Running example in $... 410s make[1]: Entering directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 410s ./runMe.sh 410s #!/bin/bash -ve 410s 410s export PERL_HASH_SEED=0 410s 410s 410s 410s ## generate alignment gff3 formatted output 410s ../../util/gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3 411s 411s 411s ## generate transcripts fasta file 411s # not including the genome here... too big, but here's how you'd do it. 411s #../../util/gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta 411s 411s ## Extract the long ORFs 411s ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S 411s CMD: mkdir -p /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir 411s * [Mon Mar 11 04:14:05 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat 411s 411s 411s -first extracting base frequencies, we'll need them later. 413s 413s 413s - extracting ORFs from transcripts. 413s -total transcripts to examine: 3501 423s [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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 423s 423s 423s ################################# 423s ### Done preparing long ORFs. ### 423s ################################## 423s 423s Use file: /tmp/autopkgtest.B13zNQ/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. 423s 423s Then, run TransDecoder.Predict for your final coding region predictions. 423s 423s 423s 423s 423s ## Predict likely ORFs 423s 423s ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS 424s * [Mon Mar 11 04:14:17 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 424s * [Mon Mar 11 04:14:18 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 424s -skipping training candidate: NM_198270.p1, not unique enough 424s -skipping training candidate: NR_104391.p1, not unique enough 424s -skipping training candidate: NR_104395.p1, not unique enough 424s -skipping training candidate: NM_001282622.p1, not unique enough 424s -skipping training candidate: MSTRG.376.1.p1, not unique enough 424s -skipping training candidate: MSTRG.839.3.p1, not unique enough 424s -skipping training candidate: NR_104394.p1, not unique enough 424s -skipping training candidate: MSTRG.397.18.p1, not unique enough 424s -skipping training candidate: NM_020717.p1, not unique enough 424s -skipping training candidate: MSTRG.505.14.p1, not unique enough 424s -skipping training candidate: NM_001136024.p1, not unique enough 424s -skipping training candidate: MSTRG.538.2.p1, not unique enough 424s -skipping training candidate: NM_001291868.p1, not unique enough 424s -skipping training candidate: MSTRG.236.1.p1, not unique enough 424s -skipping training candidate: MSTRG.404.8.p1, not unique enough 424s -skipping training candidate: NM_001555.p1, not unique enough 424s -skipping training candidate: NM_001282224.p1, not unique enough 424s -skipping training candidate: NM_001170962.p1, not unique enough 424s -skipping training candidate: NM_001291416.p1, not unique enough 424s -skipping training candidate: NM_021140.p1, not unique enough 424s -skipping training candidate: MSTRG.376.9.p1, not unique enough 424s -skipping training candidate: NM_014710.p1, not unique enough 424s -skipping training candidate: NM_001099411.p1, not unique enough 424s -skipping training candidate: NM_001184727.p1, not unique enough 424s -skipping training candidate: NM_001146702.p1, not unique enough 424s -skipping training candidate: MSTRG.258.8.p1, not unique enough 424s -skipping training candidate: NM_005096.p1, not unique enough 424s -skipping training candidate: MSTRG.258.9.p1, not unique enough 424s -skipping training candidate: MSTRG.502.3.p1, not unique enough 424s -skipping training candidate: NM_001171162.p1, not unique enough 424s -skipping training candidate: MSTRG.502.2.p1, not unique enough 424s -skipping training candidate: MSTRG.502.1.p1, not unique enough 424s -skipping training candidate: NM_001291417.p1, not unique enough 424s -skipping training candidate: NM_001168360.p1, not unique enough 424s -skipping training candidate: NM_032969.p1, not unique enough 424s -skipping training candidate: NM_001168363.p1, not unique enough 424s -skipping training candidate: MSTRG.236.3.p1, not unique enough 424s -skipping training candidate: NM_001168362.p1, not unique enough 424s -skipping training candidate: NM_001291418.p1, not unique enough 424s -skipping training candidate: NM_001169123.p1, not unique enough 424s -skipping training candidate: MSTRG.570.10.p1, not unique enough 424s -skipping training candidate: NR_111960.p1, not unique enough 424s -skipping training candidate: NM_001169122.p1, not unique enough 424s -skipping training candidate: NM_001169124.p1, not unique enough 424s -skipping training candidate: NM_001169125.p1, not unique enough 424s -skipping training candidate: MSTRG.848.14.p1, not unique enough 424s -skipping training candidate: NM_001042749.p1, not unique enough 424s -skipping training candidate: MSTRG.848.13.p1, not unique enough 424s -skipping training candidate: MSTRG.848.7.p1, not unique enough 424s -skipping training candidate: MSTRG.848.12.p1, not unique enough 424s -skipping training candidate: NM_000425.p1, not unique enough 424s -skipping training candidate: NM_024003.p1, not unique enough 424s -skipping training candidate: NM_001143963.p1, not unique enough 424s -skipping training candidate: MSTRG.477.3.p1, not unique enough 424s -skipping training candidate: NM_012310.p1, not unique enough 424s -skipping training candidate: MSTRG.848.11.p1, not unique enough 424s -skipping training candidate: NM_001042751.p1, not unique enough 424s -skipping training candidate: NM_006603.p1, not unique enough 424s -skipping training candidate: MSTRG.848.1.p1, not unique enough 424s -skipping training candidate: MSTRG.848.4.p1, not unique enough 424s -skipping training candidate: MSTRG.848.2.p1, not unique enough 424s -skipping training candidate: NM_001282418.p1, not unique enough 424s -skipping training candidate: MSTRG.848.6.p1, not unique enough 424s -skipping training candidate: NM_004022.p1, not unique enough 424s -skipping training candidate: NM_004013.p1, not unique enough 424s -skipping training candidate: MSTRG.570.9.p1, not unique enough 424s -skipping training candidate: MSTRG.147.2.p1, not unique enough 424s -skipping training candidate: NM_006044.p1, not unique enough 424s -skipping training candidate: MSTRG.331.3.p1, not unique enough 424s -skipping training candidate: MSTRG.331.2.p1, not unique enough 424s -skipping training candidate: MSTRG.331.4.p1, not unique enough 424s -skipping training candidate: NM_001281463.p1, not unique enough 424s -skipping training candidate: NM_001122670.p1, not unique enough 424s -skipping training candidate: MSTRG.147.3.p1, not unique enough 424s -skipping training candidate: NM_021949.p1, not unique enough 424s -skipping training candidate: MSTRG.456.2.p1, not unique enough 424s -skipping training candidate: NM_001130860.p1, not unique enough 424s -skipping training candidate: NM_001172436.p1, not unique enough 424s -skipping training candidate: MSTRG.442.1.p1, not unique enough 424s -skipping training candidate: NM_004023.p1, not unique enough 424s -skipping training candidate: MSTRG.945.2.p1, not unique enough 424s -skipping training candidate: MSTRG.945.3.p1, not unique enough 424s -skipping training candidate: MSTRG.945.8.p1, not unique enough 424s -skipping training candidate: MSTRG.518.1.p1, not unique enough 424s -skipping training candidate: NM_001010986.p1, not unique enough 424s -skipping training candidate: MSTRG.945.1.p1, not unique enough 424s -skipping training candidate: NM_004020.p1, not unique enough 424s -skipping training candidate: NM_153280.p1, not unique enough 424s -skipping training candidate: NM_001291421.p1, not unique enough 424s -skipping training candidate: NM_001105243.p1, not unique enough 424s -skipping training candidate: NM_020766.p1, not unique enough 424s -skipping training candidate: NM_007309.p1, not unique enough 424s -skipping training candidate: NM_005756.p1, not unique enough 424s -skipping training candidate: NM_001113490.p1, not unique enough 424s -skipping training candidate: NM_001079859.p1, not unique enough 424s -skipping training candidate: NM_001184833.p1, not unique enough 424s -skipping training candidate: MSTRG.945.6.p1, not unique enough 424s -skipping training candidate: NM_001168361.p1, not unique enough 424s -skipping training candidate: NM_001079860.p1, not unique enough 424s -skipping training candidate: NM_001184836.p1, not unique enough 424s -skipping training candidate: NM_001184837.p1, not unique enough 424s -skipping training candidate: NM_001257231.p1, not unique enough 424s -skipping training candidate: NM_001184835.p1, not unique enough 424s -skipping training candidate: NM_001282875.p1, not unique enough 424s -skipping training candidate: NM_003069.p1, not unique enough 424s -skipping training candidate: MSTRG.88.1.p1, not unique enough 424s -skipping training candidate: MSTRG.387.2.p1, not unique enough 424s -skipping training candidate: MSTRG.387.1.p1, not unique enough 424s -skipping training candidate: MSTRG.860.6.p1, not unique enough 424s -skipping training candidate: NM_001184834.p1, not unique enough 425s -skipping training candidate: NM_138636.p1, not unique enough 425s -skipping training candidate: NM_181673.p1, not unique enough 425s -skipping training candidate: NM_001271184.p1, not unique enough 425s -skipping training candidate: MSTRG.759.13.p1, not unique enough 425s -skipping training candidate: MSTRG.759.12.p1, not unique enough 425s -skipping training candidate: NM_001037343.p1, not unique enough 425s -skipping training candidate: NM_015107.p1, not unique enough 425s -skipping training candidate: NM_014725.p1, not unique enough 425s -skipping training candidate: NM_001142504.p1, not unique enough 425s -skipping training candidate: MSTRG.945.7.p1, not unique enough 425s -skipping training candidate: NM_001168647.p1, not unique enough 425s -skipping training candidate: NM_001099855.p1, not unique enough 425s -skipping training candidate: NM_004014.p1, not unique enough 425s -skipping training candidate: MSTRG.110.1.p1, not unique enough 425s -skipping training candidate: NM_001282141.p1, not unique enough 425s -skipping training candidate: NM_001666.p1, not unique enough 425s -skipping training candidate: NM_001271183.p1, not unique enough 425s -skipping training candidate: NM_001257237.p1, not unique enough 425s -skipping training candidate: NM_001257230.p1, not unique enough 425s -skipping training candidate: NM_001257234.p1, not unique enough 425s -skipping training candidate: NM_001170628.p1, not unique enough 425s -skipping training candidate: NM_015075.p1, not unique enough 425s -skipping training candidate: NM_001587.p1, not unique enough 425s -skipping training candidate: NM_001184897.p1, not unique enough 425s -skipping training candidate: NM_001171879.p1, not unique enough 425s -skipping training candidate: MSTRG.759.11.p1, not unique enough 425s -skipping training candidate: MSTRG.110.4.p1, not unique enough 425s -skipping training candidate: NM_005676.p1, not unique enough 425s -skipping training candidate: MSTRG.110.5.p1, not unique enough 425s -skipping training candidate: NM_001204467.p1, not unique enough 425s -skipping training candidate: NM_031276.p1, not unique enough 425s -skipping training candidate: NM_005369.p1, not unique enough 425s -skipping training candidate: MSTRG.250.1.p1, not unique enough 425s -skipping training candidate: MSTRG.387.3.p1, not unique enough 425s -skipping training candidate: MSTRG.1005.1.p1, not unique enough 425s -skipping training candidate: NM_001300788.p1, not unique enough 425s -skipping training candidate: MSTRG.508.1.p1, not unique enough 425s -skipping training candidate: NM_001126054.p1, not unique enough 425s -skipping training candidate: NM_003588.p1, not unique enough 425s -skipping training candidate: NM_001126055.p1, not unique enough 425s -skipping training candidate: MSTRG.110.7.p1, not unique enough 425s -skipping training candidate: NM_001184965.p1, not unique enough 425s -skipping training candidate: NM_001085354.p1, not unique enough 425s -skipping training candidate: NM_001168648.p1, not unique enough 425s -skipping training candidate: NM_001079872.p1, not unique enough 425s -skipping training candidate: NM_007325.p1, not unique enough 425s -skipping training candidate: NM_014799.p1, not unique enough 425s -skipping training candidate: MSTRG.110.8.p1, not unique enough 425s -skipping training candidate: MSTRG.855.3.p1, not unique enough 425s -skipping training candidate: NM_001171184.p1, not unique enough 425s -skipping training candidate: MSTRG.110.6.p1, not unique enough 425s -skipping training candidate: NM_001184898.p1, not unique enough 425s -skipping training candidate: MSTRG.276.2.p1, not unique enough 425s -skipping training candidate: NM_024597.p1, not unique enough 425s -skipping training candidate: MSTRG.839.4.p1, not unique enough 425s -skipping training candidate: NM_007156.p1, not unique enough 425s -skipping training candidate: MSTRG.759.1.p1, not unique enough 425s -skipping training candidate: MSTRG.759.21.p1, not unique enough 425s -skipping training candidate: MSTRG.759.22.p1, not unique enough 425s -skipping training candidate: NM_182540.p1, not unique enough 425s -skipping training candidate: NM_001171878.p1, not unique enough 425s -skipping training candidate: NM_152633.p1, not unique enough 425s -skipping training candidate: MSTRG.442.2.p1, not unique enough 425s -skipping training candidate: NM_001173516.p1, not unique enough 425s -skipping training candidate: MSTRG.921.2.p1, not unique enough 425s -skipping training candidate: NM_001204466.p1, not unique enough 425s -skipping training candidate: NM_152856.p1, not unique enough 425s -skipping training candidate: MSTRG.759.20.p1, not unique enough 425s -skipping training candidate: MSTRG.855.4.p1, not unique enough 425s -skipping training candidate: NM_001168649.p1, not unique enough 425s -skipping training candidate: NM_001077445.p1, not unique enough 425s -skipping training candidate: MSTRG.839.6.p1, not unique enough 425s -skipping training candidate: NM_001144004.p1, not unique enough 425s -skipping training candidate: NM_001144010.p1, not unique enough 425s -skipping training candidate: NM_001144003.p1, not unique enough 425s -skipping training candidate: NM_001144009.p1, not unique enough 425s -skipping training candidate: NM_001144005.p1, not unique enough 425s -skipping training candidate: NM_001144006.p1, not unique enough 425s -skipping training candidate: NM_032539.p1, not unique enough 425s -skipping training candidate: NM_139289.p1, not unique enough 425s -skipping training candidate: MSTRG.839.5.p1, not unique enough 425s -skipping training candidate: NM_001173517.p1, not unique enough 425s -skipping training candidate: NM_001184875.p1, not unique enough 425s 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MSTRG.664.1.p2, not unique enough 425s -skipping training candidate: MSTRG.664.2.p2, not unique enough 425s -skipping training candidate: NM_001171907.p1, not unique enough 425s -skipping training candidate: NM_182681.p2, not unique enough 425s -skipping training candidate: NR_026710.p1, not unique enough 425s -skipping training candidate: NR_033772_dup1.p1, not unique enough 425s -skipping training candidate: NM_001282302.p1, not unique enough 425s -skipping training candidate: MSTRG.459.2.p1, not unique enough 425s -skipping training candidate: NR_033773_dup1.p1, not unique enough 425s -skipping training candidate: NR_033773.p1, not unique enough 425s -skipping training candidate: MSTRG.1041.6.p2, not unique enough 425s -skipping training candidate: MSTRG.1041.7.p2, not unique enough 425s -skipping training candidate: MSTRG.387.3.p2, not unique enough 425s -skipping training candidate: NM_001184896.p2, not unique enough 425s -skipping training candidate: NM_001170569.p1, not unique 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NM_001079900_dup1.p1, not unique enough 426s -skipping training candidate: NM_001654.p2, not unique enough 426s -skipping training candidate: NM_001256196.p2, not unique enough 426s -skipping training candidate: MSTRG.76.2.p2, not unique enough 426s -skipping training candidate: NM_001281463.p2, not unique enough 426s -skipping training candidate: MSTRG.739.4.p1, not unique enough 426s -skipping training candidate: NM_000425.p3, not unique enough 426s -skipping training candidate: