0s autopkgtest [21:04:08]: starting date and time: 2024-03-16 21:04:08+0000 0s autopkgtest [21:04:08]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:04:08]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nvfoqqef/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:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade transdecoder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-11.secgroup --name adt-noble-arm64-transdecoder-20240316-210408-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/ 134s autopkgtest [21:06:22]: testbed dpkg architecture: arm64 135s autopkgtest [21:06:23]: testbed apt version: 2.7.12 135s autopkgtest [21:06:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 136s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 137s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 137s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 137s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 137s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3703 kB] 138s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 138s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 138s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 138s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 138s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4017 kB] 138s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 138s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 138s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 147s Fetched 9115 kB in 5s (1884 kB/s) 148s Reading package lists... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 156s Calculating upgrade... 157s The following packages will be REMOVED: 157s libglib2.0-0 libssl3 157s The following NEW packages will be installed: 157s libglib2.0-0t64 libssl3t64 xdg-user-dirs 157s The following packages have been kept back: 157s curl 157s The following packages will be upgraded: 157s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 157s 5 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 157s Need to get 4592 kB of archives. 157s After this operation, 211 kB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 157s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 158s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 158s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 158s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 158s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 158s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 158s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 159s Fetched 4592 kB in 1s (5914 kB/s) 159s (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 ... 75850 files and directories currently installed.) 159s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 159s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 160s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 160s udisks2 depends on libglib2.0-0 (>= 2.77.0). 160s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 160s python3-gi depends on libglib2.0-0 (>= 2.77.0). 160s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 160s netplan.io depends on libglib2.0-0 (>= 2.70.0). 160s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 160s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 160s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 160s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 160s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 160s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 160s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 160s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 160s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 160s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 160s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 160s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 160s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 160s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 160s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 160s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 160s fwupd depends on libglib2.0-0 (>= 2.79.0). 160s bolt depends on libglib2.0-0 (>= 2.56.0). 160s 160s (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 ... 75850 files and directories currently installed.) 160s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 160s Selecting previously unselected package libglib2.0-0t64:arm64. 160s (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 ... 75825 files and directories currently installed.) 160s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 160s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 160s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 160s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 160s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 160s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 161s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 161s wget depends on libssl3 (>= 3.0.0). 161s u-boot-tools depends on libssl3 (>= 3.0.0). 161s tnftp depends on libssl3 (>= 3.0.0). 161s tcpdump depends on libssl3 (>= 3.0.0). 161s systemd-resolved depends on libssl3 (>= 3.0.0). 161s systemd depends on libssl3 (>= 3.0.0). 161s sudo depends on libssl3 (>= 3.0.0). 161s sbsigntool depends on libssl3 (>= 3.0.0). 161s rsync depends on libssl3 (>= 3.0.0). 161s python3-cryptography depends on libssl3 (>= 3.0.0). 161s openssh-server depends on libssl3 (>= 3.0.10). 161s openssh-client depends on libssl3 (>= 3.0.10). 161s mtd-utils depends on libssl3 (>= 3.0.0). 161s mokutil depends on libssl3 (>= 3.0.0). 161s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 161s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 161s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 161s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 161s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 161s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 161s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 161s libnvme1 depends on libssl3 (>= 3.0.0). 161s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 161s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 161s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 161s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 161s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 161s kmod depends on libssl3 (>= 3.0.0). 161s dhcpcd-base depends on libssl3 (>= 3.0.0). 161s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 161s 161s (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 ... 75850 files and directories currently installed.) 161s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 161s Selecting previously unselected package libssl3t64:arm64. 161s (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 ... 75839 files and directories currently installed.) 161s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 161s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 162s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 162s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 162s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 162s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 162s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 162s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 162s Selecting previously unselected package xdg-user-dirs. 162s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 162s Unpacking xdg-user-dirs (0.18-1) ... 162s Setting up xdg-user-dirs (0.18-1) ... 162s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 162s Setting up libtirpc-common (1.3.4+ds-1.1) ... 162s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 162s No schema files found: doing nothing. 162s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 162s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 162s Setting up openssl (3.0.13-0ubuntu1) ... 162s Setting up readline-common (8.2-3.1) ... 162s Processing triggers for man-db (2.12.0-3) ... 163s Processing triggers for install-info (7.1-3) ... 164s Processing triggers for libc-bin (2.39-0ubuntu2) ... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 167s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 169s sh: Attempting to set up Debian/Ubuntu apt sources automatically 169s sh: Distribution appears to be Ubuntu 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s eatmydata is already the newest version (131-1). 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 176s dbus is already the newest version (1.14.10-4ubuntu1). 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 179s rng-tools-debian is already the newest version (2.4). 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 181s The following packages will be REMOVED: 181s cloud-init* python3-configobj* python3-debconf* 182s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 182s After this operation, 3252 kB disk space will be freed. 182s (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 ... 75866 files and directories currently installed.) 182s Removing cloud-init (24.1.1-0ubuntu1) ... 184s Removing python3-configobj (5.0.8-3) ... 184s Removing python3-debconf (1.5.86) ... 185s Processing triggers for man-db (2.12.0-3) ... 185s (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 ... 75477 files and directories currently installed.) 185s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 188s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 188s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 188s invoke-rc.d: policy-rc.d denied execution of try-restart. 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 191s linux-generic is already the newest version (6.8.0-11.11+1). 191s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 191s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 191s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 200s Reading package lists... 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Calculating upgrade... 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s Reading package lists... 204s Building dependency tree... 204s Reading state information... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 206s autopkgtest [21:07:34]: rebooting testbed after setup commands that affected boot 366s autopkgtest [21:10:14]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 370s autopkgtest [21:10:18]: @@@@@@@@@@@@@@@@@@@@ apt-source transdecoder 375s Get:1 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (dsc) [2260 B] 375s Get:2 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (tar) [15.0 MB] 375s Get:3 http://ftpmaster.internal/ubuntu noble/universe transdecoder 5.7.1-2 (diff) [5940 B] 376s gpgv: Signature made Thu Sep 14 10:39:31 2023 UTC 376s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 376s gpgv: Can't check signature: No public key 376s dpkg-source: warning: cannot verify inline signature for ./transdecoder_5.7.1-2.dsc: no acceptable signature found 377s autopkgtest [21:10:25]: testing package transdecoder version 5.7.1-2 377s autopkgtest [21:10:25]: build not needed 379s autopkgtest [21:10:27]: test run-tests: preparing testbed 380s Reading package lists... 381s Building dependency tree... 381s Reading state information... 382s Starting pkgProblemResolver with broken count: 0 382s Starting 2 pkgProblemResolver with broken count: 0 382s Done 383s The following additional packages will be installed: 383s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hmmer 383s libblas3 libcairo2 libdatrie1 libdeflate0 libdivsufsort3 libfontconfig1 383s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 383s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libmbedcrypto7 libmbedtls14 383s libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 383s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 383s libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 libxcb-render0 383s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ ncbi-data 383s r-base-core transdecoder transdecoder-doc unzip x11-common xdg-utils zip 383s Suggested packages: 383s hmmer-doc tcl8.6 tk8.6 libbusiness-isbn-perl libregexp-ipv6-perl libwww-perl 383s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 383s Recommended packages: 383s r-recommended r-base-dev r-doc-html r-cran-ggplot2 r-bioc-seqlogo 383s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 383s x11-xserver-utils 383s The following NEW packages will be installed: 383s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 383s fonts-dejavu-mono hmmer libblas3 libcairo2 libdatrie1 libdeflate0 383s libdivsufsort3 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 383s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 383s libmbedcrypto7 libmbedtls14 libmbedx509-1 libpango-1.0-0 libpangocairo-1.0-0 383s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 383s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 liburi-perl libwebp7 383s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 ncbi-blast+ 383s ncbi-data r-base-core transdecoder transdecoder-doc unzip x11-common 383s xdg-utils zip 384s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 384s Need to get 69.7 MB/69.7 MB of archives. 384s After this operation, 188 MB of additional disk space will be used. 384s Get:1 /tmp/autopkgtest.x2gTgS/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 384s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 384s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 384s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 384s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 384s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 384s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 384s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 384s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 384s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 384s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 384s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 384s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 384s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 384s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 384s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 384s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 384s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 384s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 384s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 384s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 384s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 384s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 384s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 385s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 385s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 385s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 385s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 385s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 385s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 385s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 385s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 385s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 385s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 385s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 385s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 385s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 385s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 385s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 385s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 385s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 385s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 385s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 385s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 385s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 liburi-perl all 5.27-1 [88.0 kB] 385s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 385s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 385s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 385s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 385s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 385s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 386s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 387s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder all 5.7.1-2 [204 kB] 387s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 transdecoder-doc all 5.7.1-2 [14.9 MB] 387s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 388s Preconfiguring packages ... 388s Fetched 69.7 MB in 4s (19.0 MB/s) 389s Selecting previously unselected package fonts-dejavu-mono. 389s (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 ... 75422 files and directories currently installed.) 389s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 389s Unpacking fonts-dejavu-mono (2.37-8) ... 389s Selecting previously unselected package fonts-dejavu-core. 389s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 389s Unpacking fonts-dejavu-core (2.37-8) ... 389s Selecting previously unselected package fontconfig-config. 389s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 390s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 390s Selecting previously unselected package libfontconfig1:arm64. 390s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 390s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 390s Selecting previously unselected package fontconfig. 390s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 390s Unpacking fontconfig (2.15.0-1ubuntu1) ... 390s Selecting previously unselected package libblas3:arm64. 390s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 390s Unpacking libblas3:arm64 (3.12.0-3) ... 390s Selecting previously unselected package libpixman-1-0:arm64. 390s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_arm64.deb ... 390s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 390s Selecting previously unselected package libxcb-render0:arm64. 390s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ... 390s Unpacking libxcb-render0:arm64 (1.15-1) ... 390s Selecting previously unselected package libxcb-shm0:arm64. 390s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ... 390s Unpacking libxcb-shm0:arm64 (1.15-1) ... 390s Selecting previously unselected package libxrender1:arm64. 391s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 391s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 391s Selecting previously unselected package libcairo2:arm64. 391s Preparing to unpack .../10-libcairo2_1.18.0-1_arm64.deb ... 391s Unpacking libcairo2:arm64 (1.18.0-1) ... 391s Selecting previously unselected package libdatrie1:arm64. 391s Preparing to unpack .../11-libdatrie1_0.2.13-3_arm64.deb ... 391s Unpacking libdatrie1:arm64 (0.2.13-3) ... 391s Selecting previously unselected package libdeflate0:arm64. 391s Preparing to unpack .../12-libdeflate0_1.19-1_arm64.deb ... 391s Unpacking libdeflate0:arm64 (1.19-1) ... 391s Selecting previously unselected package libdivsufsort3:arm64. 391s Preparing to unpack .../13-libdivsufsort3_2.0.1-6_arm64.deb ... 391s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 391s Selecting previously unselected package libgfortran5:arm64. 391s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 391s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 391s Selecting previously unselected package libgomp1:arm64. 391s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 391s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 391s Selecting previously unselected package libgraphite2-3:arm64. 391s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 391s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 391s Selecting previously unselected package libharfbuzz0b:arm64. 391s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 391s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 391s Selecting previously unselected package x11-common. 391s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 391s Unpacking x11-common (1:7.7+23ubuntu2) ... 392s Selecting previously unselected package libice6:arm64. 392s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 392s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 392s Selecting previously unselected package libjpeg-turbo8:arm64. 392s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 392s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 392s Selecting previously unselected package libjpeg8:arm64. 392s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 392s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 392s Selecting previously unselected package liblapack3:arm64. 392s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 392s Unpacking liblapack3:arm64 (3.12.0-3) ... 392s Selecting previously unselected package liblerc4:arm64. 392s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 392s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 392s Selecting previously unselected package libmbedcrypto7:arm64. 