NM_024003.p3, not unique enough 426s -skipping training candidate: NM_001143963.p3, not unique enough 426s -skipping training candidate: MSTRG.205.2.p1, not unique enough 426s -skipping training candidate: MSTRG.338.6.p2, not unique enough 426s -skipping training candidate: NM_001136157.p2, not unique enough 426s -skipping training candidate: NM_001136159.p2, not unique enough 426s -skipping training candidate: MSTRG.994.1.p2, not unique enough 426s -skipping training candidate: NR_033772_dup1.p2, not unique enough 426s -skipping training candidate: MSTRG.4.3.p4, not unique enough 426s -skipping training candidate: NM_018390.p4, not unique enough 426s -skipping training candidate: NM_001172672.p1, not unique enough 426s -skipping training candidate: NR_033773_dup1.p2, not unique enough 426s -skipping training candidate: NR_033773.p2, not unique enough 426s -skipping training candidate: MSTRG.17.2.p2, not unique enough 426s -skipping training candidate: MSTRG.668.2.p2, not unique enough 426s -skipping training candidate: MSTRG.759.9.p2, not unique enough 426s -skipping training candidate: NM_018466.p1, not unique enough 426s -skipping training candidate: MSTRG.116.5.p1, not unique enough 426s -skipping training candidate: MSTRG.961.7.p1, not unique enough 426s -skipping training candidate: MSTRG.216.5.p2, not unique enough 426s -skipping training candidate: NM_001098791.p2, not unique enough 426s -skipping training candidate: NM_021242.p2, not unique enough 426s -skipping training candidate: NM_001098790.p2, not unique enough 426s -skipping training candidate: NM_153183.p1, not unique enough 426s -skipping training candidate: NM_001282201.p2, not unique enough 426s -skipping training candidate: NM_001190255.p2, not unique enough 426s -skipping training candidate: NM_001282202.p2, not unique enough 426s -skipping training candidate: MSTRG.925.2.p2, not unique enough 426s -skipping training candidate: NM_001163280.p2, not unique enough 426s -skipping training candidate: NM_005393.p2, not unique enough 426s -skipping training candidate: MSTRG.763.1.p1, not unique enough 426s -skipping training candidate: MSTRG.124.9.p1, not unique enough 426s -skipping training candidate: MSTRG.124.1.p1, not unique enough 426s -skipping training candidate: MSTRG.124.8.p2, not unique enough 426s -skipping training candidate: NM_001256185.p1, not unique enough 426s -skipping training candidate: NM_001282174.p2, not unique enough 426s -skipping training candidate: NM_020717.p2, not unique enough 426s -skipping training candidate: NM_001303545.p1, not unique enough 426s -skipping training candidate: MSTRG.311.2.p1, not unique enough 426s -skipping training candidate: NR_027419.p1, not unique enough 426s -skipping training candidate: NR_033254_dup1.p1, not unique enough 426s -skipping training candidate: NR_033257_dup1.p1, not unique enough 426s -skipping training candidate: NR_033257.p1, not unique enough 426s -skipping training candidate: MSTRG.549.7.p1, not unique enough 426s -skipping training candidate: NM_205856_dup1.p1, not unique enough 426s -skipping training candidate: NM_205856.p1, not unique enough 426s -skipping training candidate: NM_001306188.p1, not unique enough 426s -skipping training candidate: NM_004780.p1, not unique enough 426s -skipping training candidate: MSTRG.694.2.p1, not unique enough 426s -skipping training candidate: NM_001006639.p1, not unique enough 426s -skipping training candidate: NM_001168400.p1, not unique enough 426s -skipping training candidate: NM_005647.p2, not unique enough 426s -skipping training candidate: MSTRG.973.4.p1, not unique enough 426s -skipping training candidate: MSTRG.973.3.p1, not unique enough 426s -skipping training candidate: NM_001013845.p1, not unique enough 426s -skipping training candidate: MSTRG.109.10.p1, not unique enough 426s -skipping training candidate: NM_005089.p2, not unique enough 426s -skipping training candidate: MSTRG.128.1.p3, not unique enough 426s -skipping training candidate: NM_001171908.p1, not unique enough 426s -skipping training candidate: NM_178124.p1, not unique enough 426s -skipping training candidate: NM_001171907.p2, not unique enough 426s -skipping training candidate: NM_001039891.p2, not unique enough 426s -skipping training candidate: NM_001190417.p2, not unique enough 426s -skipping training candidate: NM_001146291.p2, not unique enough 426s -skipping training candidate: MSTRG.266.4.p2, not unique enough 426s -skipping training candidate: NM_001278740.p1, not unique enough 426s -skipping training candidate: NM_001278741.p1, not unique enough 426s -skipping training candidate: MSTRG.324.2.p1, not unique enough 426s -skipping training candidate: NR_104107.p2, not unique enough 426s -skipping training candidate: NM_001184897.p2, not unique enough 426s -skipping training candidate: NM_015107.p3, not unique enough 426s -skipping training candidate: MSTRG.387.3.p3, not unique enough 426s -skipping training candidate: NM_001184896.p3, not unique enough 426s -skipping training candidate: MSTRG.387.1.p2, not unique enough 426s -skipping training candidate: NM_001282462.p1, not unique enough 426s -skipping training candidate: NM_001282461.p1, not unique enough 426s -skipping training candidate: NM_001012755.p2, not unique enough 426s -skipping training candidate: MSTRG.705.2.p2, not unique enough 426s -skipping training candidate: MSTRG.705.4.p2, not unique enough 426s -skipping training candidate: MSTRG.718.6.p1, not unique enough 426s -skipping training candidate: NM_001007088.p3, not unique enough 426s -skipping training candidate: NM_006962.p3, not unique enough 426s -skipping training candidate: MSTRG.294.4.p3, not unique enough 426s -skipping training candidate: NM_000054.p3, not unique enough 426s -skipping training candidate: MSTRG.53.1.p1, not unique enough 426s -skipping training candidate: NM_177537.p2, not unique enough 426s -skipping training candidate: MSTRG.1029.1.p2, not unique enough 426s -skipping training candidate: NM_019045.p2, not unique enough 426s -skipping training candidate: NM_001184966.p2, not unique enough 426s -skipping training candidate: NM_177535_dup1.p2, not unique enough 426s -skipping training candidate: NM_177537_dup1.p2, not unique enough 426s -skipping training candidate: NR_033380.p1, not unique enough 426s -skipping training candidate: MSTRG.38.1.p1, not unique enough 426s -skipping training candidate: NM_001163265.p2, not unique enough 426s -skipping training candidate: NM_001163264.p2, not unique enough 426s -skipping training candidate: NM_001135998.p1, not unique enough 426s -skipping training candidate: MSTRG.961.2.p2, not unique enough 426s -skipping training candidate: MSTRG.961.7.p2, not unique enough 426s -skipping training candidate: MSTRG.961.4.p2, not unique enough 426s -skipping training candidate: MSTRG.68.20.p1, not unique enough 426s -skipping training candidate: NM_001040612.p1, not unique enough 426s -skipping training candidate: MSTRG.925.2.p3, not unique enough 426s -skipping training candidate: NM_001163280.p3, not unique enough 426s -skipping training candidate: NM_175729.p1, not unique enough 426s -skipping training candidate: NM_175729_dup1.p1, not unique enough 426s -skipping training candidate: NR_126093.p2, not unique enough 426s -skipping training candidate: NM_001193417.p2, not unique enough 426s -skipping training candidate: NM_001356.p2, not unique enough 426s -skipping training candidate: NM_005393.p3, not unique enough 426s -skipping training candidate: MSTRG.799.2.p1, not unique enough 426s -skipping training candidate: MSTRG.275.3.p2, not unique enough 426s -skipping training candidate: MSTRG.275.4.p2, not unique enough 426s -skipping training candidate: NM_000425.p4, not unique enough 426s -skipping training candidate: NM_024003.p4, not unique enough 426s -skipping training candidate: NM_001143963.p4, not unique enough 426s -skipping training candidate: NM_170750.p1, not unique enough 426s -skipping training candidate: NM_001291421.p2, not unique enough 426s -skipping training candidate: NM_022117.p2, not unique enough 426s -skipping training candidate: MSTRG.459.1.p2, not unique enough 426s -skipping training candidate: MSTRG.459.2.p2, not unique enough 426s -skipping training candidate: NM_001146151.p3, not unique enough 426s -skipping training candidate: MSTRG.345.2.p2, not unique enough 426s -skipping training candidate: MSTRG.345.4.p2, not unique enough 426s -skipping training candidate: MSTRG.1012.4.p2, not unique enough 426s -skipping training candidate: NM_005334.p2, not unique enough 426s -skipping training candidate: MSTRG.1012.3.p2, not unique enough 426s -skipping training candidate: MSTRG.68.10.p2, not unique enough 426s -skipping training candidate: NM_015075.p3, not unique enough 426s -skipping training candidate: NR_030774.p2, not unique enough 426s -skipping training candidate: MSTRG.34.8.p1, not unique enough 426s -skipping training candidate: MSTRG.34.3.p1, not unique enough 426s -skipping training candidate: NM_001164619.p2, not unique enough 426s -skipping training candidate: NM_001164618.p2, not unique enough 426s -skipping training candidate: NM_001164617.p2, not unique enough 426s -skipping training candidate: MSTRG.663.1.p1, not unique enough 426s -skipping training candidate: MSTRG.734.6.p1, not unique enough 426s -skipping training candidate: NM_017698.p1, not unique enough 426s -skipping training candidate: NM_001005613.p1, not unique enough 426s -skipping training candidate: MSTRG.1029.12.p2, not unique enough 426s -skipping training candidate: MSTRG.216.5.p3, not unique enough 426s -skipping training candidate: NM_021242.p3, not unique enough 426s -skipping training candidate: MSTRG.994.4.p2, not unique enough 426s -skipping training candidate: NM_001130997.p2, not unique enough 426s -skipping training candidate: NM_016120.p2, not unique enough 426s -skipping training candidate: MSTRG.537.1.p2, not unique enough 426s -skipping training candidate: NM_183353.p2, not unique enough 426s -skipping training candidate: MSTRG.867.6.p1, not unique enough 426s -skipping training candidate: NM_001272062.p3, not unique enough 426s -skipping training candidate: NM_001272063.p2, not unique enough 426s -skipping training candidate: NM_177537.p3, not unique enough 426s -skipping training candidate: MSTRG.973.2.p1, not unique enough 426s -skipping training candidate: MSTRG.973.1.p1, not unique enough 426s -skipping training candidate: NM_001171909.p1, not unique enough 426s -skipping training candidate: MSTRG.963.2.p1, not unique enough 426s -skipping training candidate: MSTRG.963.3.p2, not unique enough 426s -skipping training candidate: MSTRG.963.1.p2, not unique enough 426s -skipping training candidate: NM_001097604_dup1.p1, not unique enough 426s -skipping training candidate: MSTRG.268.3.p2, not unique enough 426s -skipping training candidate: NM_001272061_dup1.p2, not unique enough 426s -skipping training candidate: NM_030801_dup1.p2, not unique enough 426s -skipping training candidate: NM_177535_dup1.p3, not unique enough 426s -skipping training candidate: NM_177537_dup1.p3, not unique enough 426s -skipping training candidate: NM_001097594_dup1.p1, not unique enough 426s -skipping training candidate: NM_001097594.p1, not unique enough 426s -skipping training candidate: NM_020717.p3, not unique enough 426s -skipping training candidate: MSTRG.302.6.p1, not unique enough 426s -skipping training candidate: MSTRG.1025.5.p1, not unique enough 426s -skipping training candidate: NM_001287760.p2, not unique enough 426s -skipping training candidate: NM_033641.p2, not unique enough 426s -skipping training candidate: NM_001847.p2, not unique enough 426s -skipping training candidate: MSTRG.131.6.p1, not unique enough 426s -skipping training candidate: MSTRG.131.5.p1, not unique enough 426s -skipping training candidate: NM_001303465.p2, not unique enough 426s -skipping training candidate: MSTRG.1029.3.p2, not unique enough 426s -skipping training candidate: NM_206917.p1, not unique enough 426s -skipping training candidate: NM_031407.p2, not unique enough 426s -skipping training candidate: MSTRG.397.21.p2, not unique enough 426s -skipping training candidate: MSTRG.397.6.p2, not unique enough 426s -skipping training candidate: MSTRG.397.7.p2, not unique enough 426s -skipping training candidate: MSTRG.397.5.p2, not unique enough 426s -skipping training candidate: MSTRG.397.18.p2, not unique enough 426s -skipping training candidate: MSTRG.397.26.p2, not unique enough 426s -skipping training candidate: MSTRG.397.17.p2, not unique enough 426s -skipping training candidate: MSTRG.397.24.p2, not unique enough 426s -skipping training candidate: MSTRG.397.2.p2, not unique enough 426s -skipping training candidate: MSTRG.397.27.p2, not unique enough 426s -skipping training candidate: MSTRG.397.8.p2, not unique enough 426s -skipping training candidate: MSTRG.397.23.p2, not unique enough 426s -skipping training candidate: MSTRG.397.12.p2, not unique enough 426s -skipping training candidate: MSTRG.397.19.p2, not unique enough 426s -skipping training candidate: MSTRG.397.22.p2, not unique enough 426s -skipping training candidate: MSTRG.397.9.p2, not unique enough 426s -skipping training candidate: MSTRG.397.14.p2, not unique enough 426s -skipping training candidate: MSTRG.397.25.p2, not unique enough 426s -skipping training candidate: MSTRG.397.10.p2, not unique enough 426s -skipping training candidate: MSTRG.397.11.p2, not unique enough 426s -skipping training candidate: MSTRG.397.15.p2, not unique enough 426s -skipping training candidate: MSTRG.397.4.p2, not unique enough 426s -skipping training candidate: MSTRG.397.28.p2, not unique enough 426s -skipping training candidate: MSTRG.397.3.p2, not unique enough 426s -skipping training candidate: MSTRG.397.20.p2, not unique enough 426s -skipping training candidate: MSTRG.397.16.p2, not unique enough 426s -skipping training candidate: NR_045560.p1, not unique enough 426s -skipping training candidate: MSTRG.268.7.p2, not unique enough 426s -skipping training candidate: NM_001291421.p3, not unique enough 426s -skipping training candidate: NM_001291417.p2, not unique enough 426s -skipping training candidate: NM_021140.p2, not unique enough 426s -skipping training candidate: NM_001291418.p2, not unique enough 426s -skipping training candidate: NM_001291416.p2, not unique enough 426s -skipping training candidate: NM_001291415.p2, not unique enough 426s -skipping training candidate: NM_001256187.p1, not unique enough 426s -skipping training candidate: MSTRG.305.1.p3, not unique enough 426s -skipping training candidate: MSTRG.459.3.p2, not unique enough 426s -skipping training candidate: NM_021783.p2, not unique enough 426s -skipping training candidate: MSTRG.459.1.p3, not unique enough 426s -skipping training candidate: NM_020994.p2, not unique enough 426s -skipping training candidate: NM_001282621.p1, not unique enough 426s -skipping training candidate: NM_001146257.p1, not unique enough 426s -skipping training candidate: MSTRG.109.1.p1, not unique enough 426s -skipping training candidate: NM_001168649.p2, not unique enough 426s -skipping training candidate: NM_014927.p2, not unique enough 426s -skipping training candidate: NM_001168647.p2, not unique enough 426s -skipping training candidate: NM_001242617.p1, not unique enough 426s -skipping training candidate: NM_021029.p1, not unique enough 426s -skipping training candidate: MSTRG.68.10.p3, not unique enough 426s -skipping training candidate: MSTRG.68.8.p2, not unique enough 426s -skipping training candidate: MSTRG.68.2.p1, not unique enough 426s -skipping training candidate: MSTRG.68.16.p2, not unique enough 426s -skipping training candidate: MSTRG.258.8.p2, not unique enough 426s -skipping training candidate: MSTRG.250.5.p1, not unique enough 426s -skipping training candidate: NM_001011658.p1, not unique enough 426s -skipping training candidate: MSTRG.258.9.p2, not unique enough 426s -skipping training candidate: NM_001184898.p2, not unique enough 426s -skipping training candidate: MSTRG.992.7.p2, not unique enough 426s -skipping training candidate: MSTRG.476.2.p1, not unique enough 426s -skipping training candidate: NM_020717.p4, not unique enough 426s -skipping training candidate: NM_001256186.p1, not unique enough 426s -skipping training candidate: NM_017711.p3, not unique enough 426s -skipping training candidate: NM_017883.p2, not unique enough 426s -skipping training candidate: NM_001171192.p3, not unique enough 426s -skipping training candidate: NM_001282621.p2, not unique enough 426s -skipping training candidate: MSTRG.921.1.p2, not unique enough 426s -skipping training candidate: MSTRG.921.3.p2, not unique enough 426s -skipping training candidate: MSTRG.921.2.p2, not unique enough 426s -skipping training candidate: MSTRG.718.1.p1, not unique enough 426s -skipping training candidate: NM_001184819.p2, not unique enough 426s -skipping training candidate: MSTRG.641.8.p1, not unique enough 426s -skipping training candidate: NM_001099857.p2, not unique enough 426s -skipping training candidate: NM_001008534.p1, not unique enough 426s -skipping training candidate: NM_001278742.p1, not unique enough 426s -skipping training candidate: MSTRG.305.6.p2, not unique enough 426s -skipping training candidate: MSTRG.306.1.p2, not unique enough 426s -skipping training candidate: NM_014725.p2, not unique enough 426s -skipping training candidate: NM_001142504.p2, not unique enough 426s -skipping training candidate: NM_001271183.p2, not unique enough 426s -skipping training candidate: MSTRG.404.8.p2, not unique enough 426s -skipping training candidate: NM_001271184.p2, not unique enough 426s -skipping training candidate: NM_001172739.p2, not unique enough 426s -skipping training candidate: MSTRG.734.6.p2, not unique enough 426s -skipping training candidate: NM_017698.p2, not unique enough 426s -skipping training candidate: MSTRG.734.5.p2, not unique enough 426s -skipping training candidate: MSTRG.734.3.p2, not unique enough 426s -skipping training candidate: MSTRG.734.2.p2, not unique enough 426s -skipping training candidate: NM_001005609.p2, not unique enough 426s -skipping training candidate: MSTRG.438.2.p1, not unique enough 426s -skipping training candidate: NR_001564.p1, not unique enough 426s -skipping training candidate: MSTRG.531.1.p1, not unique enough 426s -skipping training candidate: MSTRG.531.3.p1, not unique enough 426s -skipping training candidate: MSTRG.275.3.p3, not unique enough 426s -skipping training candidate: NM_001170460.p2, not unique enough 426s -skipping training candidate: MSTRG.275.2.p2, not unique enough 426s -skipping training candidate: MSTRG.275.4.p3, not unique enough 426s -skipping training candidate: MSTRG.275.7.p2, not unique enough 426s -skipping training candidate: MSTRG.275.6.p2, not unique enough 426s -skipping training candidate: NM_006201.p2, not unique enough 426s -skipping training candidate: MSTRG.615.2.p1, not unique enough 426s -skipping training candidate: MSTRG.615.1.p1, not unique enough 426s -skipping training candidate: MSTRG.16.1.p6, not unique enough 426s -skipping training candidate: NM_000495.p2, not unique enough 426s -skipping training candidate: MSTRG.992.3.p1, not unique enough 426s -skipping training candidate: NR_073156.p2, not unique enough 426s -skipping training candidate: MSTRG.62.2.p2, not unique enough 426s -skipping training candidate: MSTRG.62.1.p2, not unique enough 426s -skipping training candidate: NM_006521.p2, not unique enough 426s -skipping training candidate: MSTRG.488.1.p1, not unique enough 426s -skipping training candidate: NR_033212.p1, not unique enough 426s -skipping training candidate: NM_145305.p2, not unique enough 426s -skipping training candidate: NM_001005610.p1, not unique enough 426s -skipping training candidate: NR_001564.p2, not unique enough 426s -skipping training candidate: MSTRG.531.1.p2, not unique enough 426s -skipping training candidate: MSTRG.531.3.p2, not unique enough 426s -skipping training candidate: MSTRG.275.4.p4, not unique enough 426s -skipping training candidate: NM_006201.p3, not unique enough 426s -skipping training candidate: NM_001300788.p3, not unique enough 426s -skipping training candidate: NM_001144003.p2, not unique enough 426s -skipping training candidate: MSTRG.284.1.p3, not unique enough 426s -skipping training candidate: MSTRG.963.2.p2, not unique enough 426s -skipping training candidate: NM_001039582.p2, not unique enough 426s -skipping training candidate: NM_001144005.p2, not unique enough 426s -skipping training candidate: MSTRG.933.1.p2, not unique enough 426s -skipping training candidate: NM_001005609.p3, not unique enough 426s -skipping training candidate: NM_001005612.p2, not unique enough 426s -skipping training candidate: NM_001005612.p3, not unique enough 426s -skipping training candidate: MSTRG.759.10.p2, not unique enough 426s -skipping training candidate: MSTRG.759.2.p2, not unique enough 426s -skipping training candidate: MSTRG.759.21.p2, not unique enough 426s -skipping training candidate: MSTRG.759.11.p2, not unique enough 426s -skipping training candidate: NM_001168385.p1, not unique enough 426s -skipping training candidate: NM_001143982.p2, not unique enough 426s -skipping training candidate: MSTRG.305.8.p2, not unique enough 426s -skipping training candidate: NM_145234.p2, not unique enough 426s -skipping training candidate: MSTRG.641.7.p1, not unique enough 426s -skipping training candidate: NM_001145252.p2, not unique enough 426s -skipping training candidate: NM_001143981.p2, not unique enough 426s -skipping training candidate: NM_174951.p2, not unique enough 426s -skipping training candidate: NR_027383.p4, not unique enough 426s -skipping training candidate: MSTRG.32.4.p4, not unique enough 426s -skipping training candidate: MSTRG.327.3.p3, not unique enough 426s -skipping training candidate: NM_003173.p3, not unique enough 426s -skipping training candidate: NR_024048.p2, not unique enough 426s -skipping training candidate: NM_001123385.p2, not unique enough 426s -skipping training candidate: NM_130467.p1, not unique enough 426s -skipping training candidate: NM_005676.p2, not unique enough 426s -skipping training candidate: NM_001204468.p2, not unique enough 426s -skipping training candidate: NR_029427.p3, not unique enough 426s -skipping training candidate: MSTRG.325.4.p2, not unique enough 426s -skipping training candidate: NM_001166426.p2, not unique enough 426s -skipping training candidate: NM_017883.p3, not unique enough 426s -skipping training candidate: NM_001080851.p2, not unique enough 426s -skipping training candidate: NM_001278743.p1, not unique enough 426s -skipping training candidate: MSTRG.822.4.p1, not unique enough 426s -skipping training candidate: NM_033053.p2, not unique enough 426s -skipping training candidate: NM_033053_dup1.p2, not unique enough 426s -skipping training candidate: NM_005647.p3, not unique enough 426s -skipping training candidate: MSTRG.1023.3.p2, not unique enough 426s -skipping training candidate: MSTRG.1023.2.p2, not unique enough 426s -skipping training candidate: NM_001166700.p1, not unique enough 426s -skipping training candidate: MSTRG.1074.8.p2, not unique enough 426s -skipping training candidate: NR_026594.p1, not unique enough 426s -skipping training candidate: NR_110830.p3, not unique enough 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NM_003918.p2, not unique enough 426s -skipping training candidate: MSTRG.913.3.p1, not unique enough 426s -skipping training candidate: NM_001129826_dup1.p1, not unique enough 426s -skipping training candidate: MSTRG.502.3.p2, not unique enough 426s -skipping training candidate: NM_001171162.p2, not unique enough 426s -skipping training candidate: NM_005096.p2, not unique enough 426s -skipping training candidate: MSTRG.502.2.p2, not unique enough 426s -skipping training candidate: MSTRG.502.1.p2, not unique enough 426s -skipping training candidate: MSTRG.9.3.p2, not unique enough 426s -skipping training candidate: MSTRG.654.2.p2, not unique enough 426s -skipping training candidate: MSTRG.654.1.p2, not unique enough 426s -skipping training candidate: MSTRG.654.3.p2, not unique enough 426s -skipping training candidate: MSTRG.794.2.p2, not unique enough 426s -skipping training candidate: NM_001109879.p2, not unique enough 426s -skipping training candidate: MSTRG.230.7.p2, not unique 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NM_001146256.p2, not unique enough 426s -skipping training candidate: NM_001146257.p2, not unique enough 426s -skipping training candidate: MSTRG.208.3.p2, not unique enough 426s -skipping training candidate: NM_152787.p2, not unique enough 426s -skipping training candidate: MSTRG.208.2.p2, not unique enough 426s -skipping training candidate: NM_021048.p2, not unique enough 426s -skipping training candidate: NM_001011543.p2, not unique enough 426s -skipping training candidate: MSTRG.147.4.p2, not unique enough 426s -skipping training candidate: NM_001170931.p2, not unique enough 426s -skipping training candidate: MSTRG.1041.5.p1, not unique enough 426s -skipping training candidate: MSTRG.794.3.p2, not unique enough 426s -skipping training candidate: NM_001356.p3, not unique enough 426s -skipping training candidate: MSTRG.68.1.p2, not unique enough 426s -skipping training candidate: MSTRG.68.18.p3, not unique enough 426s -skipping training candidate: MSTRG.68.10.p4, not unique enough 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NM_006746.p2, not unique enough 426s -skipping training candidate: MSTRG.541.3.p2, not unique enough 426s -skipping training candidate: NM_005088.p3, not unique enough 426s -skipping training candidate: NM_001080485.p3, not unique enough 426s -skipping training candidate: NM_020922.p2, not unique enough 426s -skipping training candidate: MSTRG.604.2.p2, not unique enough 426s -skipping training candidate: MSTRG.311.3.p1, not unique enough 426s -skipping training candidate: NM_001080425.p1, not unique enough 426s -skipping training candidate: MSTRG.68.17.p3, not unique enough 426s -skipping training candidate: NR_130733.p1, not unique enough 426s -skipping training candidate: NM_001282535.p3, not unique enough 426s -skipping training candidate: NM_001282607.p2, not unique enough 426s -skipping training candidate: NR_026551.p2, not unique enough 426s -skipping training candidate: NM_013423.p2, not unique enough 426s -skipping training candidate: NM_001287242.p2, not unique enough 426s 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NM_001170703.p2, not unique enough 426s -skipping training candidate: MSTRG.889.4.p3, not unique enough 426s -skipping training candidate: MSTRG.889.3.p2, not unique enough 426s -skipping training candidate: MSTRG.889.2.p2, not unique enough 426s -skipping training candidate: NM_133486.p2, not unique enough 426s -skipping training candidate: NM_018388.p2, not unique enough 426s -skipping training candidate: NM_001170701.p2, not unique enough 426s -skipping training candidate: NM_001170702.p2, not unique enough 426s -skipping training candidate: MSTRG.889.1.p2, not unique enough 426s -skipping training candidate: NR_033835.p2, not unique enough 426s -skipping training candidate: NM_178151.p2, not unique enough 426s -skipping training candidate: MSTRG.4.3.p6, not unique enough 426s -skipping training candidate: NM_018390.p6, not unique enough 426s -skipping training candidate: NM_001171706.p1, not unique enough 426s -skipping training candidate: NR_104390.p2, not unique enough 426s 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NR_034116_dup1.p1, not unique enough 426s -skipping training candidate: NM_002414.p2, not unique enough 426s -skipping training candidate: NM_001277710.p2, not unique enough 426s -skipping training candidate: NM_001654.p3, not unique enough 426s -skipping training candidate: NM_001256196.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.9.p1, not unique enough 426s -skipping training candidate: NM_001141920.p2, not unique enough 426s -skipping training candidate: NM_198511.p3, not unique enough 426s -skipping training candidate: NM_021806.p2, not unique enough 426s -skipping training candidate: NM_001282311.p2, not unique enough 426s -skipping training candidate: MSTRG.1037.1.p2, not unique enough 426s -skipping training candidate: NM_001171134.p2, not unique enough 426s -skipping training candidate: NR_120493.p1, not unique enough 426s -skipping training candidate: NR_120493_dup1.p1, not unique enough 426s -skipping training candidate: NM_002893.p3, not unique enough 426s -skipping training candidate: MSTRG.376.9.p2, not unique enough 426s -skipping training candidate: MSTRG.376.4.p3, not unique enough 426s -skipping training candidate: NM_004187.p2, not unique enough 426s -skipping training candidate: NM_001282622.p2, not unique enough 426s -skipping training candidate: MSTRG.376.2.p3, not unique enough 426s -skipping training candidate: MSTRG.376.8.p3, not unique enough 426s -skipping training candidate: MSTRG.376.1.p2, not unique enough 426s -skipping training candidate: NM_001146702.p2, not unique enough 426s -skipping training candidate: NM_014380.p1, not unique enough 426s -skipping training candidate: MSTRG.799.2.p2, not unique enough 426s -skipping training candidate: NM_001282161.p3, not unique enough 426s -skipping training candidate: NM_022117.p3, not unique enough 426s -skipping training candidate: NM_134445.p2, not unique enough 426s -skipping training candidate: NM_134446.p2, not unique enough 426s -skipping training candidate: NM_001242614.p2, not unique enough 426s -skipping training candidate: NM_001184808.p2, not unique enough 426s -skipping training candidate: NM_001291868.p3, not unique enough 426s -skipping training candidate: NM_001025242.p3, not unique enough 426s -skipping training candidate: NM_001025243.p3, not unique enough 426s -skipping training candidate: NR_033348.p3, not unique enough 426s -skipping training candidate: NM_024087.p2, not unique enough 426s -skipping training candidate: NM_001168530.p2, not unique enough 426s -skipping training candidate: NM_001159560.p1, not unique enough 426s -skipping training candidate: MSTRG.702.2.p3, not unique enough 426s -skipping training candidate: NM_001195578.p1, not unique enough 426s -skipping training candidate: NM_001195576.p1, not unique enough 426s -skipping training candidate: NM_175569.p2, not unique enough 426s -skipping training candidate: NM_000044.p2, not unique enough 426s -skipping training candidate: NM_001291867.p3, not unique enough 426s -skipping training candidate: NM_001136024.p3, not unique enough 426s -skipping training candidate: NM_130776.p1, not unique enough 426s -skipping training candidate: NM_207339.p1, not unique enough 426s -skipping training candidate: MSTRG.719.3.p1, not unique enough 426s -skipping training candidate: MSTRG.17.1.p2, not unique enough 426s -skipping training candidate: MSTRG.17.2.p3, not unique enough 426s -skipping training candidate: NM_004192.p2, not unique enough 426s -skipping training candidate: NM_001173473.p2, not unique enough 426s -skipping training candidate: NM_001173474.p2, not unique enough 426s -skipping training candidate: MSTRG.17.6.p3, not unique enough 426s -skipping training candidate: NR_001564.p3, not unique enough 426s -skipping training candidate: MSTRG.531.1.p3, not unique enough 426s -skipping training candidate: MSTRG.531.3.p3, not unique enough 426s -skipping training candidate: MSTRG.26.2.p2, not unique enough 426s -skipping training candidate: MSTRG.763.3.p2, not unique enough 426s -skipping training candidate: MSTRG.397.6.p3, not unique enough 426s -skipping training candidate: MSTRG.397.7.p3, not unique enough 426s -skipping training candidate: MSTRG.397.5.p3, not unique enough 426s -skipping training candidate: MSTRG.397.2.p3, not unique enough 426s -skipping training candidate: MSTRG.397.8.p3, not unique enough 426s -skipping training candidate: MSTRG.397.4.p3, not unique enough 426s -skipping training candidate: MSTRG.397.3.p3, not unique enough 426s -skipping training candidate: NM_001129828.p1, not unique enough 426s -skipping training candidate: NM_001129828_dup1.p1, not unique enough 426s -skipping training candidate: MSTRG.68.19.p2, not unique enough 426s -skipping training candidate: NM_000425.p6, not unique enough 426s -skipping training candidate: NM_024003.p6, not unique enough 426s -skipping training candidate: NM_001143963.p6, not unique enough 426s -skipping training candidate: NM_001244892_dup1.p1, not unique enough 426s -skipping training candidate: NR_037927.p1, not unique enough 426s -skipping training candidate: NM_001144064_dup1.p1, not unique enough 426s -skipping training candidate: NM_001144064.p1, not unique enough 426s -skipping training candidate: NM_001145414.p1, not unique enough 426s -skipping training candidate: MSTRG.36.2.p1, not unique enough 426s -skipping training candidate: MSTRG.36.1.p1, not unique enough 426s -skipping training candidate: MSTRG.1041.5.p2, not unique enough 426s -skipping training candidate: NM_001134321.p1, not unique enough 426s -skipping training candidate: NM_033380.p4, not unique enough 426s -skipping training candidate: MSTRG.992.4.p2, not unique enough 426s -skipping training candidate: NM_001184875.p4, not unique enough 426s -skipping training candidate: NM_138437.p4, not unique enough 426s -skipping training candidate: NM_001004051.p4, not unique enough 426s -skipping training candidate: NM_001184874.p4, not unique enough 426s -skipping training candidate: NM_001145409.p2, not unique enough 426s -skipping training candidate: NM_001145410.p2, not unique enough 426s -skipping training candidate: NM_007363.p2, not unique enough 426s -skipping training candidate: MSTRG.693.4.p2, not unique enough 426s -skipping training candidate: NM_001006933.p2, not unique enough 426s -skipping training candidate: MSTRG.693.3.p2, not unique enough 426s -skipping training candidate: NM_001145140_dup1.p3, not unique enough 426s -skipping training candidate: NM_014725.p3, not unique enough 426s -skipping training candidate: NM_001142504.p3, not unique enough 426s -skipping training candidate: MSTRG.992.3.p3, not unique enough 426s -skipping training candidate: MSTRG.992.6.p2, not unique enough 426s -skipping training candidate: MSTRG.992.7.p3, not unique enough 426s -skipping training candidate: NM_001184704.p2, not unique enough 426s -skipping training candidate: MSTRG.108.3.p2, not unique enough 426s -skipping training candidate: NM_001042480.p3, not unique enough 426s -skipping training candidate: NM_001042479.p2, not unique enough 426s -skipping training candidate: MSTRG.108.1.p2, not unique enough 426s -skipping training candidate: NM_017856.p2, not unique enough 426s -skipping training candidate: NM_001448.p4, not unique enough 426s -skipping training candidate: NM_001145139_dup1.p3, not unique enough 426s -skipping training candidate: NM_001145139.p3, not unique enough 426s -skipping training candidate: NM_001018024.p1, not unique enough 426s -skipping training candidate: NR_033772_dup1.p3, not unique enough 426s -skipping training candidate: NR_120499.p1, not unique enough 426s -skipping training candidate: NR_120499_dup1.p1, not unique enough 426s -skipping training candidate: MSTRG.364.2.p2, not unique enough 426s -skipping training candidate: MSTRG.364.3.p2, not unique enough 426s -skipping training candidate: NM_001171095.p2, not unique enough 426s -skipping training candidate: MSTRG.369.2.p2, not unique enough 426s -skipping training candidate: NR_120494_dup1.p1, not unique enough 426s -skipping training candidate: NR_120494.p1, not unique enough 426s -skipping training candidate: MSTRG.702.3.p1, not unique enough 426s -skipping training candidate: NM_001171092.p2, not unique enough 426s -skipping training candidate: NM_001114123.p2, not unique enough 426s -skipping training candidate: NR_033773_dup1.p3, not unique enough 426s -skipping training candidate: NR_033773.p3, not unique enough 426s -skipping training candidate: NM_133499.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.2.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.12.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.1.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.4.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.3.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.11.p2, not unique enough 426s -skipping training candidate: MSTRG.992.5.p3, not unique enough 426s -skipping training candidate: MSTRG.331.3.p2, not unique enough 426s -skipping training candidate: MSTRG.331.1.p2, not unique enough 426s -skipping training candidate: MSTRG.331.2.p2, not unique enough 426s -skipping training candidate: MSTRG.331.4.p2, not unique enough 426s -skipping training candidate: NM_001104544.p2, not unique enough 426s -skipping training candidate: MSTRG.822.4.p2, not unique enough 426s -skipping training candidate: NM_001104545.p2, not unique enough 426s -skipping training candidate: NR_033181.p2, not unique enough 426s -skipping training candidate: NM_001128167.p3, not unique enough 426s -skipping training candidate: MSTRG.16.1.p9, not unique enough 426s -skipping training candidate: NM_001184830.p2, not unique enough 426s -skipping training candidate: MSTRG.945.1.p2, not unique enough 426s -skipping training candidate: MSTRG.887.7.p1, not unique enough 426s -skipping training candidate: NM_005676.p4, not unique enough 426s -skipping training candidate: NM_001204466.p3, not unique enough 426s -skipping training candidate: NM_001204468.p4, not unique enough 426s -skipping training candidate: NM_152856.p3, not unique enough 426s -skipping training candidate: MSTRG.973.1.p3, not unique enough 426s -skipping training candidate: NM_001171909.p2, not unique enough 426s -skipping training candidate: MSTRG.963.2.p3, not unique enough 426s -skipping training candidate: MSTRG.963.2.p4, not unique enough 426s -skipping training candidate: MSTRG.963.3.p3, not unique enough 426s -skipping training candidate: MSTRG.963.1.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.10.p2, not unique enough 426s -skipping training candidate: MSTRG.1074.1.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.2.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.5.p2, not unique enough 426s -skipping training candidate: MSTRG.1074.3.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.8.p3, not unique enough 426s -skipping training candidate: NM_198511.p4, not unique enough 426s -skipping training candidate: NM_004595.p2, not unique enough 426s -skipping training candidate: NM_001199972.p1, not unique enough 426s -skipping training candidate: NR_024499.p1, not unique enough 426s -skipping training candidate: MSTRG.74.2.p1, not unique enough 426s -skipping training candidate: MSTRG.108.1.p3, not unique enough 426s -skipping training candidate: MSTRG.862.1.p3, not unique enough 426s -skipping training candidate: NM_001127197.p2, not unique enough 426s -skipping training candidate: MSTRG.862.3.p2, not unique enough 426s -skipping training candidate: NM_001421.p2, not unique enough 426s -skipping training candidate: MSTRG.862.4.p2, not unique enough 426s -skipping training candidate: MSTRG.68.12.p2, not unique enough 426s -skipping training candidate: MSTRG.68.9.p2, not unique enough 426s -skipping training candidate: MSTRG.68.13.p2, not unique enough 426s -skipping training candidate: MSTRG.68.8.p4, not unique enough 426s -skipping training candidate: MSTRG.68.3.p4, not unique enough 426s -skipping training candidate: MSTRG.68.6.p3, not unique enough 426s -skipping training candidate: MSTRG.68.16.p5, not unique enough 426s -skipping training candidate: NR_034031.p4, not unique enough 426s -skipping training candidate: MSTRG.68.14.p4, not unique enough 426s -skipping training candidate: MSTRG.68.17.p5, not unique enough 426s -skipping training candidate: NM_001256789.p3, not unique enough 426s -skipping training candidate: MSTRG.860.1.p2, not unique enough 426s -skipping training candidate: NM_001184772.p2, not unique enough 426s -skipping training candidate: MSTRG.860.3.p2, not unique enough 426s -skipping training candidate: MSTRG.860.6.p2, not unique enough 426s -skipping training candidate: MSTRG.860.2.p2, not unique enough 426s -skipping training candidate: NM_021949.p4, not unique enough 426s -skipping training candidate: NM_001143983.p3, not unique enough 426s -skipping training candidate: NM_153280.p2, not unique enough 426s -skipping training candidate: NM_001586.p2, not unique enough 426s -skipping training candidate: NM_005183.p3, not unique enough 426s -skipping training candidate: NM_032591.p3, not unique enough 426s -skipping training candidate: MSTRG.268.7.p3, not unique enough 426s -skipping training candidate: NM_001257291.p3, not unique enough 426s -skipping training candidate: MSTRG.268.2.p2, not unique enough 426s -skipping training candidate: MSTRG.268.1.p2, not unique enough 426s -skipping training candidate: MSTRG.268.3.p3, not unique enough 426s -skipping training candidate: MSTRG.268.6.p2, not unique enough 426s -skipping training candidate: NM_001143981.p3, not unique enough 426s -skipping training candidate: MSTRG.876.1.p3, not unique enough 426s -skipping training candidate: NM_203474.p2, not unique enough 426s -skipping training candidate: NM_022825.p2, not unique enough 426s -skipping training candidate: MSTRG.305.8.p3, not unique enough 426s -skipping training candidate: MSTRG.305.6.p3, not unique enough 426s -skipping training candidate: NM_203475.p2, not unique enough 426s -skipping training candidate: NM_203473.p2, not unique enough 426s -skipping training candidate: MSTRG.305.7.p3, not unique enough 426s -skipping training candidate: NM_001282167.p3, not unique enough 426s -skipping training candidate: MSTRG.2.1.p2, not unique enough 426s -skipping training candidate: NM_007213.p3, not unique enough 426s -skipping training candidate: MSTRG.68.10.p5, not unique enough 426s -skipping training candidate: MSTRG.68.5.p4, not unique enough 426s -skipping training candidate: MSTRG.468.4.p2, not unique enough 426s -skipping training candidate: NM_032926.p3, not unique enough 426s -skipping training candidate: NM_016303.p1, not unique enough 426s -skipping training candidate: NM_001006612.p1, not unique enough 426s -skipping training candidate: NM_001006614.p1, not unique enough 426s -skipping training candidate: NM_153280.p3, not unique enough 426s -skipping training candidate: NM_000533.p2, not unique enough 426s -skipping training candidate: NM_001145140_dup1.p4, not unique enough 426s -skipping training candidate: NM_001171184.p2, not unique enough 426s -skipping training candidate: NM_014927.p3, not unique enough 426s -skipping training candidate: NM_001168647.p3, not unique enough 426s -skipping training candidate: NM_024597.p2, not unique enough 426s -skipping training candidate: MSTRG.17.6.p4, not unique enough 426s -skipping training candidate: NM_001145139_dup1.p4, not unique enough 426s -skipping training candidate: NM_001145139.p4, not unique enough 426s -skipping training candidate: NM_199478.p2, not unique enough 426s -skipping training candidate: MSTRG.889.17.p2, not unique enough 426s -skipping training candidate: NM_033215.p3, not unique enough 426s -skipping training candidate: MSTRG.549.7.p2, not unique enough 426s -skipping training candidate: NM_017848.p3, not unique enough 426s -skipping training candidate: NM_001300788.p4, not unique enough 426s -skipping training candidate: NM_134445.p3, not unique enough 426s -skipping training candidate: NM_134446.p3, not unique enough 426s -skipping training candidate: NM_001242614.p3, not unique enough 426s -skipping training candidate: NM_001184808.p3, not unique enough 426s -skipping training candidate: NR_029427.p4, not unique enough 426s -skipping training candidate: MSTRG.325.4.p3, not unique enough 426s -skipping training candidate: NM_001166426.p4, not unique enough 426s -skipping training candidate: NM_017883.p4, not unique enough 426s -skipping training candidate: MSTRG.301.3.p2, not unique enough 426s -skipping training candidate: MSTRG.301.2.p3, not unique enough 426s -skipping training candidate: MSTRG.1074.11.p2, not unique enough 426s -skipping training candidate: MSTRG.1074.9.p2, not unique enough 426s -skipping training candidate: MSTRG.1074.10.p3, not unique enough 426s -skipping training candidate: NM_014799.p3, not unique enough 426s -skipping training candidate: NM_138737.p3, not unique enough 426s -skipping training candidate: MSTRG.456.2.p3, not unique enough 426s -skipping training candidate: NM_001040663.p2, not unique enough 426s -skipping training candidate: MSTRG.862.1.p4, not unique enough 426s -skipping training candidate: NM_001127197.p3, not unique enough 426s -skipping training candidate: MSTRG.862.3.p3, not unique enough 426s -skipping training candidate: NM_001421.p3, not unique enough 426s -skipping training candidate: MSTRG.862.4.p3, not unique enough 426s -skipping training candidate: NM_206917.p2, not unique enough 426s -skipping training candidate: NM_001282157.p2, not unique enough 426s -skipping training candidate: NM_012280.p2, not unique enough 426s -skipping training candidate: NM_006013.p2, not unique enough 426s -skipping training candidate: MSTRG.1025.5.p3, not unique enough 426s -skipping training candidate: NM_001256577.p2, not unique enough 426s -skipping training candidate: NM_001303625.p2, not unique enough 426s -skipping training candidate: NM_001303624.p3, not unique enough 426s -skipping training candidate: NM_001256580.p2, not unique enough 426s -skipping training candidate: MSTRG.1025.1.p2, not unique enough 426s -skipping training candidate: NM_152634.p2, not unique enough 426s -skipping training candidate: NM_001297563.p2, not unique enough 426s -skipping training candidate: NM_000513.p2, not unique enough 426s -skipping training candidate: NM_000513_dup2.p2, not unique enough 426s -skipping training candidate: NM_001300788.p5, not unique enough 426s -skipping training candidate: NM_004651.p3, not unique enough 426s -skipping training candidate: MSTRG.597.1.p2, not unique enough 426s -skipping training candidate: MSTRG.597.3.p2, not unique enough 426s -skipping training candidate: NM_001017931.p2, not unique enough 426s -skipping training candidate: NM_001128835.p2, not unique enough 426s -skipping training candidate: NM_000451.p2, not unique enough 426s -skipping training candidate: NM_001114123.p3, not unique enough 426s -skipping training candidate: MSTRG.907.2.p1, not unique enough 426s -skipping training candidate: NM_000402.p3, not unique enough 426s -skipping training candidate: NM_001042351.p2, not unique enough 426s -skipping training candidate: NM_032539.p2, not unique enough 426s -skipping training candidate: NM_006013.p3, not unique enough 426s -skipping training candidate: MSTRG.1025.5.p4, not unique enough 426s -skipping training candidate: NM_001256577.p3, not unique enough 426s -skipping training candidate: NM_001303625.p3, not unique enough 426s -skipping training candidate: NM_001303624.p4, not unique enough 426s -skipping training candidate: NM_001256580.p3, not unique enough 426s -skipping training candidate: MSTRG.1025.1.p3, not unique enough 426s -skipping training candidate: NM_033290.p2, not unique enough 426s -skipping training candidate: MSTRG.1042.3.p2, not unique enough 426s -skipping training candidate: MSTRG.1042.1.p3, not unique enough 426s -skipping training candidate: NM_002637.p2, not unique enough 426s -skipping training candidate: NM_001172436.p2, not unique enough 426s -skipping training candidate: MSTRG.306.3.p2, not unique enough 426s -skipping training candidate: NM_001098624.p2, not unique enough 426s -skipping training candidate: MSTRG.128.4.p2, not unique enough 426s -skipping training candidate: MSTRG.1074.5.p3, not unique enough 426s -skipping training candidate: NM_033289.p2, not unique enough 426s -skipping training candidate: NM_001145255.p3, not unique enough 426s -skipping training candidate: MSTRG.1041.6.p4, not unique enough 426s -skipping training candidate: NM_003639.p2, not unique enough 426s -skipping training candidate: NM_001099857.p3, not unique enough 426s -skipping training candidate: MSTRG.1041.7.p3, not unique enough 426s -skipping training candidate: MSTRG.1041.9.p2, not unique enough 426s -skipping training candidate: NM_001099856.p2, not unique enough 426s -skipping training candidate: NM_001303465.p3, not unique enough 426s -skipping training candidate: MSTRG.1029.3.p4, not unique enough 426s -skipping training candidate: NM_001193277.p2, not unique enough 426s -skipping training candidate: NM_147175.p2, not unique enough 426s -skipping training candidate: NM_198450.p2, not unique enough 426s -skipping training candidate: MSTRG.108.1.p4, not unique enough 426s -skipping training candidate: NM_001184835.p2, not unique enough 426s -skipping training candidate: NM_001079859.p2, not unique enough 426s -skipping training candidate: NM_032498.p2, not unique enough 426s -skipping training candidate: NM_001830.p3, not unique enough 426s -skipping training candidate: MSTRG.961.7.p4, not unique enough 426s -skipping training candidate: NM_000202.p2, not unique enough 426s -skipping training candidate: MSTRG.961.3.p2, not unique enough 426s -skipping training candidate: MSTRG.961.4.p4, not unique enough 426s -skipping training candidate: NM_001166550.p2, not unique