392s Preparing to unpack .../24-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 392s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 392s Selecting previously unselected package libmbedx509-1:arm64. 392s Preparing to unpack .../25-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 392s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 392s Selecting previously unselected package libmbedtls14:arm64. 392s Preparing to unpack .../26-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 392s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 392s Selecting previously unselected package libthai-data. 392s Preparing to unpack .../27-libthai-data_0.1.29-2_all.deb ... 392s Unpacking libthai-data (0.1.29-2) ... 392s Selecting previously unselected package libthai0:arm64. 393s Preparing to unpack .../28-libthai0_0.1.29-2_arm64.deb ... 393s Unpacking libthai0:arm64 (0.1.29-2) ... 393s Selecting previously unselected package libpango-1.0-0:arm64. 393s Preparing to unpack .../29-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 393s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 393s Selecting previously unselected package libpangoft2-1.0-0:arm64. 393s Preparing to unpack .../30-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 393s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 393s Selecting previously unselected package libpangocairo-1.0-0:arm64. 393s Preparing to unpack .../31-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 393s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 393s Selecting previously unselected package libpaper1:arm64. 393s Preparing to unpack .../32-libpaper1_1.1.29_arm64.deb ... 393s Unpacking libpaper1:arm64 (1.1.29) ... 393s Selecting previously unselected package libpaper-utils. 393s Preparing to unpack .../33-libpaper-utils_1.1.29_arm64.deb ... 393s Unpacking libpaper-utils (1.1.29) ... 393s Selecting previously unselected package libsharpyuv0:arm64. 393s Preparing to unpack .../34-libsharpyuv0_1.3.2-0.4_arm64.deb ... 393s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 393s Selecting previously unselected package libsm6:arm64. 393s Preparing to unpack .../35-libsm6_2%3a1.2.3-1build2_arm64.deb ... 393s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 393s Selecting previously unselected package libtcl8.6:arm64. 393s Preparing to unpack .../36-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 393s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 394s Selecting previously unselected package libjbig0:arm64. 394s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 394s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 394s Selecting previously unselected package libwebp7:arm64. 394s Preparing to unpack .../38-libwebp7_1.3.2-0.4_arm64.deb ... 394s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 394s Selecting previously unselected package libtiff6:arm64. 394s Preparing to unpack .../39-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 394s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 394s Selecting previously unselected package libxft2:arm64. 394s Preparing to unpack .../40-libxft2_2.3.6-1_arm64.deb ... 394s Unpacking libxft2:arm64 (2.3.6-1) ... 394s Selecting previously unselected package libxss1:arm64. 394s Preparing to unpack .../41-libxss1_1%3a1.2.3-1build2_arm64.deb ... 394s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 394s Selecting previously unselected package libtk8.6:arm64. 394s Preparing to unpack .../42-libtk8.6_8.6.13-2_arm64.deb ... 394s Unpacking libtk8.6:arm64 (8.6.13-2) ... 394s Selecting previously unselected package liburi-perl. 394s Preparing to unpack .../43-liburi-perl_5.27-1_all.deb ... 394s Unpacking liburi-perl (5.27-1) ... 394s Selecting previously unselected package libxt6:arm64. 394s Preparing to unpack .../44-libxt6_1%3a1.2.1-1.1_arm64.deb ... 394s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 394s Selecting previously unselected package ncbi-data. 394s Preparing to unpack .../45-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 394s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 395s Selecting previously unselected package ncbi-blast+. 395s Preparing to unpack .../46-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 395s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 396s Selecting previously unselected package zip. 396s Preparing to unpack .../47-zip_3.0-13_arm64.deb ... 396s Unpacking zip (3.0-13) ... 396s Selecting previously unselected package unzip. 396s Preparing to unpack .../48-unzip_6.0-28ubuntu3_arm64.deb ... 396s Unpacking unzip (6.0-28ubuntu3) ... 396s Selecting previously unselected package xdg-utils. 396s Preparing to unpack .../49-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 396s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 396s Selecting previously unselected package r-base-core. 396s Preparing to unpack .../50-r-base-core_4.3.2-1build1_arm64.deb ... 397s Unpacking r-base-core (4.3.2-1build1) ... 398s Selecting previously unselected package transdecoder. 398s Preparing to unpack .../51-transdecoder_5.7.1-2_all.deb ... 398s Unpacking transdecoder (5.7.1-2) ... 398s Selecting previously unselected package transdecoder-doc. 398s Preparing to unpack .../52-transdecoder-doc_5.7.1-2_all.deb ... 398s Unpacking transdecoder-doc (5.7.1-2) ... 399s Selecting previously unselected package hmmer. 399s Preparing to unpack .../53-hmmer_3.4+dfsg-2_arm64.deb ... 399s Unpacking hmmer (3.4+dfsg-2) ... 399s Selecting previously unselected package autopkgtest-satdep. 399s Preparing to unpack .../54-1-autopkgtest-satdep.deb ... 399s Unpacking autopkgtest-satdep (0) ... 399s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 399s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 399s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 399s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 399s Setting up libpaper1:arm64 (1.1.29) ... 400s 400s Creating config file /etc/papersize with new version 400s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 400s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 400s Setting up libdatrie1:arm64 (0.2.13-3) ... 400s Setting up libxcb-render0:arm64 (1.15-1) ... 400s Setting up unzip (6.0-28ubuntu3) ... 400s Setting up x11-common (1:7.7+23ubuntu2) ... 402s Setting up libdeflate0:arm64 (1.19-1) ... 402s Setting up libxcb-shm0:arm64 (1.15-1) ... 402s Setting up libpaper-utils (1.1.29) ... 402s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 402s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 402s Setting up transdecoder-doc (5.7.1-2) ... 402s Setting up zip (3.0-13) ... 402s Setting up libblas3:arm64 (3.12.0-3) ... 402s 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 402s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 402s Setting up fonts-dejavu-mono (2.37-8) ... 402s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 402s Setting up fonts-dejavu-core (2.37-8) ... 402s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 402s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 402s Setting up libwebp7:arm64 (1.3.2-0.4) ... 402s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 402s Setting up libthai-data (0.1.29-2) ... 402s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 402s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 402s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 402s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 402s Setting up liburi-perl (5.27-1) ... 402s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 402s Setting up libice6:arm64 (2:1.0.10-1build2) ... 402s Setting up liblapack3:arm64 (3.12.0-3) ... 402s 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 402s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 402s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 402s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 402s Setting up ncbi-blast+ (2.12.0+ds-4) ... 402s Setting up libthai0:arm64 (0.1.29-2) ... 402s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 402s Setting up hmmer (3.4+dfsg-2) ... 403s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 403s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 403s Setting up fontconfig (2.15.0-1ubuntu1) ... 405s Regenerating fonts cache... done. 405s Setting up libxft2:arm64 (2.3.6-1) ... 405s Setting up libtk8.6:arm64 (8.6.13-2) ... 405s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 405s Setting up libcairo2:arm64 (1.18.0-1) ... 405s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 405s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 405s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 405s Setting up r-base-core (4.3.2-1build1) ... 405s 405s Creating config file /etc/R/Renviron with new version 406s Setting up transdecoder (5.7.1-2) ... 406s Setting up autopkgtest-satdep (0) ... 406s Processing triggers for man-db (2.12.0-3) ... 408s Processing triggers for install-info (7.1-3) ... 408s Processing triggers for libc-bin (2.39-0ubuntu2) ... 417s (Reading database ... 77921 files and directories currently installed.) 417s Removing autopkgtest-satdep (0) ... 418s autopkgtest [21:11:06]: test run-tests: [----------------------- 418s Running example in $... 418s make[1]: Entering directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 418s ./runMe.sh incl_pfam_n_blast 418s 418s export PERL_HASH_SEED=0 418s 418s if [ ! -e test.genome.fasta ]; then 418s gunzip -c test.genome.fasta.gz > test.genome.fasta 418s fi 418s 418s 418s if [ ! -e transcripts.gtf ]; then 418s gunzip -c transcripts.gtf.gz > transcripts.gtf 418s fi 418s 418s if [ ! -e mini_Pfam-A.hmm ]; then 418s gunzip -c mini_Pfam-A.hmm.gz > mini_Pfam-A.hmm 418s fi 418s 418s if [ ! -e mini_sprot.db.pep ]; then 418s gunzip -c mini_sprot.db.pep.gz > mini_sprot.db.pep 418s fi 418s 418s 418s ## generate alignment gff3 formatted output 418s ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 418s 418s ## generate transcripts fasta file 418s ../../util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta 419s -parsing cufflinks output: transcripts.gtf 419s -parsing genome fasta: test.genome.fasta 419s -done parsing genome. 419s // processing 7000000090838467 419s 419s ## Extract the long ORFs 419s ../../TransDecoder.LongOrfs -t transcripts.fasta 419s CMD: mkdir -p /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir 419s * [Sat Mar 16 21:11:07 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 419s 419s 419s -first extracting base frequencies, we'll need them later. 419s 419s 419s - extracting ORFs from transcripts. 