enough 426s -skipping training candidate: MSTRG.961.1.p3, not unique enough 426s -skipping training candidate: NM_001163278.p2, not unique enough 426s -skipping training candidate: NR_109985.p1, not unique enough 426s -skipping training candidate: NM_001079860.p2, not unique enough 426s -skipping training candidate: NM_007137.p2, not unique enough 426s -skipping training candidate: MSTRG.292.4.p2, not unique enough 426s -skipping training candidate: NM_014253.p2, not unique enough 426s -skipping training candidate: MSTRG.109.9.p2, not unique enough 426s -skipping training candidate: NM_001001994.p2, not unique enough 426s -skipping training candidate: NM_005278.p2, not unique enough 426s -skipping training candidate: NR_027401.p2, not unique enough 426s -skipping training candidate: MSTRG.841.1.p3, not unique enough 426s -skipping training candidate: NM_001079858.p2, not unique enough 426s -skipping training candidate: NM_001184834.p2, not unique enough 426s -skipping training candidate: NM_001449.p3, not unique enough 426s -skipping training candidate: NM_001159703.p3, not unique enough 426s -skipping training candidate: NM_005756.p2, not unique enough 426s -skipping training candidate: NM_001099685.p2, not unique enough 426s -skipping training candidate: NM_001099685_dup1.p2, not unique enough 426s -skipping training candidate: NM_001141920.p3, not unique enough 426s -skipping training candidate: NM_001142529.p2, not unique enough 426s -skipping training candidate: NM_030639.p2, not unique enough 426s -skipping training candidate: NM_001142528.p2, not unique enough 426s -skipping training candidate: NM_001142530.p2, not unique enough 426s -skipping training candidate: NM_001142526.p2, not unique enough 426s -skipping training candidate: NM_001142527.p2, not unique enough 426s -skipping training candidate: NM_001142524.p2, not unique enough 426s -skipping training candidate: NM_001184836.p2, not unique enough 426s -skipping training candidate: NM_175569.p3, not unique enough 426s -skipping training candidate: NR_026594.p2, not unique enough 426s -skipping training candidate: NM_001184837.p2, not unique enough 426s -skipping training candidate: NM_177537_dup1.p4, not unique enough 426s -skipping training candidate: NR_103770.p1, not unique enough 426s -skipping training candidate: MSTRG.945.3.p2, not unique enough 426s 426s -redundancy-minimized set includes 1645 / 4259 = 38.62% 426s 426s * [Mon Mar 11 04:14:20 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 426s PCT_GC: 46 426s * [Mon Mar 11 04:14:20 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores 429s * [Mon Mar 11 04:14:23 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 464s * [Mon Mar 11 04:14:58 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 464s Selecting best orfs 465s * [Mon Mar 11 04:14:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement 465s Training start codon pattern recognition* [Mon Mar 11 04:14:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 466s * [Mon Mar 11 04:15:00 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 466s -round: 1 471s -round: 2 476s -round: 3 482s -round: 4 487s -round: 5 492s * [Mon Mar 11 04:15:26 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 492s -parsing scores 498s * [Mon Mar 11 04:15:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 499s Error in library(ggplot2) : there is no package called ‘ggplot2’ 499s Execution halted 499s * [Mon Mar 11 04:15:33 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 499s Error in library(ggplot2) : there is no package called ‘ggplot2’ 499s Execution halted 499s * [Mon Mar 11 04:15:33 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 499s Error in library(seqLogo) : there is no package called ‘seqLogo’ 499s Execution halted 499s * [Mon Mar 11 04:15:33 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 500s Error in library(seqLogo) : there is no package called ‘seqLogo’ 500s Execution halted 500s * [Mon Mar 11 04:15:34 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced 500s num features: 336 num_incorporate: 100 500s -feature swap of score: 3.78911079353454 instead of -4.15762669956 500s -feature swap of score: 4.3075564869904 instead of -3.54241712691985 500s -feature swap of score: -1.55002091334646 instead of -2.55010664779592 500s -feature swap of score: 4.83949655109525 instead of -2.24867860418506 500s -feature swap of score: 0.392270533069581 instead of -2.32345623662297 500s -feature swap of score: 3.78855323991787 instead of -2.2988029392048 500s -feature swap of score: 3.99836372804798 instead of -2.19588732342881 500s -feature swap of score: 3.64835524788969 instead of -2.09663793619562 500s -feature swap of score: 4.88229074177495 instead of -2.0071137297779 500s -feature swap of score: -1.8083423728436 instead of -1.93321879934806 500s -feature swap of score: 3.92879192464595 instead of -1.772614249871 500s -feature swap of score: -0.465948676008031 instead of -2.00439257184315 500s -feature swap of score: 0.0546515421473758 instead of -1.60684025496409 500s -feature swap of score: 0.803622088306608 instead of -1.17227320164039 500s -feature swap of score: 4.45581598878225 instead of -1.27696269799764 500s -feature swap of score: 2.07236230159122 instead of -1.40605769767333 500s -feature swap of score: 4.02245547784082 instead of -1.5805710473436 500s -feature swap of score: 0.586330906031762 instead of -0.825175240434032 500s -feature swap of score: 3.96397529913446 instead of -0.871836639747919 500s -feature swap of score: 1.28205341901886 instead of -0.854499557546068 500s -feature swap of score: 2.51752465071796 instead of -0.880497045171406 500s -feature swap of score: 7.60013808606777 instead of -0.651902109016902 500s -feature swap of score: 5.56752159508171 instead of -0.585113517527429 500s -feature swap of score: 4.16682533874051 instead of -0.591263924699593 500s -feature swap of score: 5.98692288702727 instead of -0.550933752346117 500s -feature swap of score: 2.78461992524222 instead of -0.361642943889318 500s -feature swap of score: -0.14086687166401 instead of -0.260141330736644 500s -feature swap of score: 1.30640970749369 instead of -0.208633020456475 500s -feature swap of score: 0.305536787416525 instead of 0.0104847431676378 500s -feature swap of score: 3.55759636533095 instead of -0.120486034233916 500s -feature swap of score: 2.46987628753496 instead of -0.103803542507822 500s -feature swap of score: 2.0546736913397 instead of 0.0935269368540257 500s -feature swap of score: 1.31912484703918 instead of 0.229231280733345 500s -feature swap of score: 1.89359151880524 instead of 0.232351263114116 500s -feature swap of score: 5.43521751645765 instead of 0.195794099551117 500s -feature swap of score: 4.33834387795496 instead of -0.054616396540288 500s -feature swap of score: 6.43704991515938 instead of 0.111124242596921 500s -feature swap of score: 4.25846830983975 instead of 0.127430589246059 500s -feature swap of score: 0.771786455336691 instead of 0.285671737045457 500s -feature swap of score: 6.60911073864081 instead of 0.0418054250163035 500s -feature swap of score: 6.79809024958936 instead of 0.555671326116825 500s -feature swap of score: 7.27612094216219 instead of 0.559863976992066 500s -feature swap of score: 3.36215544495879 instead of 0.702288739001579 500s -feature swap of score: 4.38866473472805 instead of 0.440911348584446 500s -feature swap of score: 0.836843797008186 instead of 0.157766373683364 500s -feature swap of score: 2.13420236534183 instead of 0.949736946003556 500s -feature swap of score: 1.64354527137561 instead of 0.773162924133292 500s -feature swap of score: 2.38988424268632 instead of 0.941592652583747 500s -feature swap of score: 4.91107243910547 instead of 1.09251723189791 500s -feature swap of score: 2.49264242586391 instead of 0.856412735226522 500s -feature swap of score: 6.28552706210459 instead of 1.07932791455603 500s -feature swap of score: 4.67930772689507 instead of 1.27353927782704 500s -feature swap of score: 7.50973191408739 instead of 1.12100700928058 500s -feature swap of score: 5.55751937051127 instead of 1.21030026759988 500s -feature swap of score: 2.60074697345087 instead of 1.47109964978436 500s -feature swap of score: 3.74655896712747 instead of 1.48225927554747 500s -feature swap of score: 3.99301668862372 instead of 1.24561259795263 500s -feature swap of score: 1.72372236527001 instead of 1.02241527158741 500s -feature swap of score: 6.86300883201794 instead of 1.14563582053961 500s -feature swap of score: 5.54190533772704 instead of 1.28297492173032 500s -feature swap of score: 2.51308026289154 instead of 1.4180584754329 500s -feature swap of score: 3.38846514773249 instead of 1.2857641622143 500s -feature swap of score: 2.49385651598659 instead of 1.55130322997112 500s -feature swap of score: 2.65351701617127 instead of 1.23066210648887 500s -feature swap of score: 2.60425530523188 instead of 1.47665351441682 500s -feature swap of score: 7.60582369996651 instead of 1.55381032974607 500s -feature swap of score: 2.9807664000693 instead of 1.59725854839862 500s -feature swap of score: 4.52648695626297 instead of 1.66034729751211 500s -feature swap of score: 7.21055045635181 instead of 1.7858663752496 500s -feature swap of score: 4.25795336260412 instead of 1.84036163713462 500s -feature swap of score: 9.54168129081765 instead of 1.91931805946798 500s -feature swap of score: 8.89437210131165 instead of 1.47973460790513 500s -feature swap of score: 3.3622755750855 instead of 1.94740840499986 500s -feature swap of score: 6.78489489553093 instead of 1.90264556019824 500s -feature swap of score: 9.60405031469725 instead of 2.1040236037399 500s -feature swap of score: 5.57780850222194 instead of 1.85621488376428 500s -feature swap of score: 3.43303080359017 instead of 0.865435946387495 500s -feature swap of score: 2.67597182314123 instead of 1.80627212503354 500s -feature swap of score: 6.43244682385697 instead of 1.78041450678908 500s -feature swap of score: 3.95962793695356 instead of 1.84794334938432 500s -feature swap of score: 3.98432173082736 instead of 1.875580806845 500s -feature swap of score: 3.21236503540814 instead of 2.21808523494257 500s -feature swap of score: 7.03718379305501 instead of 2.08706655299514 500s -feature swap of score: 5.90582904633149 instead of 1.87026115503397 500s -feature swap of score: 5.79478155363706 instead of 1.80883534807753 500s -feature swap of score: 5.36619160368881 instead of 1.98766010735596 500s -feature swap of score: 6.07858328906771 instead of 2.06576129141207 500s -feature swap of score: 5.86937251981998 instead of 1.90511689506347 500s -feature swap of score: 3.38462816070108 instead of 2.13933881189727 500s -feature swap of score: 6.37449231938971 instead of 2.82058094033957 500s -feature swap of score: 6.72646305674668 instead of 2.83352026076865 500s -feature swap of score: 4.82560543584288 instead of 2.70443214397618 500s -feature swap of score: 4.42177781286965 instead of 2.8151180947157 500s -feature swap of score: 8.98279247275997 instead of 2.94679407717209 500s -feature swap of score: 4.60893969392588 instead of 2.9477877072234 500s -feature swap of score: 7.85133157245333 instead of 1.91369736378323 500s -feature swap of score: 5.99853031964839 instead of 2.93641177087966 500s -feature swap of score: 4.29682354807149 instead of 3.14449015818142 500s -feature swap of score: 3.52291944162443 instead of 3.13111126617467 500s -feature swap of score: 4.76551376672987 instead of 3.16811466075655 500s -num feature swaps: 100 500s * [Mon Mar 11 04:15:34 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 500s -round: 1 505s -round: 2 510s -round: 3 515s -round: 4 520s -round: 5 525s * [Mon Mar 11 04:15:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 525s -parsing scores 531s * [Mon Mar 11 04:16:05 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 531s Error in library(ggplot2) : there is no package called ‘ggplot2’ 531s Execution halted 531s * [Mon Mar 11 04:16:05 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 531s Error in library(ggplot2) : there is no package called ‘ggplot2’ 531s Execution halted 531s * [Mon Mar 11 04:16:05 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 531s Error in library(seqLogo) : there is no package called ‘seqLogo’ 531s Execution halted 531s * [Mon Mar 11 04:16:05 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 532s Refining start codon selections. 532s -number of revised start positions: 247 532s * [Mon Mar 11 04:16:06 2024] Running CMD: cp /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 532s copying output to final output file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Mon Mar 11 04:16:06 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 533s Making bed file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 533s * [Mon Mar 11 04:16:07 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 534s Making pep file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 534s * [Mon Mar 11 04:16:08 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/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.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 536s Making cds file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 537s transdecoder is finished. See output files /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* 537s 537s 537s 537s 537s ## convert to genome coordinates 537s ../../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 538s 539s 539s 539s Done. 3037 / 3037 transcript orfs could be propagated to the genome 539s 540s 540s 540s ## make bed files for viewing with GenomeView 540s 540s # covert cufflinks gtf to bed 540s ../../util/gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed 541s 541s # convert the genome-based gene-gff3 file to bed 541s ../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed 542s 543s 543s 543s ../../util/fasta_prot_checker.pl stringtie_merged.transcripts.fasta.transdecoder.pep 543s 543s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 543s 543s 543s exit 0 543s make[1]: Leaving directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 543s Running example in $... 543s make[1]: Entering directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 543s ./runMe.sh 543s + ../../util/gtf_to_alignment_gff3.pl supertranscripts.gtf 543s + ../../util/gtf_genome_to_cdna_fasta.pl supertranscripts.gtf supertranscripts.fasta 543s -parsing cufflinks output: supertranscripts.gtf 543s -parsing genome fasta: supertranscripts.fasta 543s -done parsing genome. 543s // processing ADD1 543s // processing ATPsyn-d 543s // processing AdipoR 543s // processing Aldh-III 543s // processing CG10082 543s // processing CG10237 543s // processing CG12581 543s // processing CG13255 543s // processing CG13284 543s // processing CG13887 543s // processing CG14995 543s // processing CG15715 543s // processing CG30438 543s // processing CG31639 543s // processing CG31948 543s // processing CG32082 543s // processing CG33125 543s // processing CG33970 543s // processing CG3530 543s // processing CG6024 543s // processing CG6091 543s // processing CG6145 543s // processing CG6424 543s // processing CG6852 543s // processing CG7564 543s // processing CG8136 543s // processing CG8312 543s // processing Calx 543s // processing CanB2 543s // processing Cdep 543s // processing Cnx99A 543s // processing Dat 543s // processing Dgk 543s // processing Eno 543s // processing Est-6 543s // processing Gale 543s // processing Galk 543s // processing His4r 543s // processing Hsc70-1 543s // processing IP3K1 543s // processing Irk2 543s // processing Klp10A 543s // processing Lip4 543s // processing Mgstl 543s // processing Myo61F 543s // processing Npl4 543s // processing RpL15 543s // processing S-Lap3 543s // processing Sec16 543s // processing Tm1 543s // processing bdg 543s // processing bic 543s // processing cdi 543s // processing ctp 543s // processing eIF5B 543s // processing eff 543s // processing gukh 543s // processing hrg 543s // processing kto 543s // processing l(1)G0193 543s // processing l(3)05822 543s // processing mGluR 543s // processing mge 543s // processing nmo 543s // processing ogre 543s // processing regucalcin 543s // processing sqd 543s // processing stas 543s // processing trc 543s + ../../TransDecoder.LongOrfs -t transcripts.fasta 543s CMD: mkdir -p /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir 543s * [Mon Mar 11 04:16:17 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 543s 543s 543s -first extracting base frequencies, we'll need them later. 544s 544s 544s - extracting ORFs from transcripts. 544s -total transcripts to examine: 279 545s [100/279] = 35.84% done [200/279] = 71.68% done CMD: touch /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 545s 545s 545s ################################# 545s ### Done preparing long ORFs. ### 545s ################################## 545s 545s Use file: /tmp/autopkgtest.B13zNQ/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. 545s 545s Then, run TransDecoder.Predict for your final coding region predictions. 545s 545s 545s + cmd='../../TransDecoder.Predict -t transcripts.fasta' 545s + '[' ']' 545s + eval ../../TransDecoder.Predict -t transcripts.fasta 545s ++ ../../TransDecoder.Predict -t transcripts.fasta 545s * [Mon Mar 11 04:16:19 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 545s * [Mon Mar 11 04:16:19 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 545s -skipping training candidate: bdg_i2.p1, not unique enough 545s -skipping training candidate: bdg_i4.p1, not unique enough 545s -skipping training candidate: bdg_i1.p1, not unique enough 545s -skipping training candidate: Dgk_i7.p1, not unique enough 545s -skipping training candidate: Cdep_i1.p1, not unique enough 545s -skipping training candidate: eIF5B_i2.p1, not unique enough 545s -skipping training candidate: eIF5B_i4.p1, not unique enough 545s -skipping training candidate: Dgk_i1.p1, not unique enough 545s -skipping training candidate: eIF5B_i5.p1, not unique enough 545s -skipping training candidate: Dgk_i3.p1, not unique enough 545s -skipping training candidate: Dgk_i6.p1, not unique enough 545s -skipping training candidate: eIF5B_i1.p1, not unique enough 545s -skipping training candidate: Myo61F_i3.p1, not unique enough 545s -skipping training candidate: Myo61F_i2.p1, not unique enough 545s -skipping training candidate: Myo61F_i4.p1, not unique enough 545s -skipping training candidate: ADD1_i3.p1, not unique enough 545s -skipping training candidate: mGluR_i4.p1, not unique enough 545s -skipping training candidate: Calx_i3.p1, not unique enough 545s -skipping training candidate: Calx_i9.p1, not unique enough 545s -skipping training candidate: Calx_i8.p1, not unique enough 545s -skipping training candidate: Calx_i1.p1, not unique enough 545s -skipping training candidate: Calx_i4.p1, not unique enough 545s -skipping training candidate: Calx_i2.p1, not unique enough 545s -skipping training candidate: Calx_i5.p1, not unique enough 545s -skipping training candidate: cdi_i1.p1, not unique enough 545s -skipping training candidate: CG8312_i2.p1, not unique enough 545s -skipping training candidate: CG8312_i4.p1, not unique enough 545s -skipping training candidate: Klp10A_i1.p1, not unique enough 545s -skipping training candidate: Klp10A_i6.p1, not unique enough 545s -skipping training candidate: Klp10A_i2.p1, not unique enough 545s -skipping training candidate: Klp10A_i4.p1, not unique enough 545s -skipping training candidate: Klp10A_i3.p1, not unique enough 545s -skipping training candidate: CG6424_i1.p1, not unique enough 545s -skipping training candidate: CG6424_i3.p1, not unique enough 545s -skipping training candidate: CG6424_i4.p1, not unique enough 545s -skipping training candidate: Dgk_i4.p1, not unique enough 545s -skipping training candidate: CG33970_i1.p1, not unique enough 545s -skipping training candidate: Dgk_i5.p1, not unique enough 545s -skipping training candidate: CG33125_i1.p1, not unique enough 545s -skipping training candidate: CG3530_i2.p1, not unique enough 545s -skipping training candidate: CG10082_i2.p1, not unique enough 545s -skipping training candidate: CG12581_i1.p1, not unique enough 545s -skipping training candidate: CG6091_i3.p1, not unique enough 545s -skipping training candidate: hrg_i3.p1, not unique enough 545s -skipping training candidate: hrg_i2.p1, not unique enough 545s -skipping training candidate: hrg_i4.p1, not unique enough 545s -skipping training candidate: Calx_i7.p1, not unique enough 545s -skipping training candidate: CG32082_i1.p1, not unique enough 545s -skipping training candidate: Npl4_i3.p1, not unique enough 545s -skipping training candidate: Npl4_i1.p1, not unique enough 545s -skipping training candidate: CG3530_i3.p1, not unique enough 545s -skipping training candidate: CG32082_i3.p1, not unique enough 545s -skipping training candidate: CG32082_i2.p1, not unique enough 545s -skipping training candidate: l(3)05822_i3.p1, not unique enough 545s -skipping training candidate: Cnx99A_i4.p1, not unique enough 545s -skipping training candidate: Cnx99A_i3.p1, not unique enough 545s -skipping training candidate: Cnx99A_i2.p1, not unique enough 545s -skipping training candidate: l(3)05822_i4.p1, not unique enough 545s -skipping training candidate: l(3)05822_i1.p1, not unique enough 545s -skipping training candidate: CG6091_i4.p1, not unique enough 545s -skipping training candidate: Aldh-III_i5.p1, not unique enough 545s -skipping training candidate: Aldh-III_i12.p1, not unique enough 545s -skipping training candidate: Aldh-III_i9.p1, not unique enough 545s -skipping training candidate: Aldh-III_i1.p1, not unique enough 545s -skipping training candidate: Hsc70-1_i3.p1, not unique enough 545s -skipping training candidate: Hsc70-1_i2.p1, not unique enough 545s -skipping training candidate: Est-6_i2.p1, not unique enough 545s -skipping training candidate: S-Lap3_i2.p1, not unique enough 545s -skipping training candidate: S-Lap3_i3.p1, not unique enough 545s -skipping training candidate: gukh_i4.p1, not unique enough 545s -skipping training candidate: mGluR_i2.p1, not unique enough 545s -skipping training candidate: CG30438_i5.p1, not unique enough 545s -skipping training candidate: CG30438_i2.p1, not unique enough 545s -skipping training candidate: CG30438_i3.p1, not unique enough 545s -skipping training candidate: CG6145_i4.p1, not unique enough 545s -skipping training candidate: CG33970_i3.p1, not unique enough 545s -skipping training candidate: Aldh-III_i11.p1, not unique enough 545s -skipping training candidate: mGluR_i1.p1, not unique enough 545s -skipping training candidate: Eno_i3.p1, not unique enough 545s -skipping training candidate: Eno_i4.p1, not unique enough 545s -skipping training candidate: Eno_i5.p1, not unique enough 545s -skipping training candidate: CG6091_i2.p1, not unique enough 545s -skipping training candidate: Aldh-III_i7.p1, not unique enough 545s -skipping training candidate: Aldh-III_i3.p1, not unique enough 545s -skipping training candidate: Aldh-III_i4.p1, not unique enough 545s -skipping training candidate: Aldh-III_i6.p1, not unique enough 545s -skipping training candidate: Aldh-III_i10.p1, not unique enough 545s -skipping training candidate: Aldh-III_i8.p1, not unique enough 545s -skipping training candidate: Galk_i1.p1, not unique enough 545s -skipping training candidate: Galk_i3.p1, not unique enough 545s -skipping training candidate: Galk_i4.p1, not unique enough 545s -skipping training candidate: CG6145_i1.p1, not unique enough 545s -skipping training candidate: CG6145_i2.p1, not unique enough 545s -skipping training candidate: Eno_i1.p2, not unique enough 545s -skipping training candidate: Eno_i3.p2, not unique enough 545s -skipping training candidate: Eno_i4.p2, not unique enough 545s -skipping training candidate: Eno_i5.p2, not unique enough 545s -skipping training candidate: Eno_i6.p1, not unique enough 545s -skipping training candidate: CG6424_i2.p2, not unique enough 545s -skipping training candidate: CG6424_i3.p2, not unique enough 545s -skipping training candidate: CG6424_i4.p2, not unique enough 545s -skipping training candidate: Eno_i6.p2, not unique enough 545s -skipping training candidate: Eno_i2.p2, not unique enough 545s -skipping training candidate: trc_i2.p1, not unique enough 545s -skipping training candidate: Irk2_i4.p1, not unique enough 545s -skipping training candidate: Irk2_i1.p1, not unique enough 545s -skipping training candidate: Lip4_i2.p1, not unique enough 545s -skipping training candidate: CG8312_i1.p1, not unique enough 545s -skipping training candidate: AdipoR_i4.p1, not unique enough 545s -skipping training candidate: AdipoR_i2.p1, not unique enough 545s -skipping training candidate: AdipoR_i3.p1, not unique enough 545s -skipping training candidate: Tm1_i5.p1, not unique enough 545s -skipping training candidate: Tm1_i14.p1, not unique enough 545s -skipping training candidate: CG8136_i4.p1, not unique enough 545s -skipping training candidate: kto_i1.p2, not unique enough 545s -skipping training candidate: CG30438_i4.p1, not unique enough 545s -skipping training candidate: Lip4_i1.p1, not unique enough 545s -skipping training candidate: nmo_i3.p1, not unique enough 545s -skipping training candidate: nmo_i6.p1, not unique enough 545s -skipping training candidate: nmo_i7.p1, not unique enough 545s -skipping training candidate: CG8136_i1.p1, not unique enough 545s -skipping training candidate: CG8136_i3.p1, not unique enough 545s -skipping training candidate: CG6145_i3.p1, not unique enough 545s -skipping training candidate: CG7564_i3.p1, not unique enough 545s -skipping training candidate: CG7564_i4.p1, not unique enough 545s -skipping training candidate: CG7564_i2.p3, not unique enough 545s -skipping training candidate: CG14995_i7.p1, not unique enough 545s -skipping training candidate: nmo_i2.p1, not unique enough 545s -skipping training candidate: nmo_i4.p1, not unique enough 545s -skipping training candidate: nmo_i5.p1, not unique enough 545s -skipping training candidate: CG14995_i3.p1, not unique enough 545s -skipping training candidate: Cdep_i4.p1, not unique enough 545s -skipping training candidate: CG14995_i2.p1, not unique enough 545s -skipping training candidate: CG6024_i2.p1, not unique enough 545s -skipping training candidate: gukh_i4.p2, not unique enough 545s -skipping training candidate: AdipoR_i1.p1, not unique enough 545s -skipping training candidate: CG14995_i4.p1, not unique enough 545s -skipping training candidate: ogre_i4.p1, not unique enough 545s -skipping training candidate: ogre_i1.p1, not unique enough 545s -skipping training candidate: ogre_i3.p1, not unique enough 545s -skipping training candidate: ogre_i2.p1, not unique enough 545s -skipping training candidate: ogre_i5.p1, not unique enough 545s -skipping training candidate: IP3K1_i2.p1, not unique enough 545s -skipping training candidate: CG14995_i1.p1, not unique enough 545s -skipping training candidate: Gale_i1.p1, not unique enough 545s -skipping training candidate: CG33125_i1.p2, not unique enough 545s -skipping training candidate: CG13284_i5.p1, not unique enough 545s -skipping training candidate: CG13284_i1.p1, not unique enough 545s -skipping training candidate: CG13284_i2.p1, not unique enough 545s -skipping training candidate: CG13284_i4.p1, not unique enough 545s -skipping training candidate: sqd_i4.p1, not unique enough 545s -skipping training candidate: Klp10A_i1.p2, not unique enough 545s -skipping training candidate: Klp10A_i6.p2, not unique enough 545s -skipping training candidate: Klp10A_i2.p2, not unique enough 545s -skipping training candidate: Klp10A_i4.p2, not unique enough 545s -skipping training candidate: Klp10A_i3.p2, not unique enough 545s -skipping training candidate: Calx_i7.p2, not unique enough 545s -skipping training candidate: sqd_i1.p1, not unique enough 545s -skipping training candidate: sqd_i2.p1, not unique enough 545s -skipping training candidate: CG10237_i4.p1, not unique enough 545s -skipping training candidate: CG10237_i5.p1, not unique enough 545s -skipping training candidate: CG31948_i2.p1, not unique enough 545s -skipping training candidate: regucalcin_i2.p1, not unique enough 545s -skipping training candidate: regucalcin_i1.p1, not unique enough 545s -skipping training candidate: regucalcin_i4.p1, not unique enough 545s -skipping training candidate: CG10237_i1.p1, not unique enough 545s -skipping training candidate: CG10237_i3.p1, not unique enough 545s -skipping training candidate: l(3)05822_i4.p2, not unique enough 545s -skipping training candidate: l(3)05822_i2.p2, not unique enough 545s -skipping training candidate: l(3)05822_i1.p2, not unique enough 545s -skipping training candidate: Tm1_i6.p1, not unique enough 545s -skipping training candidate: Tm1_i3.p1, not unique enough 545s -skipping training candidate: Tm1_i4.p1, not unique enough 545s -skipping training candidate: Tm1_i2.p1, not unique enough 545s -skipping training candidate: Tm1_i9.p1, not unique enough 545s -skipping training candidate: Tm1_i11.p1, not unique enough 545s -skipping training candidate: Npl4_i2.p2, not unique enough 545s -skipping training candidate: Npl4_i1.p2, not unique enough 545s -skipping training candidate: Sec16_i1.p2, not unique enough 545s -skipping training candidate: Sec16_i2.p2, not unique enough 545s -skipping training candidate: Sec16_i5.p2, not unique enough 545s -skipping training candidate: CG8312_i2.p2, not unique enough 545s -skipping training candidate: CG8312_i4.p2, not unique enough 545s -skipping training candidate: Dgk_i7.p2, not unique enough 545s -skipping training candidate: eIF5B_i5.p2, not unique enough 545s -skipping training candidate: eIF5B_i2.p2, not unique enough 545s -skipping training candidate: eIF5B_i1.p2, not unique enough 545s -skipping training candidate: eIF5B_i4.p2, not unique enough 545s -skipping training candidate: Dgk_i3.p2, not unique enough 545s -skipping training candidate: Dgk_i2.p2, not unique enough 545s -skipping training candidate: Dgk_i6.p2, not unique enough 545s -skipping training candidate: l(1)G0193_i1.p2, not unique enough 545s -skipping training candidate: Tm1_i12.p1, not unique enough 545s -skipping training candidate: Dgk_i1.p3, not unique enough 545s -skipping training candidate: Dgk_i7.p3, not unique enough 545s -skipping training candidate: Dat_i1.p1, not unique enough 545s -skipping training candidate: Dgk_i3.p3, not unique enough 545s -skipping training candidate: Dgk_i4.p3, not unique enough 545s -skipping training candidate: Dgk_i2.p3, not unique enough 545s -skipping training candidate: Dgk_i6.p3, not unique enough 545s -skipping training candidate: l(3)05822_i4.p3, not unique enough 545s -skipping training candidate: l(3)05822_i2.p3, not unique enough 545s -skipping training candidate: l(3)05822_i1.p3, not unique enough 545s -skipping training candidate: CG14995_i5.p1, not unique enough 545s -skipping training candidate: CG6024_i2.p2, not unique enough 545s -skipping training candidate: Sec16_i5.p3, not unique enough 545s -skipping training candidate: Sec16_i6.p2, not unique enough 545s -skipping training candidate: CG13887_i2.p1, not unique enough 545s -skipping training candidate: CG13887_i1.p1, not unique enough 545s -skipping training candidate: CG14995_i7.p2, not unique enough 545s -skipping training candidate: Dgk_i5.p3, not unique enough 545s -skipping training candidate: nmo_i3.p2, not unique enough 545s -skipping training candidate: nmo_i2.p2, not unique enough 545s -skipping training candidate: nmo_i4.p2, not unique enough 545s -skipping training candidate: nmo_i5.p2, not unique enough 545s -skipping training candidate: nmo_i6.p2, not unique enough 545s -skipping training candidate: nmo_i7.p2, not unique enough 545s -skipping training candidate: RpL15_i6.p1, not unique enough 545s -skipping training candidate: regucalcin_i1.p2, not unique enough 545s -skipping training candidate: Hsc70-1_i3.p2, not unique enough 545s -skipping training candidate: RpL15_i7.p1, not unique enough 545s -skipping training candidate: regucalcin_i3.p2, not unique enough 545s -skipping training candidate: regucalcin_i2.p2, not unique enough 545s -skipping training candidate: gukh_i4.p3, not unique enough 545s -skipping training candidate: gukh_i1.p2, not unique enough 545s -skipping training candidate: cdi_i1.p2, not unique enough 545s -skipping training candidate: Hsc70-1_i2.p2, not unique enough 545s -skipping training candidate: RpL15_i1.p1, not unique enough 545s -skipping training candidate: RpL15_i3.p1, not unique enough 545s -skipping training candidate: RpL15_i4.p1, not unique enough 545s -skipping training candidate: RpL15_i2.p1, not unique enough 545s -skipping training candidate: RpL15_i5.p1, not unique enough 545s -skipping training candidate: Npl4_i2.p3, not unique enough 545s -skipping training candidate: Npl4_i1.p3, not unique enough 545s -skipping training candidate: trc_i1.p2, not unique enough 545s -skipping