419s -total transcripts to examine: 64 420s CMD: touch /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 420s 420s 420s ################################# 420s ### Done preparing long ORFs. ### 420s ################################## 420s 420s Use file: /tmp/autopkgtest.x2gTgS/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. 420s 420s Then, run TransDecoder.Predict for your final coding region predictions. 420s 420s 420s 420s cmd="" 420s ## Predict likely ORFs 420s if [ "$1" == "" ]; then # always doing this now. 420s # just coding metrics 420s cmd="../../TransDecoder.Predict -t transcripts.fasta" 420s 420s else 420s 420s # this is how I would have run blast and pfam but I'm using precomputed results for ease of demonstration. 420s #BLASTDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/uniprot_sprot.pep 420s #PFAMDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/Pfam-A.hmm 420s # 420s ## run blast 420s #blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db $BLASTDB -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 420s 420s makeblastdb -in mini_sprot.db.pep -dbtype prot 420s 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 420s 420s # 420s ## run pfam 420s #hmmsearch --domtblout pfam.domtblout $PFAMDB transcripts.fasta.transdecoder_dir/longest_orfs.pep > pfam.log 420s 420s hmmpress -f mini_Pfam-A.hmm 420s hmmsearch --domtblout pfam.domtblout mini_Pfam-A.hmm transcripts.fasta.transdecoder_dir/longest_orfs.pep 420s 420s ## use pfam and blast results: 420s cmd="../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v" 420s 420s fi 420s 420s 420s Building a new DB, current time: 03/16/2024 21:11:08 420s New DB name: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/mini_sprot.db.pep 420s New DB title: mini_sprot.db.pep 420s Sequence type: Protein 420s Keep MBits: T 420s Maximum file size: 1000000000B 420s Adding sequences from FASTA; added 240 sequences in 0.023876 seconds. 420s 420s 420s Warning: [blastp] Examining 5 or more matches is recommended 422s Working... done. 422s Pressed and indexed 118 HMMs (118 names and 118 accessions). 422s Models pressed into binary file: mini_Pfam-A.hmm.h3m 422s SSI index for binary model file: mini_Pfam-A.hmm.h3i 422s Profiles (MSV part) pressed into: mini_Pfam-A.hmm.h3f 422s Profiles (remainder) pressed into: mini_Pfam-A.hmm.h3p 422s # hmmsearch :: search profile(s) against a sequence database 422s # HMMER 3.4 (Aug 2023); http://hmmer.org/ 422s # Copyright (C) 2023 Howard Hughes Medical Institute. 422s # Freely distributed under the BSD open source license. 422s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s # query HMM file: mini_Pfam-A.hmm 422s # target sequence database: transcripts.fasta.transdecoder_dir/longest_orfs.pep 422s # per-dom hits tabular output: pfam.domtblout 422s # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s 422s Query: AA_permease [M=479] 422s Accession: PF00324.20 422s Description: Amino acid permease 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 80.0 51.2 7.7e-27 7.3e-25 19 463 .. 70 500 .. 53 509 .. 0.76 422s 422s Alignments for each domain: 422s == domain 1 score: 80.0 bits; conditional E-value: 7.7e-27 422s AA_permease 19 lgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpe....lGfviGlnylfswitvlaleltaasiliqfwelvtdlp 111 422s + + ++G++g++ ++++++++++ v +slge+a+ +p sgg y+++ +p+ l +v+G+ ++ ++t +a + as+++q + + + + 422s CUFF.38.1.p2 70 SLIFSMNCGGGGMVWSWIIGCICLIPVSISLGELASSMPTSGGLYFWIFTLASPSsrafLCWVCGYVSVLGYATIYASTVYSASSMVQALAVIGSPS 166 422s 44455689999************************************99999987222255555555555566666666666666666664444333 PP 422s 422s AA_permease 112 kawvt..........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkga..gfrflgdngsifknnlppgfakeeeg 196 422s + a +l+v+++++ + +v +++ +i + + ++ i++ii ++ ++ + +n g ++ f++++g n+ 422s CUFF.38.1.p2 167 ----YsptkyeqygiYAALLFVISAMTAIPSRVIAKVNIINITFQFLVSIILIIALAAGSDSTTRNSGSfiFGDFTNYSGW---SNM---------- 246 422s ....02345666666999**********************99999999999999996555555555553333333333333...111.......... PP 422s 422s AA_permease 197 afknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplin 293 422s +fi f + v +G+e+ a++a+E+ + +k+ P a+++ + ti+ +++++++++++ + +l +s+ + + ++ g++++ ++ 422s CUFF.38.1.p2 247 -GWAFILSFTTPVWVVSGFESSAAVAEESTNAAKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSSLGQ-PVAQVLVNNVGNKGALGIFS 341 422s .246888888899999*******************************************************99966.7888889999********** PP 422s 422s AA_permease 294 aviltaalssansslysasRvlyslakdglaP..kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388 422s +++++ +l++ +s+l++asR ++++++dg +P ++l+ ++k++vPl+aill+++ sll+ ll +n+ ais + +l++ l i+ + 422s CUFF.38.1.p2 342 LLVIALCLNC-ISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILVNVT---------AISSVFNLAIIALYIAYSG 428 422s *999999998.79************************************************99999999.........4444444444444444444 PP 422s 422s AA_permease 389 rfRkalkyqgrsieelgfkaallplgvi..lvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463 422s +++ + y++ + + + + p ++ +++ ++i++ll+ + ++ + + +++a +++ +++v++++ ++ 422s CUFF.38.1.p2 429 PLMCRFVYNKFQPGVFYVGKWSKPAALWslVWMWFMILMLLFPQYQKPNQ-----DEMNWAIVVLGFVMVFCVVYYY 500 422s 55555555555555555555666555540045555555555555555555.....6788888899999998888777 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (479 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 422s # Mc/sec: 518.67 422s // 422s Query: AA_permease_2 [M=425] 422s Accession: PF13520.5 422s Description: Amino acid permease 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 183.8 57.6 2.7e-58 2.6e-56 1 425 [] 48 491 .. 48 491 .. 0.85 422s 422s Alignments for each domain: 422s == domain 1 score: 183.8 bits; conditional E-value: 2.7e-58 422s AA_permease_2 1 lsllsafalvigsv......igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf....gkkvaflsawfnwf 86 422s +s++s f+ ++gs+ +gs if +++ gg +++++i+++++ ++v++ + El+s +p+sgG+y + + ++ +++++ +++ 422s CUFF.38.1.p2 48 FSYVSIFGQSFGSMglcpamAGSLIF---SMNCGGGGMVWSWIIGCICL-IPVSISLGELASSMPTSGGLYFWIFTLAspssRAFLCWVCGYVSVL 139 422s 799***********777755555555...57888888888888888888.9*********888***********8886333356666********* PP 422s 422s AA_permease_2 87 ayvpvlasilsvaasyl..lnalg.pdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfssl.ste 178 422s +y+ as++++a s+ l ++g p++ ++++ +y+i++a+l ++ +++++ + +ak++ i +++ +l + iili ++l++++ ++ ++ s++ 422s CUFF.38.1.p2 140 GYATIYASTVYSASSMVqaLAVIGsPSYSPTKYEQYGIYAALLFVISAMTAIPSRVIAKVNIINITFQFL-VSIILI-IALAAGSDSTTRNSgSFI 233 422s ****9999888777777433345547*******************************************5.555454.566666555444334444 PP 422s 422s AA_permease_2 179 tdtffpn.gwp..g..vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsn.lgs.vaalffe 265 422s + f++ gw+ g ++l++++ +w+++Gfes+a v+ee + k +p+a++++l+++++l++ + i++++ ++ d a l++ lg+ va+++++ 422s CUFF.38.1.p2 234 FGDFTNYsGWSnmGwaFILSFTTPVWVVSGFESSAAVAEESTNaaKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSsLGQpVAQVLVN 329 422s 4444444477743133699*********************8887789*****************************999887773444569***** PP 422s 422s AA_permease_2 266 avggkvvaiivvilialsllgaintavigssrvlealardgvlP..rffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgli 359 422s +vg+k + +i++ l++++l+++ ++++i++sr ++a++rdg++P r+++ k++ p++ai l++++sl+++ll+l+ + +a++ +++++ ++l+ 422s CUFF.38.1.p2 330 NVGNKGALGIFS-LLVIALCLNCISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILV-NVTAISSVFNLAIIALY 423 422s ***999999999.8999****************************************************888877765.69*************** PP 422s 422s AA_permease_2 360 isyllliigalilrkkrphl...krpgkilvaiigalfllfllvalffppkgpatqssliytiiltval 425 422s i y ++ +++++ k +p +++ + a+ ++++ f++ +l fp+ + +q++++++i++++++ 422s CUFF.38.1.p2 424 IAYSGPLMCRFVYNKFQPGVfyvGKW-SKPAALWSLVWMWFMILMLLFPQYQKPNQDEMNWAIVVLGFV 491 422s **********9999999977444444.468**********************************99875 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (425 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 422s # Mc/sec: 504.28 422s // 422s Query: Acetyltransf_1 [M=117] 422s Accession: PF00583.24 422s Description: Acetyltransferase (GNAT) family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 48.3 0.0 1.2e-16 5.6e-15 18 117 .] 35 129 .. 16 129 .. 0.77 422s 422s Alignments for each domain: 422s == domain 1 score: 48.3 bits; conditional E-value: 1.2e-16 422s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 422s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 422s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 422s CUFF.34.1.p2 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 422s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 422s 422s HHHHH.TTE CS 422s Acetyltransf_1 110 rlYek.lGF 117 422s +lY + +GF 422s CUFF.34.1.p2 122 PLY-RsVGF 129 422s ***.65**9 PP 422s 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 48.1 0.0 1.3e-16 6.2e-15 18 117 .] 35 129 .. 16 129 .. 0.77 422s 422s Alignments for each domain: 422s == domain 1 score: 48.1 bits; conditional E-value: 1.3e-16 422s HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS 422s Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 422s ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ 422s CUFF.35.1.p1 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 422s 4444443333..2556345558888***********999...9*********************************877344466...99***** PP 422s 422s HHHHH.TTE CS 422s Acetyltransf_1 110 rlYek.lGF 117 422s +lY + +GF 422s CUFF.35.1.p1 122 PLY-RsVGF 129 422s ***.65**9 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (117 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 612.24 422s // 422s Query: Acetyltransf_10 [M=127] 422s Accession: PF13673.6 422s Description: Acetyltransferase (GNAT) domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+) 422s 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- 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 70.8 0.0 1.1e-23 5.3e-22 32 127 .] 50 150 .. 28 150 .. 0.90 422s 422s Alignments for each domain: 422s == domain 1 score: 70.8 bits; conditional E-value: 1.1e-23 422s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 422s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 422s CUFF.35.1.p1 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 422s 67888899*******9986666799***************************98888888888889999************************* PP 422s 422s Acetyltransf_10 121 vpMekel 127 422s v+M++el 422s CUFF.35.1.p1 144 VEMRLEL 150 422s ****986 PP 422s 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 65.7 0.0 4.1e-22 2e-20 32 123 .. 50 146 .] 28 146 .] 0.90 422s 422s Alignments for each domain: 422s == domain 1 score: 65.7 bits; conditional E-value: 4.1e-22 422s Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 422s +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + 422s CUFF.34.1.p2 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 422s 67888899*******9986666799***************************98888888888889999************************* PP 422s 422s Acetyltransf_10 121 vpM 123 422s v+M 422s CUFF.34.1.p2 144 VEM 146 422s **9 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (127 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 650.70 422s // 422s Query: Acetyltransf_15 [M=210] 422s Accession: PF17013.4 422s Description: Putative acetyl-transferase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+) 422s 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- 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 19.4 0.1 6.3e-08 3e-06 28 154 .. 5 149 .. 1 150 [. 0.84 422s 422s Alignments for each domain: 422s == domain 1 score: 19.4 bits; conditional E-value: 6.3e-08 422s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 422s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 422s CUFF.35.1.p1 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 422s 5578888888888888888888999999988734444479999999999999999999987777889999************************ PP 422s 422s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksgPeelkkrle 154 422s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g ++++ rle 422s CUFF.35.1.p1 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDGIPHVEMRLE 149 422s **********9888774........6789999*******99744499999998888876 PP 422s 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 17.4 0.1 2.6e-07 1.2e-05 28 145 .. 5 140 .. 1 146 [] 0.81 422s 422s Alignments for each domain: 422s == domain 1 score: 17.4 bits; conditional E-value: 2.6e-07 422s Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 422s e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ 422s CUFF.34.1.p2 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 422s 5678888888888888888888999999988734444479999999999999999999987777889999************************ PP 422s 422s Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksg 145 422s l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g 422s CUFF.34.1.p2 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDG 140 422s *********99887774........5677888888888887633366655 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (210 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 422s # Mc/sec: 233.51 422s // 422s Query: Acetyltransf_5 [M=101] 422s Accession: PF13444.5 422s Description: Acetyltransferase (GNAT) domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 22.2 0.0 2e-08 9.5e-07 1 82 [. 25 102 .. 25 123 .. 0.81 422s 422s Alignments for each domain: 422s == domain 1 score: 22.2 bits; conditional E-value: 2e-08 422s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 422s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 422s CUFF.34.1.p2 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 422s 7888888888888777......*************988889*********9999987777776666665555443555666666 PP 422s 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 21.7 0.0 2.7e-08 1.3e-06 1 82 [. 25 102 .. 25 106 .. 0.78 422s 422s Alignments for each domain: 422s == domain 1 score: 21.7 bits; conditional E-value: 2.7e-08 422s Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 422s LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ 422s CUFF.35.1.p1 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 422s 7888888888888777......*************988889*********9999877777776666665555443555677666 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (101 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 185.90 422s // 422s Query: Acetyltransf_7 [M=76] 422s Accession: PF13508.6 422s Description: Acetyltransferase (GNAT) domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 41.8 0.0 1.2e-14 5.6e-13 5 76 .] 29 131 .. 25 131 .. 0.68 422s 422s Alignments for each domain: 422s == domain 1 score: 41.8 bits; conditional E-value: 1.2e-14 422s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 422s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 422s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 422s CUFF.34.1.p2 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 422s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 422s 422s HHHHHTTEEE CS 422s Acetyltransf_7 67 kfYeklGFee 76 422s ++Y++ GF++ 422s CUFF.34.1.p2 122 PLYRSVGFKK 131 422s ********95 PP 422s 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 41.7 0.0 1.3e-14 6.2e-13 5 76 .] 29 131 .. 25 131 .. 0.68 422s 422s Alignments for each domain: 422s == domain 1 score: 41.7 bits; conditional E-value: 1.3e-14 422s EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS 422s Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 422s vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ 422s CUFF.35.1.p1 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 422s 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP 422s 422s HHHHHTTEEE CS 422s Acetyltransf_7 67 kfYeklGFee 76 422s ++Y++ GF++ 422s CUFF.35.1.p1 122 PLYRSVGFKK 131 422s ********95 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (76 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 763.28 422s // 422s Query: Acetyltransf_9 [M=128] 422s Accession: PF13527.6 422s Description: Acetyltransferase (GNAT) domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 21.8 0.0 1.7e-08 8.3e-07 72 127 .. 72 131 .. 11 132 .. 0.71 422s 422s Alignments for each domain: 422s == domain 1 score: 21.8 bits; conditional E-value: 1.7e-08 422s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 422s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 422s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 422s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 422s 4567999*************************9986556666667566669******975 PP 422s 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 21.6 0.0 1.9e-08 9.2e-07 72 127 .. 72 131 .. 11 132 .. 0.71 422s 422s Alignments for each domain: 422s == domain 1 score: 21.6 bits; conditional E-value: 1.9e-08 422s EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS 422s Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 422s ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ 422s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 422s 4567999*************************9986556666667566669******975 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (128 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 422s # Mc/sec: 192.95 422s // 422s Query: Acetyltransf_CG [M=80] 422s Accession: PF14542.5 422s Description: GCN5-related N-acetyl-transferase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 17.2 0.0 4.8e-07 2.3e-05 8 56 .. 57 105 .. 50 108 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: 17.2 bits; conditional E-value: 4.8e-07 422s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 422s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 422s CUFF.34.1.p2 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 422s 5677888888778999***************************998875 PP 422s 422s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 17.1 0.0 5.2e-07 2.5e-05 8 56 .. 57 105 .. 50 108 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: 17.1 bits; conditional E-value: 5.2e-07 422s Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 422s +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e 422s CUFF.35.1.p1 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 422s 5677888888778999***************************998875 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (80 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 628.88 422s // 422s Query: Aldo_ket_red [M=292] 422s Accession: PF00248.20 422s Description: Aldo/keto reductase family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 225.3 0.0 4.8e-71 4.6e-69 1 289 [. 21 340 .. 21 342 .. 0.91 422s 422s Alignments for each domain: 422s == domain 1 score: 225.3 bits; conditional E-value: 4.8e-71 422s .EEEE-SSS-ST.......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..................... CS 422s Aldo_ket_red 1 elglGtwqlgsk......eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..................... 70 422s +l+lG +++g k ++ee+++++++a++aGi++fDtA+ Y g seel+G++++k++ +r +++i +K+ 422s CUFF.17.1.p1 21 KLILGCMSYGKKeywedwVLEDEEEVFKIMKAAYDAGIRTFDTANCYSAGVSEELVGKFIRKYEIPRSSIVILSKCffpvrkdlikifgdlssrgvh 117 422s 689999999999888663334678999*********************************************************************9 PP 422s 422s ..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH....HHTTT--EEEEE- CS 422s Aldo_ket_red 71 ..dkrdaeiksglskenieesleeslkrLgtdyvDllllHrpdpslpieevldaleelvkeGkiraiGvSnfsveqleka....kkkkkvkivavqv 161 422s d +++ gls+++i ++e+s+krLgt y+D+l++Hr dp ++ eev++al+++v++Gk+r+iG S q ++ +k++ +k+++ q+ 422s CUFF.17.1.p1 118 flDSPELANQCGLSRKHIFDAVEDSVKRLGT-YIDVLQIHRYDPHVSAEEVMRALNDVVESGKVRYIGASTMRCYQFIELqntaEKHGWHKFISMQN 213 422s 998888889999******************6.**************************************88866655566778************* PP 422s 422s B-BTTB-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------....S-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT CS 422s Aldo_ket_red 162 eynllkreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr....rtsknqdaaeelselakehgvsiaqvalryalsqpa 254 422s +nll ++ee++++++c+k gv+li++spl++Gllt+ + +e++ + +++ ++ + +++++elak+++vs+a++a ++ l + 422s CUFF.17.1.p1 214 YHNLL-YREEEREMIPYCQKTGVGLIPWSPLARGLLTRSIDANEETIRSKTD-LY-TraleFGAGYKAILSRVEELAKKYNVSMATLATAWSL--HK 305 422s *****.*******************************999988887743332.33.2479555556666799*********************..9* PP 422s 422s -SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS 422s Aldo_ket_red 255 vgivipgasnieqlednldalelklseeevaelde 289 422s + +i+g s++e+l+d l+a+elklsee++++l+e 422s CUFF.17.1.p1 306 GDYPIVGISKVERLKDALAAVELKLSEEDIKYLEE 340 422s *******************************9986 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (292 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 689.39 422s // 422s Query: Amidohydro_1 [M=344] 422s Accession: PF01979.19 422s Description: Amidohydrolase family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 268.4 0.4 1.1e-83 5.3e-82 1 343 [. 55 420 .. 55 421 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 422s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 422s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 422s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 422s CUFF.26.1.p1 55 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 149 422s 79************************************************************************************9..