training candidate: Hsc70-1_i2.p3, not unique enough 545s -skipping training candidate: Hsc70-1_i1.p3, not unique enough 545s -skipping training candidate: CG14995_i5.p2, not unique enough 545s -skipping training candidate: CG14995_i1.p2, not unique enough 545s -skipping training candidate: CG14995_i2.p2, not unique enough 545s -skipping training candidate: CG14995_i4.p2, not unique enough 545s -skipping training candidate: CG10237_i5.p2, not unique enough 545s -skipping training candidate: CG10237_i1.p2, not unique enough 545s -skipping training candidate: CG10237_i3.p2, not unique enough 545s -skipping training candidate: CG10237_i2.p2, not unique enough 545s -skipping training candidate: Eno_i3.p3, not unique enough 545s -skipping training candidate: Eno_i2.p3, not unique enough 545s -skipping training candidate: Eno_i4.p3, not unique enough 545s -skipping training candidate: Eno_i5.p3, not unique enough 545s -skipping training candidate: Eno_i6.p3, not unique enough 545s -skipping training candidate: Sec16_i1.p3, not unique enough 545s -skipping training candidate: Sec16_i3.p2, not unique enough 545s -skipping training candidate: CG14995_i3.p3, not unique enough 545s -skipping training candidate: CG14995_i7.p3, not unique enough 545s -skipping training candidate: CG13887_i3.p1, not unique enough 545s -skipping training candidate: gukh_i1.p3, not unique enough 545s -skipping training candidate: ATPsyn-d_i3.p1, not unique enough 545s -skipping training candidate: ATPsyn-d_i1.p1, not unique enough 545s -skipping training candidate: CG10082_i1.p2, not unique enough 545s -skipping training candidate: sqd_i5.p1, not unique enough 545s -skipping training candidate: CG14995_i5.p3, not unique enough 545s -skipping training candidate: CG14995_i6.p3, not unique enough 545s -skipping training candidate: CG30438_i1.p2, not unique enough 545s -skipping training candidate: CG30438_i5.p2, not unique enough 545s -skipping training candidate: CG30438_i2.p2, not unique enough 545s -skipping training candidate: CG30438_i3.p2, not unique enough 545s -skipping training candidate: CG14995_i5.p4, not unique enough 545s -skipping training candidate: stas_i1.p1, not unique enough 545s -skipping training candidate: cdi_i1.p3, not unique enough 545s -skipping training candidate: CG14995_i1.p3, not unique enough 545s -skipping training candidate: CG14995_i2.p3, not unique enough 545s -skipping training candidate: CG14995_i4.p3, not unique enough 545s -skipping training candidate: CanB2_i2.p1, not unique enough 545s -skipping training candidate: ADD1_i2.p2, not unique enough 545s -skipping training candidate: Sec16_i1.p4, not unique enough 545s -skipping training candidate: Sec16_i3.p3, not unique enough 545s -skipping training candidate: bic_i2.p1, not unique enough 545s -skipping training candidate: CG12581_i1.p2, not unique enough 545s -skipping training candidate: Mgstl_i1.p1, not unique enough 545s -skipping training candidate: ctp_i2.p1, not unique enough 545s -skipping training candidate: ctp_i3.p1, not unique enough 545s -skipping training candidate: ctp_i1.p1, not unique enough 545s -skipping training candidate: hrg_i3.p2, not unique enough 545s -skipping training candidate: hrg_i4.p2, not unique enough 545s -skipping training candidate: Eno_i3.p4, not unique enough 545s -skipping training candidate: Eno_i2.p4, not unique enough 545s -skipping training candidate: Eno_i4.p4, not unique enough 545s -skipping training candidate: Eno_i5.p4, not unique enough 545s -skipping training candidate: Eno_i6.p4, not unique enough 545s -skipping training candidate: Klp10A_i1.p3, not unique enough 545s -skipping training candidate: Klp10A_i6.p3, not unique enough 545s -skipping training candidate: Klp10A_i2.p4, not unique enough 545s -skipping training candidate: Klp10A_i4.p3, not unique enough 545s -skipping training candidate: Klp10A_i3.p3, not unique enough 545s -skipping training candidate: Calx_i7.p3, not unique enough 545s -skipping training candidate: Calx_i4.p2, not unique enough 545s -skipping training candidate: Calx_i6.p2, not unique enough 545s -skipping training candidate: Calx_i8.p2, not unique enough 545s -skipping training candidate: Calx_i9.p2, not unique enough 545s -skipping training candidate: Calx_i2.p2, not unique enough 545s -skipping training candidate: Calx_i5.p2, not unique enough 545s -skipping training candidate: Calx_i3.p2, not unique enough 545s -skipping training candidate: CG7564_i1.p2, not unique enough 545s -skipping training candidate: CG7564_i3.p3, not unique enough 545s -skipping training candidate: CG7564_i4.p2, not unique enough 545s -skipping training candidate: CG7564_i4.p3, not unique enough 545s -skipping training candidate: CG7564_i2.p4, not unique enough 545s -skipping training candidate: CG7564_i2.p5, not unique enough 545s -skipping training candidate: Gale_i1.p2, not unique enough 545s -skipping training candidate: eIF5B_i5.p3, not unique enough 545s -skipping training candidate: eIF5B_i2.p3, not unique enough 545s -skipping training candidate: eIF5B_i1.p3, not unique enough 545s -skipping training candidate: eIF5B_i4.p3, not unique enough 545s -skipping training candidate: Dgk_i7.p4, not unique enough 545s -skipping training candidate: Mgstl_i3.p2, not unique enough 545s -skipping training candidate: AdipoR_i3.p2, not unique enough 545s -skipping training candidate: CG6424_i2.p3, not unique enough 545s -skipping training candidate: CG6424_i3.p3, not unique enough 545s -skipping training candidate: CG6424_i3.p4, not unique enough 545s -skipping training candidate: CG6424_i4.p3, not unique enough 545s -skipping training candidate: Tm1_i5.p2, not unique enough 545s -skipping training candidate: Tm1_i16.p2, not unique enough 545s -skipping training candidate: Tm1_i14.p2, not unique enough 545s -skipping training candidate: Dgk_i1.p4, not unique enough 545s -skipping training candidate: Dgk_i2.p5, not unique enough 545s -skipping training candidate: Dgk_i6.p4, not unique enough 545s -skipping training candidate: Dgk_i7.p5, not unique enough 545s -skipping training candidate: cdi_i1.p4, not unique enough 545s -skipping training candidate: eff_i3.p1, not unique enough 545s -skipping training candidate: eff_i1.p1, not unique enough 545s -skipping training candidate: CG6852_i2.p1, not unique enough 545s -skipping training candidate: eIF5B_i5.p4, not unique enough 545s -skipping training candidate: eIF5B_i2.p4, not unique enough 545s -skipping training candidate: eIF5B_i1.p4, not unique enough 545s -skipping training candidate: eIF5B_i4.p5, not unique enough 545s -skipping training candidate: Sec16_i1.p5, not unique enough 545s -skipping training candidate: Sec16_i2.p5, not unique enough 545s -skipping training candidate: Sec16_i5.p4, not unique enough 545s -skipping training candidate: Sec16_i6.p3, not unique enough 545s -skipping training candidate: Sec16_i3.p4, not unique enough 545s -skipping training candidate: CG32082_i3.p2, not unique enough 545s -skipping training candidate: CG32082_i2.p2, not unique enough 545s -skipping training candidate: CG32082_i4.p2, not unique enough 545s -skipping training candidate: CG3530_i2.p2, not unique enough 545s -skipping training candidate: CG3530_i1.p2, not unique enough 545s -skipping training candidate: Dgk_i7.p6, not unique enough 545s -skipping training candidate: l(3)05822_i4.p4, not unique enough 545s -skipping training candidate: l(3)05822_i2.p4, not unique enough 545s -skipping training candidate: l(3)05822_i1.p5, not unique enough 545s -skipping training candidate: sqd_i2.p2, not unique enough 545s -skipping training candidate: CG7564_i3.p4, not unique enough 545s -skipping training candidate: CG7564_i4.p4, not unique enough 545s -skipping training candidate: CG7564_i2.p6, not unique enough 545s -skipping training candidate: S-Lap3_i2.p2, not unique enough 545s -skipping training candidate: S-Lap3_i3.p2, not unique enough 545s -skipping training candidate: cdi_i1.p5, not unique enough 545s -skipping training candidate: CG6091_i2.p2, not unique enough 545s -skipping training candidate: CG6091_i4.p2, not unique enough 545s -skipping training candidate: CG6091_i3.p2, not unique enough 545s -skipping training candidate: Cdep_i1.p2, not unique enough 545s -skipping training candidate: Cdep_i3.p2, not unique enough 545s -skipping training candidate: Cnx99A_i4.p2, not unique enough 545s -skipping training candidate: Cnx99A_i3.p2, not unique enough 545s -skipping training candidate: Cnx99A_i1.p2, not unique enough 545s -skipping training candidate: Sec16_i5.p5, not unique enough 545s -skipping training candidate: Sec16_i6.p4, not unique enough 545s -skipping training candidate: Sec16_i3.p5, not unique enough 545s -skipping training candidate: ogre_i3.p2, not unique enough 545s -skipping training candidate: CG6024_i2.p3, not unique enough 545s -skipping training candidate: hrg_i3.p3, not unique enough 545s -skipping training candidate: hrg_i4.p3, not unique enough 545s -skipping training candidate: ATPsyn-d_i1.p2, not unique enough 545s -skipping training candidate: CG6091_i4.p3, not unique enough 545s -skipping training candidate: CG6091_i3.p3, not unique enough 545s -skipping training candidate: ATPsyn-d_i2.p2, not unique enough 545s -skipping training candidate: CG33970_i3.p2, not unique enough 545s -skipping training candidate: CG33970_i1.p2, not unique enough 545s -skipping training candidate: eIF5B_i3.p5, not unique enough 545s -skipping training candidate: eIF5B_i5.p5, not unique enough 545s -skipping training candidate: eIF5B_i1.p5, not unique enough 545s -skipping training candidate: Aldh-III_i11.p2, not unique enough 545s -skipping training candidate: Aldh-III_i8.p2, not unique enough 545s -skipping training candidate: CG13284_i3.p2, not unique enough 545s -skipping training candidate: CG13284_i1.p2, not unique enough 545s -skipping training candidate: CG13284_i5.p2, not unique enough 545s -skipping training candidate: CG13284_i4.p2, not unique enough 545s -skipping training candidate: Lip4_i3.p2, not unique enough 545s -skipping training candidate: Lip4_i1.p2, not unique enough 545s -skipping training candidate: Dgk_i1.p5, not unique enough 545s -skipping training candidate: Dgk_i4.p4, not unique enough 545s -skipping training candidate: Dgk_i2.p7, not unique enough 545s -skipping training candidate: Dgk_i6.p5, not unique enough 545s -skipping training candidate: Dgk_i5.p4, not unique enough 545s -skipping training candidate: Dgk_i7.p7, not unique enough 545s -skipping training candidate: Tm1_i5.p3, not unique enough 545s -skipping training candidate: Tm1_i16.p3, not unique enough 545s -skipping training candidate: Tm1_i14.p3, not unique enough 545s -skipping training candidate: CG8312_i3.p3, not unique enough 545s -skipping training candidate: CG8312_i3.p4, not unique enough 545s -skipping training candidate: CG8312_i2.p3, not unique enough 545s -skipping training candidate: CG8312_i2.p4, not unique enough 545s -skipping training candidate: CG8312_i4.p3, not unique enough 545s -skipping training candidate: CG8312_i4.p4, not unique enough 545s -skipping training candidate: Klp10A_i1.p4, not unique enough 545s -skipping training candidate: Klp10A_i6.p4, not unique enough 545s -skipping training candidate: Klp10A_i2.p6, not unique enough 545s -skipping training candidate: Klp10A_i4.p4, not unique enough 545s -skipping training candidate: Klp10A_i3.p4, not unique enough 545s -skipping training candidate: eff_i3.p2, not unique enough 545s -skipping training candidate: eff_i1.p2, not unique enough 545s -skipping training candidate: CG14995_i5.p5, not unique enough 545s -skipping training candidate: CG14995_i3.p4, not unique enough 545s -skipping training candidate: CG14995_i4.p4, not unique enough 545s -skipping training candidate: CG14995_i7.p4, not unique enough 545s -skipping training candidate: CG14995_i6.p4, not unique enough 545s -skipping training candidate: CG6424_i2.p4, not unique enough 545s -skipping training candidate: CG6424_i3.p5, not unique enough 545s -skipping training candidate: CG6424_i4.p4, not unique enough 545s -skipping training candidate: CG12581_i1.p3, not unique enough 545s -skipping training candidate: CG32082_i3.p3, not unique enough 545s -skipping training candidate: CG32082_i2.p3, not unique enough 545s -skipping training candidate: CG32082_i4.p5, not unique enough 545s -skipping training candidate: Cnx99A_i3.p3, not unique enough 545s -skipping training candidate: Cnx99A_i1.p3, not unique enough 545s -skipping training candidate: Cdep_i2.p6, not unique enough 545s -skipping training candidate: Cdep_i3.p3, not unique enough 545s -skipping training candidate: Sec16_i2.p6, not unique enough 545s -skipping training candidate: CG33970_i3.p3, not unique enough 545s -skipping training candidate: CG33970_i1.p3, not unique enough 545s -skipping training candidate: Sec16_i4.p7, not unique enough 545s -skipping training candidate: Sec16_i1.p7, not unique enough 545s -skipping training candidate: Sec16_i2.p7, not unique enough 545s -skipping training candidate: Sec16_i5.p6, not unique enough 545s -skipping training candidate: Sec16_i6.p5, not unique enough 545s -skipping training candidate: Sec16_i3.p6, not unique enough 545s -skipping training candidate: mge_i3.p1, not unique enough 545s -skipping training candidate: CG6024_i2.p4, not unique enough 545s -skipping training candidate: Myo61F_i4.p2, not unique enough 545s -skipping training candidate: Myo61F_i3.p2, not unique enough 545s -skipping training candidate: Myo61F_i1.p2, not unique enough 545s -skipping training candidate: Cdep_i1.p3, not unique enough 545s -skipping training candidate: Cnx99A_i3.p4, not unique enough 545s -skipping training candidate: Cnx99A_i1.p4, not unique enough 545s -skipping training candidate: CG13887_i2.p2, not unique enough 545s -skipping training candidate: CG13887_i1.p2, not unique enough 545s -skipping training candidate: CG6145_i4.p2, not unique enough 545s -skipping training candidate: CG6145_i2.p2, not unique enough 545s -skipping training candidate: CG6145_i1.p2, not unique enough 545s -skipping training candidate: CG6145_i5.p2, not unique enough 545s -skipping training candidate: Calx_i7.p5, not unique enough 545s -skipping training candidate: Calx_i4.p3, not unique enough 545s -skipping training candidate: Calx_i6.p3, not unique enough 545s -skipping training candidate: Calx_i8.p3, not unique enough 545s -skipping training candidate: Calx_i9.p3, not unique enough 545s -skipping training candidate: Calx_i2.p3, not unique enough 545s -skipping training candidate: Calx_i5.p3, not unique enough 545s -skipping training candidate: Calx_i3.p3, not unique enough 545s -skipping training candidate: mge_i2.p2, not unique enough 545s -skipping training candidate: AdipoR_i1.p2, not unique enough 545s -skipping training candidate: AdipoR_i4.p3, not unique enough 545s -skipping training candidate: AdipoR_i2.p2, not unique enough 545s -skipping training candidate: AdipoR_i3.p3, not unique enough 545s -skipping training candidate: Aldh-III_i7.p2, not unique enough 545s -skipping training candidate: Aldh-III_i10.p3, not unique enough 545s -skipping training candidate: Aldh-III_i9.p2, not unique enough 545s -skipping training candidate: Aldh-III_i1.p2, not unique enough 545s -skipping training candidate: Aldh-III_i4.p2, not unique enough 545s -skipping training candidate: Aldh-III_i6.p2, not unique enough 545s -skipping training candidate: Cdep_i4.p3, not unique enough 545s -skipping training candidate: Cdep_i2.p9, not unique enough 545s -skipping training candidate: Cdep_i3.p4, not unique enough 545s -skipping training candidate: hrg_i3.p4, not unique enough 545s -skipping training candidate: hrg_i2.p2, not unique enough 545s -skipping training candidate: hrg_i4.p4, not unique enough 545s -skipping training candidate: CG33125_i2.p2, not unique enough 545s -skipping training candidate: Calx_i9.p4, not unique enough 545s -skipping training candidate: mge_i3.p2, not unique enough 545s -skipping training candidate: CG12581_i1.p4, not unique enough 545s -skipping training candidate: Sec16_i1.p8, not unique enough 545s -skipping training candidate: Sec16_i1.p9, not unique enough 545s -skipping training candidate: Sec16_i2.p8, not unique enough 545s -skipping training candidate: Sec16_i2.p9, not unique enough 545s -skipping training candidate: Sec16_i5.p7, not unique enough 545s -skipping training candidate: Sec16_i5.p8, not unique enough 545s -skipping training candidate: Sec16_i6.p6, not