******** PP 422s 422s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 422s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 422s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 422s CUFF.26.1.p1 150 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 238 422s ******************9988899999999999999....*******************************************9999996....67 PP 422s 422s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 422s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 422s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 422s CUFF.26.1.p1 239 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 332 422s 76.6677.8*************.************************************************************************** PP 422s 422s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 422s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 422s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 422s CUFF.26.1.p1 333 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 420 422s ***99998888.6677.89999***************6.******************972255668888********************97 PP 422s 422s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 268.4 0.4 1.1e-83 5.4e-82 1 343 [. 57 422 .. 57 423 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 422s EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS 422s Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 422s iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk 422s CUFF.27.1.p1 57 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 151 422s 79************************************************************************************9..******** PP 422s 422s SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS 422s Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 422s v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + 422s CUFF.27.1.p1 152 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 240 422s ******************9988899999999999999....*******************************************9999996....67 PP 422s 422s HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS 422s Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 422s f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ 422s CUFF.27.1.p1 241 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 334 422s 76.6677.8*************.************************************************************************** PP 422s 422s HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS 422s Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 422s +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl 422s CUFF.27.1.p1 335 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 422 422s ***99998888.6677.89999***************6.******************972255668888********************97 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (344 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 422s # Mc/sec: 467.51 422s // 422s Query: Amidohydro_3 [M=473] 422s Accession: PF07969.10 422s Description: Amidohydrolase family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 10.0 0.1 4.8e-05 0.0023 5 25 .. 51 71 .. 50 82 .. 0.86 422s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 211 421 .. 163 422 .. 0.75 422s 422s Alignments for each domain: 422s == domain 1 score: 10.0 bits; conditional E-value: 4.8e-05 422s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 422s ++G +v+PG++ H Hla 422s CUFF.26.1.p1 51 LEGHIVMPGLISLHVHLAQSL 71 422s 89**************99865 PP 422s 422s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 422s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 422s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 422s CUFF.26.1.p1 211 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 298 422s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 422s 422s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 422s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 422s CUFF.26.1.p1 299 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 389 422s 9******************.....4444444444433333333666999***************************8.***************9555 PP 422s 422s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 422s l ++p ++ v +v+dG+ + 422s CUFF.26.1.p1 390 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 421 422s 55555443333346666888899999999876 PP 422s 422s >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 10.0 0.1 4.9e-05 0.0023 5 25 .. 53 73 .. 52 84 .. 0.86 422s 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 213 423 .. 165 424 .. 0.75 422s 422s Alignments for each domain: 422s == domain 1 score: 10.0 bits; conditional E-value: 4.9e-05 422s Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 422s ++G +v+PG++ H Hla 422s CUFF.27.1.p1 53 LEGHIVMPGLISLHVHLAQSL 73 422s 89**************99865 PP 422s 422s == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 422s Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 422s +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g 422s CUFF.27.1.p1 213 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 300 422s 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP 422s 422s Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 422s ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + 422s CUFF.27.1.p1 301 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 391 422s 9******************.....4444444444433333333666999***************************8.***************9555 PP 422s 422s Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 422s l ++p ++ v +v+dG+ + 422s CUFF.27.1.p1 392 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 423 422s 55555443333346666888899999999876 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (473 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 422s # Mc/sec: 552.27 422s // 422s Query: Aminotran_1_2 [M=363] 422s Accession: PF00155.20 422s Description: Aminotransferase class I and II 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 17.9 0.0 7.6e-08 7.3e-06 48 334 .. 65 357 .. 61 375 .. 0.71 422s 422s Alignments for each domain: 422s == domain 1 score: 17.9 bits; conditional E-value: 7.6e-08 422s HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHH...HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS 422s Aminotran_1_2 48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyk...nilrlsggevvryplyseedfhldlealeealk 140 422s e ++ lak+l+ ++++++++ +++++++++ + lk pgd++++ d +++ +l++ g+ev+ +p +e ++h ++ + ++ 422s CUFF.40.1.p1 65 ETRSLLAKLLN------ASTKDSITFTRDTTEGLNLFQRSLKWKPGDNVVILDNEHPNQGfgwIALQNDGLEVRLVP--NEGQYHANASTFAPYVD 152 422s 778999*****......45555***********************************987333568999********..77999999999*99999 PP 422s 422s THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTTSGGG-EEEEEEE CS 422s Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgn 236 422s + +tk i + s+ +G+ +++++++++ + ++++++ D + +++ ++ +v++ +++ s+ K +G++ +G ++++ 422s CUFF.40.1.p1 153 S------RTKAIGLSSVMFHSGQ---KNDVKDIANAFRPKGIHVLADLTQQVGLSK--------IDVQDLNVSACAFSCHKGLGCPT-GLGVLYVS 230 422s 9......9***********9*97...5677777777*************9999998........55555544688889999999975.58999998 PP 422s 422s H.........................HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHS.....TEEE CS 422s Aminotran_1_2 237 a.........................avvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLael.....glkv 299 422s + +++ ++ ++++ + + ++++ +al++ l+ +++ + lq + k l +eL++l g k 422s CUFF.40.1.p1 231 PlaiselrstppfvgggavedfkedlKLKLNAKYHQSALRYeHTNNAYMLITALRAYLKFLLkvGISNVERYLQGLGKDLIKELESLnvsviGYKD 326 422s 866666666666666666666666555555555555555555555666666666666555554434444444555555666666555444444444 PP 422s 422s ECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEE CS 422s Aminotran_1_2 300 lasq.sgmflltdlsaetakelskkLleevgvyvtp 334 422s ++++ s+ ++l l++e ++ L+++ gv v++ 422s CUFF.40.1.p1 327 FDKHsSHSYVLKILNPE----WFDFLRQQ-GVCVSR 357 422s 44444555555555555....44445555.666655 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (363 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 422s # Mc/sec: 348.39 422s // 422s Query: Aminotran_5 [M=371] 422s Accession: PF00266.18 422s Description: Aminotransferase class-V 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 152.3 0.0 9.2e-49 8.8e-47 41 369 .. 59 376 .. 25 378 .. 0.89 422s 422s Alignments for each domain: 422s == domain 1 score: 152.3 bits; conditional E-value: 9.2e-49 422s HHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCHHH-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS 422s Aminotran_5 41 atkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137 422s ++ ee+r+ +a+l+na++++ i ft+ tte++nl+ +sl ++kpgd++v+ ++eh + w +l+ g++v+ +p + + + + ++++ +++ 422s CUFF.40.1.p1 59 WKERTEETRSLLAKLLNASTKDSITFTRDTTEGLNLFQRSL--KWKPGDNVVILDNEHPNQGFGWIALQ-NDGLEVRLVPNEGQYHANASTFAPYVD 152 422s 56789************************************..59***********************8.67************************* PP 422s 422s TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHHS.....SS.STTS CS 422s Aminotran_5 138 ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl...eplllggem 230 422s +tk++ ++ v +G ++v++i+++++ kg+ vl+D +q+vg +idv++l+v afs hK l PtG+Gvlyv++ ++ +l +p+ +gg+ 422s CUFF.40.1.p1 153 SRTKAIGLSSVMFHSGQKNDVKDIANAFRPKGIHVLADLTQQVGLSKIDVQDLNVSACAFSCHKgLGCPTGLGVLYVSPLAISELrstPPF-VGGGA 248 422s ****************************************************************8888*************9999774455.55555 PP 422s 422s EEEEET.....TEEEEHHTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTSSHH CS 422s Aminotran_5 231 veevsl.....eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhae 322 422s ve+ + +++++++ ++e+ + i +l+a l++l ++g++++e++ + l + l ++l+sl+ + g k+ ++s s ++k +++e 422s CUFF.40.1.p1 249 VEDFKEdlklkLNAKYHQSALRYEHTNNAYMLITALRAYLKFLLKVGISNVERYLQGLGKDLIKELESLNVSVI-G-YKDFDKHSSHSYVLKILNPE 343 422s 665554110044555999*******555578899***********************************98766.8.67899999999999999998 PP 422s 422s HHHHHHHHTTEEEEEE-TTTHHHHHHHT.S-EEEEE--TTS-HHHHH CS 422s Aminotran_5 323 dvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369 422s + +L+++g++v+ e+++R+S+++ynt++++ 422s CUFF.40.1.p1 344 WF-DFLRQQGVCVSR-------------FESGIRVSFGLYNTSKDII 376 422s 65.79******9974.............45999***********996 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (371 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 422s # Mc/sec: 326.80 422s // 422s Query: Arginase [M=280] 422s Accession: PF00491.20 422s Description: Arginase family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 298.2 0.0 3.6e-93 3.4e-91 2 277 .. 75 373 .. 74 374 .] 0.93 422s 422s Alignments for each domain: 422s == domain 1 score: 298.2 bits; conditional E-value: 3.6e-93 422s EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE...SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEE......... CS 422s Arginase 2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv...leelkivdlgdvavtpvdneevleqieeavaeilkagklp......... 86 422s d+a+lG+Pfd+++s+rpGarfGP+ ire+s+rl+ + +yn+ ++ +++kivd+gd+++t +dn+ +++qie+ e+l+++ + 422s CUFF.38.1.p4 75 DIAFLGAPFDTGTSYRPGARFGPSGIREGSRRLNLYGGYNVPMETnpfNNWAKIVDCGDIPLTSYDNAVAIKQIENGHFELLTRKPTSysekdgyal 171 422s 89********************************8778888887788999******************9***************4444555555555 PP 422s 422s ........EEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSC......TTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH..HHHH CS 422s Arginase 87 ........ivlGGDHsialgilralaekygkplgvihfDAHaDlrtpe......tegsgnshGtpfrraaeegllkpkklvqiGirsvdne..eyel 167 422s i+lGGDH+i l+ilr+++++yg p+++ihfD+H+D ++p+ ++ +++hGt+f++a++egl+++++ +++Gir++ ++ +y+ 422s CUFF.38.1.p4 172 dgsvlprvITLGGDHTIVLPILRSVSRAYG-PVSIIHFDSHLDSWKPKvfgggkSSVGSINHGTYFYHASQEGLVSNDSNIHAGIRTTLSGlsDYDN 267 422s 55555666********************99.6****************99988877778********************************999999 PP 422s 422s HHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTT CS 422s Arginase 168 akelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteae 264 422s ++++g+++i++reid +g++a++++i++rvg ++ ylS+DiDvlDpa+aP+tGtpe G+t+rel+++lr+l + +lvgaD+vEv+Pa+d ae 422s CUFF.38.1.p4 268 DADCGFEIIEAREIDTIGIDAIIKRIRDRVG--DGIAYLSIDIDVLDPAYAPATGTPESAGWTTRELRTILRGLDG-IKLVGADIVEVAPAYDF-AE 360 422s 999***************************8..57***************************************99.*****************.67 PP 422s 422s HHHHHHHHHHHHH CS 422s Arginase 265 qtarlaarlvrel 277 422s t+++aa++++e+ 422s CUFF.38.1.p4 361 VTTLAAADILFEV 373 422s ***********95 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (280 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 969.16 422s // 422s Query: Asparaginase [M=191] 422s Accession: PF00710.19 422s Description: Asparaginase, N-terminal 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-1103(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 176.1 0.6 3.1e-56 2.9e-54 1 182 [. 47 233 .. 47 241 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: 176.1 bits; conditional E-value: 3.1e-56 422s EEEEEEEESGGGBB-SSSS--SS-B...S-HHHHHTTSTTHHHHSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHH.HT.--EEEEE--STTHHHHH CS 422s Asparaginase 1 kvlvlatGGTiasekdesggalapa...lsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee.ydgfVvlhGTDTlaytA 92 422s +v v a+GGTia +++s + +++ + +e+l+ea+p+++ ia+++ q++n+ S+n+tpad+lkla+ i +++ + ++g+V++hGTD+l++tA 422s CUFF.15.1.p1 47 NVTVFAMGGTIAGCANSSLEIVNYIpgsVGIEKLIEAVPAIKAIANINGVQVTNMGSENLTPADVLKLAKLILAEVaKPnVHGIVITHGTDSLEETA 143 422s 599***************99999878899***********************************************7669***************** PP 422s 422s HHHHHH---.-S-EEEE--SS-TTSTT-SHHHHHHHHHHHHHSGG.TTS-SEEEETTEEEETTT-EE-BSSSSS-EE-TTT--SEEEETTE CS 422s Asparaginase 93 saLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasse.riagvlvvfngkllranrvtKvhtssldaFespnlgplaevegsk 182 422s ++L+l++ + +kp+v++G++rp++++++Dgp+Nll+A++va+s++ ++g lv +n+++ +a ++tK++ ++ld+F+s ++g+l+ v ++k 422s CUFF.15.1.p1 144 MFLDLTIST-AKPIVVVGAMRPSTAIGADGPMNLLNAVAVASSNQsMGRGTLVLLNDRIGSAFYTTKTNGNTLDTFKSYEAGSLGIVLNQK 233 422s *******99.***************************************************************************986655 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (191 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 422s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 827.75 422s // 422s Query: Asp_Glu_race [M=224] 422s Accession: PF01177.21 422s Description: Asp/Glu/Hydantoin racemase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 18.9 0.0 1.2e-07 5.8e-06 49 98 .. 157 205 .. 141 211 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: 18.9 bits; conditional E-value: 1.2e-07 422s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 422s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 422s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 422s CUFF.52.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 422s 34455667**********************99.****************7 PP 422s 422s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 18.6 0.0 1.4e-07 6.9e-06 49 98 .. 157 205 .. 141 212 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: 18.6 bits; conditional E-value: 1.4e-07 422s H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS 422s Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 422s +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi 422s CUFF.50.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 422s 34455667**********************99.****************7 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (224 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 964.83 422s // 422s Query: Beta_elim_lyase [M=293] 422s Accession: PF01212.20 422s Description: Beta-eliminating lyase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 18.8 0.0 4.4e-08 4.2e-06 29 201 .. 619 786 .. 611 886 .. 0.76 422s 422s Alignments for each domain: 422s == domain 1 score: 18.8 bits; conditional E-value: 4.4e-08 422s T--HHHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT........-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS 422s Beta_elim_lyase 29 gedktvnrLedavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep........ahihfdetgaiaelagvklrdlknkeaGkmdlek 113 422s g + +++L+ ++ ++g++aa f p +G a++ l+++ + ++ +++ ah+ ++ a a++ag +++++k ++G++d+++ 422s CUFF.57.1.p1 619 GYRHVIEDLQLMLTTITGFDAACFQPnSGAAGEYTGLSVIRAYQRSIGQGHRniclipvsAHG---TNPASAAMAGFTVIPVKCLNNGYLDMQD 709 422s 555667788999999*********9956*******9977765555555555445444344443...55677889*********9999******* PP 422s 422s HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH...HHHTS-CHHHHTTSSEEEEESSSTT- CS 422s Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa...kslgeivkemfsyvDsvtmslkKdll 201 422s l+++ + h++k ++ ++t G ++e+ ++ +++g ++ +DgA +na+ ++ ++ ++D++ + l K + 422s CUFF.57.1.p1 710 LKEKASK---HADKLAAFMVTYPSTF--GI--FEPDVKEALEVIHEHGGQVYFDGAN-MNAMvglC----KAGDI--GADVCHLNLHKTFC 786 422s ***9999...8889999999888887..54..44579*******************5.45552332....33333..23444444444444 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (293 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 601.86 422s // 422s Query: Chitin_synth_1 [M=163] 422s Accession: PF01644.16 422s Description: Chitin synthase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 422s 422s Alignments for each domain: 422s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 422s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 422s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 422s CUFF.60.1.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 422s 9********************************************************************************************** PP 422s 422s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 422s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 422s CUFF.60.1.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 422s ******************************************************************98 PP 422s 422s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 422s 422s Alignments for each domain: 422s == domain 1 score: 270.1 bits; conditional E-value: 7e-85 422s Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 422s mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ 422s CUFF.60.2.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 422s 9********************************************************************************************** PP 422s 422s Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 422s +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f 422s CUFF.60.2.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 422s ******************************************************************98 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (163 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 454.86 422s // 422s Query: Chitin_synth_1N [M=73] 422s Accession: PF08407.10 422s Description: Chitin synthase N-terminal 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 422s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 422s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 422s CUFF.60.1.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 422s 89***********************65..9******************************8779*********9 PP 422s 422s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 422s Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 422s k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT 422s CUFF.60.2.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 422s 89***********************65..9******************************8779*********9 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (73 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 422s # Mc/sec: 374.29 422s // 422s Query: Chitin_synth_2 [M=527] 422s Accession: PF03142.14 422s Description: Chitin synthase 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 422s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 422s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 422s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: -3.5 bits; conditional E-value: 0.33 422s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 422s + + +t y ede + +t+ s+ 422s CUFF.60.1.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 422s 3446999*****99999999986 PP 422s 422s == domain 2 score: -3.2 bits; conditional E-value: 0.27 422s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 422s G tki ++ ++++ai v++ i+++++ 422s CUFF.60.1.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 422s 38899999999999999999988887776 PP 422s 422s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 422s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 422s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 422s CUFF.60.1.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 422s 8899********************************9876543244222225789************************************9886 PP 422s 422s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 422s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 422s CUFF.60.1.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 422s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 422s 422s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 422s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 422s CUFF.60.1.