unique enough 545s -skipping training candidate: Sec16_i6.p7, not unique enough 545s -skipping training candidate: Sec16_i3.p7, not unique enough 545s -skipping training candidate: Sec16_i3.p8, not unique enough 545s -skipping training candidate: Aldh-III_i4.p3, not unique enough 545s -skipping training candidate: l(3)05822_i2.p5, not unique enough 545s -skipping training candidate: CG6091_i2.p3, not unique enough 545s -skipping training candidate: CG6091_i4.p4, not unique enough 545s -skipping training candidate: CG6091_i3.p4, not unique enough 545s -skipping training candidate: CanB2_i2.p2, not unique enough 545s -skipping training candidate: IP3K1_i2.p2, not unique enough 545s -skipping training candidate: Klp10A_i1.p6, not unique enough 545s -skipping training candidate: Klp10A_i6.p5, not unique enough 545s -skipping training candidate: Klp10A_i2.p8, not unique enough 545s -skipping training candidate: Klp10A_i4.p5, not unique enough 545s -skipping training candidate: Klp10A_i3.p5, not unique enough 545s -skipping training candidate: AdipoR_i2.p3, not unique enough 545s -skipping training candidate: Cdep_i4.p4, not unique enough 545s -skipping training candidate: Cdep_i2.p10, not unique enough 545s -skipping training candidate: Cdep_i3.p5, not unique enough 545s -skipping training candidate: Est-6_i2.p2, not unique enough 545s -skipping training candidate: Klp10A_i1.p7, not unique enough 545s -skipping training candidate: Klp10A_i6.p6, not unique enough 545s -skipping training candidate: Klp10A_i2.p9, not unique enough 545s -skipping training candidate: Klp10A_i4.p6, not unique enough 545s -skipping training candidate: Klp10A_i3.p6, not unique enough 545s -skipping training candidate: l(3)05822_i3.p5, not unique enough 545s -skipping training candidate: ADD1_i2.p3, not unique enough 545s -skipping training candidate: AdipoR_i5.p3, not unique enough 545s -skipping training candidate: Cnx99A_i4.p3, not unique enough 545s -skipping training candidate: Cnx99A_i3.p5, not unique enough 545s -skipping training candidate: Cnx99A_i1.p5, not unique enough 545s -skipping training candidate: Myo61F_i4.p3, not unique enough 545s -skipping training candidate: Myo61F_i3.p3, not unique enough 545s -skipping training candidate: Myo61F_i1.p3, not unique enough 545s -skipping training candidate: Myo61F_i4.p4, not unique enough 545s -skipping training candidate: Myo61F_i3.p4, not unique enough 545s -skipping training candidate: Myo61F_i1.p4, not unique enough 545s -skipping training candidate: bic_i2.p2, not unique enough 545s -skipping training candidate: CG10082_i1.p5, not unique enough 545s -skipping training candidate: CG32082_i3.p4, not unique enough 545s -skipping training candidate: CG32082_i2.p4, not unique enough 545s -skipping training candidate: CG32082_i4.p6, not unique enough 545s -skipping training candidate: Eno_i3.p5, not unique enough 545s -skipping training candidate: Eno_i2.p5, not unique enough 545s -skipping training candidate: Eno_i4.p6, not unique enough 545s -skipping training candidate: Eno_i5.p6, not unique enough 545s -skipping training candidate: Eno_i6.p5, not unique enough 545s -skipping training candidate: Sec16_i4.p10, not unique enough 545s -skipping training candidate: Sec16_i1.p10, not unique enough 545s -skipping training candidate: Sec16_i3.p9, not unique enough 545s -skipping training candidate: Dgk_i1.p6, not unique enough 545s -skipping training candidate: Dgk_i4.p5, not unique enough 545s -skipping training candidate: Dgk_i2.p8, not unique enough 545s -skipping training candidate: Dgk_i6.p6, not unique enough 545s -skipping training candidate: Dgk_i5.p5, not unique enough 545s -skipping training candidate: Dgk_i7.p8, not unique enough 545s -skipping training candidate: nmo_i6.p3, not unique enough 545s -skipping training candidate: CG33970_i1.p4, not unique enough 545s -skipping training candidate: sqd_i5.p3, not unique enough 545s -skipping training candidate: Dgk_i1.p7, not unique enough 545s -skipping training candidate: Dgk_i6.p7, not unique enough 545s -skipping training candidate: His4r_i4.p1, not unique enough 545s -skipping training candidate: His4r_i3.p1, not unique enough 545s -skipping training candidate: His4r_i2.p1, not unique enough 545s -skipping training candidate: Hsc70-1_i2.p5, not unique enough 545s -skipping training candidate: Hsc70-1_i1.p4, not unique enough 545s -skipping training candidate: hrg_i3.p5, not unique enough 545s -skipping training candidate: hrg_i4.p6, not unique enough 545s -skipping training candidate: CG8136_i4.p2, not unique enough 545s -skipping training candidate: CG8136_i3.p2, not unique enough 545s -skipping training candidate: CG8136_i2.p2, not unique enough 545s -skipping training candidate: Myo61F_i4.p5, not unique enough 545s -skipping training candidate: Myo61F_i3.p5, not unique enough 545s -skipping training candidate: Myo61F_i1.p5, not unique enough 545s -skipping training candidate: CG6091_i2.p4, not unique enough 545s -skipping training candidate: CG6091_i4.p5, not unique enough 545s -skipping training candidate: CG6091_i3.p5, not unique enough 545s -skipping training candidate: CG6145_i4.p3, not unique enough 545s -skipping training candidate: CG6145_i2.p3, not unique enough 545s -skipping training candidate: CG6145_i1.p3, not unique enough 545s -skipping training candidate: CG6145_i5.p3, not unique enough 545s -skipping training candidate: gukh_i1.p4, not unique enough 545s -skipping training candidate: sqd_i5.p4, not unique enough 545s -skipping training candidate: CG33125_i2.p3, not unique enough 545s -skipping training candidate: gukh_i1.p5, not unique enough 545s 545s -redundancy-minimized set includes 286 / 856 = 33.41% 545s 545s * [Mon Mar 11 04:16:19 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 545s PCT_GC: 49.4 545s * [Mon Mar 11 04:16:19 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores 546s * [Mon Mar 11 04:16:20 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 551s * [Mon Mar 11 04:16:25 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 552s Selecting best orfs 552s * [Mon Mar 11 04:16:26 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement 552s Training start codon pattern recognition* [Mon Mar 11 04:16:26 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 552s * [Mon Mar 11 04:16:26 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 552s -round: 1 557s -round: 2 562s -round: 3 567s -round: 4 572s -round: 5 578s * [Mon Mar 11 04:16:51 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 578s -parsing scores 583s * [Mon Mar 11 04:16:57 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 585s Error in library(ggplot2) : there is no package called ‘ggplot2’ 585s Execution halted 585s * [Mon Mar 11 04:16:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 585s Error in library(ggplot2) : there is no package called ‘ggplot2’ 585s Execution halted 585s * [Mon Mar 11 04:16:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 585s Error in library(seqLogo) : there is no package called ‘seqLogo’ 585s Execution halted 585s * [Mon Mar 11 04:16:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 585s Error in library(seqLogo) : there is no package called ‘seqLogo’ 585s Execution halted 585s * [Mon Mar 11 04:16:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 585s num features: 253 num_incorporate: 75 585s -feature swap of score: -1.43286869263653 instead of -3.63059664394637 585s -feature swap of score: -1.4028203227612 instead of -3.42214593354962 585s -feature swap of score: -1.65235455073734 instead of -2.96950519527322 585s -feature swap of score: -1.15010853519738 instead of -1.45868269011156 585s -feature swap of score: -0.813886629528334 instead of -1.13692002650278 585s -feature swap of score: 1.96348046732965 instead of -1.08012229212525 585s -feature swap of score: -0.635794759354978 instead of -1.03212995534755 585s -feature swap of score: 2.83567333046555 instead of -0.895880832698561 585s -feature swap of score: -0.637039071436482 instead of -1.23483306781291 585s -feature swap of score: -0.933843069308462 instead of -0.950823994842839 585s -feature swap of score: 2.01232704973349 instead of -0.95953488819523 585s -feature swap of score: -0.705582004017741 instead of -1.34212433171185 585s -feature swap of score: 0.583411460043679 instead of -0.957064103066338 585s -feature swap of score: 1.10305033655561 instead of -1.24703754250196 585s -feature swap of score: 1.83232543008355 instead of -0.951968509592419 585s -feature swap of score: 0.540818581866311 instead of -1.08744005878758 585s -feature swap of score: 0.425493922428895 instead of -1.08967460784045 585s -feature swap of score: -0.185963068332888 instead of -0.929560375743657 585s -feature swap of score: 1.37143334080202 instead of -0.980753506208269 585s -feature swap of score: 2.44651619451709 instead of -0.932697870486119 585s -feature swap of score: 1.41147899178151 instead of -0.784908139951971 585s -feature swap of score: 0.819141228453244 instead of -0.90731158428258 585s -feature swap of score: -0.176563286063105 instead of -0.925368967472165 585s -feature swap of score: 0.994617501951542 instead of -0.411180836956245 585s -feature swap of score: -0.28374102380697 instead of -0.522471712050905 585s -feature swap of score: -0.405400787911506 instead of -0.48278539839252 585s -feature swap of score: -0.175642383908524 instead of -0.329208332413826 585s -feature swap of score: 0.504163448897735 instead of -0.0481147301807235 585s -feature swap of score: 3.02285680297352 instead of -1.44300187901426 585s -feature swap of score: 0.980858416696839 instead of 0.0358138645113575 585s -feature swap of score: 2.90709248651279 instead of -0.124377942092526 585s -feature swap of score: 0.558333657401046 instead of -0.00976827128658703 585s -feature swap of score: 2.79448595103502 instead of -0.324114544222203 585s -feature swap of score: 1.92550852852682 instead of -0.632754076691147 585s -feature swap of score: 1.07685637390087 instead of -0.756323734795527 585s -feature swap of score: 0.55820875367115 instead of -0.823256404869549 585s -feature swap of score: 0.205236226711453 instead of -0.433226329175022 585s -feature swap of score: 1.43765088688194 instead of -0.412184863804844 585s -feature swap of score: 1.28384327023684 instead of -0.400726687245895 585s -feature swap of score: -0.254802543498908 instead of -0.37540186286152 585s -feature swap of score: 0.840706228591159 instead of -0.0271379125895788 585s -feature swap of score: 2.31870665960491 instead of -0.164578308427216 585s -feature swap of score: -0.189490104637422 instead of -0.431552790659908 585s -feature swap of score: 0.18500079760525 instead of 0.136001562878459 585s -feature swap of score: 0.73978416096296 instead of 0.138684944675558 585s -feature swap of score: 0.578960858986632 instead of -0.519534099624593 585s -feature swap of score: 0.728855016906631 instead of 0.370289276148057 586s -feature swap of score: 1.32704730850315 instead of 0.226270163954469 586s -feature swap of score: 0.827794287297401 instead of 0.200164040027186 586s -feature swap of score: 3.39105104739569 instead of 0.348675710660047 586s -feature swap of score: 0.4480670438854 instead of 0.0788564272395142 586s -feature swap of score: 1.56772622645417 instead of 0.303390255565333 586s -feature swap of score: 2.05485966025529 instead of 0.0638152937251669 586s -feature swap of score: 1.46069525656899 instead of 0.379971926227356 586s -feature swap of score: 8.21132426954048 instead of 0.532492558463152 586s -feature swap of score: 4.40149480395309 instead of 0.467598475245225 586s -feature swap of score: 9.29934963484387 instead of 0.365257083201006 586s -num feature swaps: 57 586s * [Mon Mar 11 04:16:59 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 586s -round: 1 591s -round: 2 596s -round: 3 601s -round: 4 606s -round: 5 611s * [Mon Mar 11 04:17:25 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 611s -parsing scores 617s * [Mon Mar 11 04:17:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 617s Error in library(ggplot2) : there is no package called ‘ggplot2’ 617s Execution halted 618s * [Mon Mar 11 04:17:31 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 618s Error in library(ggplot2) : there is no package called ‘ggplot2’ 618s Execution halted 618s * [Mon Mar 11 04:17:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 618s Error in library(seqLogo) : there is no package called ‘seqLogo’ 618s Execution halted 618s * [Mon Mar 11 04:17:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 618s Refining start codon selections. 618s -number of revised start positions: 15 618s * [Mon Mar 11 04:17:32 2024] Running CMD: cp /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 618s copying output to final output file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Mon Mar 11 04:17:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 618s Making bed file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 618s * [Mon Mar 11 04:17:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 618s Making pep file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 618s * [Mon Mar 11 04:17:32 2024] Running CMD: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 619s Making cds file: /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 619s transdecoder is finished. See output files /tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* 619s 619s 619s + ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 supertranscripts.gff3 transcripts.fasta 619s 619s -Warning [1], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG10082_i1.p3. 619s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i1.p3. 619s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i2.p3. 619s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i3.p3. 619s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i4.p5. 619s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6091_i4.p2. 619s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. 619s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. 619s -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. 619s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. 619s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. 619s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. 619s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. 619s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. 619s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. 619s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i3.p5. 619s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i4.p4. 619s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Galk_i4.p2. 619s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Klp10A_i2.p3. 619s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Tm1_i14.p4. 619s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry bic_i2.p3. 619s -Warning [22], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i1.p2. 619s -Warning [23], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i3.p2. 619s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i4.p2. 619s -Warning [25], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i1.p2. 619s -Warning [26], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i2.p2. 619s -Warning [27], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i3.p2. 619s -Warning [28], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i3.p2. 619s -Warning [29], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i6.p2. 619s 619s 619s Done. 305 / 334 transcript orfs could be propagated to the genome 619s 619s + ../../util/gff3_file_to_bed.pl supertranscripts.wOrfs.gff3 619s 619s + ../../util/gff3_gene_to_gtf_format.pl supertranscripts.wOrfs.gff3 supertranscripts.fasta 619s -missing faidx file: supertranscripts.fasta.fai, extracting positions directly. 619s -Fasta_retriever:: begin initializing for supertranscripts.fasta 619s -Fasta_retriever:: done initializing for supertranscripts.fasta 619s 620s + echo Done 620s Done 620s make[1]: Leaving directory '/tmp/autopkgtest.B13zNQ/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 620s autopkgtest [04:17:34]: test run-tests: -----------------------] 621s autopkgtest [04:17:35]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 621s run-tests PASS 621s autopkgtest [04:17:35]: @@@@@@@@@@@@@@@@@@@@ summary 621s run-tests PASS 639s Creating nova instance adt-noble-arm64-transdecoder-20240311-040714-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...