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 422s 4445556778888887776522256665111344556666666666655555555 PP 422s 422s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 422s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 422s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 422s CUFF.60.1.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 422s 34558999*************************************************6 PP 422s 422s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 422s 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 422s 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 422s 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 422s 422s Alignments for each domain: 422s == domain 1 score: -3.5 bits; conditional E-value: 0.33 422s Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 422s + + +t y ede + +t+ s+ 422s CUFF.60.2.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 422s 3446999*****99999999986 PP 422s 422s == domain 2 score: -3.2 bits; conditional E-value: 0.27 422s Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 422s G tki ++ ++++ai v++ i+++++ 422s CUFF.60.2.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 422s 38899999999999999999988887776 PP 422s 422s == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 422s Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 422s e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ 422s CUFF.60.2.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 422s 8899********************************9876543244222225789************************************9886 PP 422s 422s Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 422s ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + 422s CUFF.60.2.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 422s 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP 422s 422s Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 422s r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + 422s CUFF.60.2.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 422s 4445556778888887776522256665111344556666666666655555555 PP 422s 422s == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 422s Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 422s ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG 422s CUFF.60.2.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 422s 34558999*************************************************6 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (527 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) 422s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 422s # Mc/sec: 338.22 422s // 422s Query: CO_dh [M=168] 422s Accession: PF02552.15 422s Description: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -1.3 0.0 0.091 8.6 18 41 .. 130 154 .. 125 156 .. 0.80 422s 2 ! 20.0 0.0 2.5e-08 2.4e-06 14 78 .. 194 257 .. 175 297 .. 0.74 422s 422s Alignments for each domain: 422s == domain 1 score: -1.3 bits; conditional E-value: 0.091 422s --EEE--SHHHHHHHHHS.SSEEEE CS 422s CO_dh 18 katleealkvvakmikka.krPlli 41 422s + ++ ++l+ +a +ik+a + P++i 422s CUFF.32.1.p1 130 QMEIAKKLTCAAVAIKRAeDAPVMI 154 422s 6788899999*******93468877 PP 422s 422s == domain 2 score: 20.0 bits; conditional E-value: 2.5e-08 422s XXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G. CS 422s CO_dh 14 anskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkd 78 422s s k +le+a +a++i+k ++P+l+ Gp+++ a e a++k + + + + +g + 422s CUFF.32.1.p1 194 EISDKESLEKATDIAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMP-AAKGFYS 257 422s 455677899999*******************************99887776654444.3555554 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (168 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 741.69 422s // 422s Query: CRCB [M=95] 422s Accession: PF02537.14 422s Description: CrcB-like protein, Camphor Resistance (CrcB) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 56.7 7.3 1.2e-19 1.2e-17 3 92 .. 8 118 .. 6 123 .. 0.83 422s 2 ? -2.4 0.1 0.33 32 44 56 .. 166 180 .. 143 183 .. 0.58 422s 3 ! 58.0 3.7 5e-20 4.8e-18 3 93 .. 190 296 .. 188 299 .. 0.86 422s 422s Alignments for each domain: 422s == domain 1 score: 56.7 bits; conditional E-value: 1.2e-19 422s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHH.. CS 422s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkal.. 77 422s +++++lG+l+R++l ++ln+ + g l+v ++G++++g++ + ++ttGf+G+lTTfS+++l++++ +++ + ++ + 422s CUFF.14.1.p1 8 FCIMSMLGTLARLGL-TALNTYpgapFSGLLWVQFVGCVIMGFCQTesvffprpkhnatfllAITTGFCGSLTTFSSWMLQMFTGMANLDPFERRgr 103 422s 6899***********.7677777997569**************99988887777777777666*********************8877665555566 PP 422s 422s HHHHHHHHHHHHHHH CS 422s CRCB 78 lyvllsvvlgllavv 92 422s y +lsvv +++++ 422s CUFF.14.1.p1 104 GYSFLSVVSDFMVTM 118 422s 999999998887665 PP 422s 422s == domain 2 score: -2.4 bits; conditional E-value: 0.33 422s H..HHTTTHHHHH-- CS 422s CRCB 44 a..llttGflGglTT 56 422s +++ f ++TT 422s CUFF.14.1.p1 166 IcfFVGAAFYTAYTT 180 422s 122455555555555 PP 422s 422s == domain 3 score: 58.0 bits; conditional E-value: 5e-20 422s HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHHHH CS 422s CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkally 79 422s ++++++ al+R++l++ ln+ p+gtl++Nv++++ll ++++ +++Gf+ l+T Stf++el+++ + +a +y 422s CUFF.14.1.p1 190 SLIFSPFAALTRLYLARFLNSPqyfiPYGTLCANVFATLLLSIMYMipqithctpvsrsvmyGIQNGFCAVLSTLSTFSNELHTMP----IKRAYIY 282 422s 689************9988888***999***************99977766666655555555*********************96....4458999 PP 422s 422s HHHHHHHHHHHHHH CS 422s CRCB 80 vllsvvlgllavvl 93 422s +++sv++++ ++v+ 422s CUFF.14.1.p1 283 CIISVAISFSICVI 296 422s 9****999987765 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (95 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 647.94 422s // 422s Query: CTP_transf_like [M=143] 422s Accession: PF01467.25 422s Description: Cytidylyltransferase-like 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 12.4 0.0 7.3e-06 0.00069 9 43 .. 33 66 .. 29 73 .. 0.88 422s 422s Alignments for each domain: 422s == domain 1 score: 12.4 bits; conditional E-value: 7.3e-06 422s --HHHHHHHHHHHHHSSESEEEEEESSTHCCST-S CS 422s CTP_transf_like 9 iHlGHlrlleqakklleedlivgvpsdeppkkkkk 43 422s +H GH l+++ak++ e+ ++v + ++ ++ + 422s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAEK-VVVSIFVNPMQFNNPQ 66 422s 7*****************.9999999988887754 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (143 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 1109.48 422s // 422s Query: Dak1 [M=307] 422s Accession: PF02733.16 422s Description: Dak1 domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 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- 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 359.4 0.4 1.3e-111 6.1e-110 2 304 .. 75 396 .. 74 399 .. 0.92 422s 422s Alignments for each domain: 422s == domain 1 score: 359.4 bits; conditional E-value: 1.3e-111 422s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 422s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 422s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 422s CUFF.19.1.p1 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 422s 899*****************94444666779****************************************************************** PP 422s 422s HHHHHHHHHHHHTT--EEEEEE--B-SSS.SSTTCSSSB--THHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTEEEEEEEEE--B-TTTSSBSS-- CS 422s Dak1 95 lnfglAaekakaegikvetvvvdDDvave.dseekagrRGvagtvlveKiaGaaaeegasLeevaelaekvnenlrsigvalsactvpgagkpsfel 190 422s ++fglAae+aka g++ve v v+DDv+v+ +++ +grRG+++tvlv+KiaG aa+ g +L++va++a++v++n ++i+++l++c vpg++ +++ l 422s CUFF.19.1.p1 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGkKRGALVGRRGLGATVLVHKIAGSAAALGLDLHQVAQVAQSVIDNAATIAASLDHCAVPGRKFETN-L 267 422s ****************************9799999********************************************************8886.* PP 422s 422s -TTEEEETE-TTS---SEEEE.---HHHHHHHHHHHHHH............TT-EEEEEEEE-BSS-HHHHHHHHHHHHHHHHHTT-EEEEEEEESS CS 422s Dak1 191 eedemelGvGiHgEpGverek.lksadelveelleklled...........kgdevvllvnglGgtsllelyivarevaelleekgikvvrvlvGey 275 422s ++de+e+G+GiH+EpG+ +++ l s+ elv+e+l+ l+ + ++d+v+llvn++Gg+s+lel ++ v e+l+++gi ++r+++G++ 422s CUFF.19.1.p1 268 GPDEYEIGMGIHNEPGTFKSSpLPSIPELVTEMLSILFGEknpdnsfvefsSKDDVILLVNNMGGMSNLELGYATEVVSEQLAKRGIIPKRTMSGTF 364 422s ****************977651566789**********64356666666655********************************************* PP 422s 422s S--TTBEEEEEEEEEE-...HHHHHHHHS-EE CS 422s Dak1 276 vTsldmaGfsitllkld...dellelldapve 304 422s vT+l+++Gf itl++++ ++ +++d p++ 422s CUFF.19.1.p1 365 VTALNGPGFGITLVNASkatPDIFKYFDLPTT 396 422s ***************98444566667776665 PP 422s 422s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 170.8 1.0 3.5e-54 1.7e-52 2 125 .. 75 202 .. 74 204 .] 0.95 422s 422s Alignments for each domain: 422s == domain 1 score: 170.8 bits; conditional E-value: 3.5e-54 422s HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS 422s Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 422s Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ 422s CUFF.20.1.p2 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 422s 899*****************94444666779****************************************************************** PP 422s 422s HHHHHHHHHHHHTT--EEEEEE--B-SSSSS CS 422s Dak1 95 lnfglAaekakaegikvetvvvdDDvaveds 125 422s ++fglAae+aka g++ve v v+DDv+v+++ 422s CUFF.20.1.p2 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGKK 202 422s ****************************876 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (307 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 2 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 588.66 422s // 422s Query: Dak2 [M=174] 422s Accession: PF02734.16 422s Description: DAK2 domain 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -2.4 0.0 0.22 21 70 88 .. 437 455 .. 422 460 .. 0.64 422s 2 ! 146.1 2.0 5.2e-47 4.9e-45 2 173 .. 467 642 .. 466 643 .. 0.96 422s 422s Alignments for each domain: 422s == domain 1 score: -2.4 bits; conditional E-value: 0.22 422s TT---HHHHHHHHHHHHHH CS 422s Dak2 70 ldaedlaaalkaaleaiqa 88 422s +d + + ++lkaa++ai++ 422s CUFF.19.1.p1 437 ADPKMFTKILKAAVDAINE 455 422s 5666677777777777765 PP 422s 422s == domain 2 score: 146.1 bits; conditional E-value: 5.2e-47 422s TS-S-HHHHHHHHHHHHHHHHHC-..--SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.......TT---HHHHHHHHHHHHHHHH---T CS 422s Dak2 2 vGDGDtGtnmargaeavlkaleel..eeaslaevlkalakallsgagGtsGvlysqflralakalke..keeldaedlaaalkaaleaiqavgkarp 94 422s +GDGD+Gt++ +g ea++ka++++ + ++ + +++la ++++++gGtsG lys++l+alak ++e +el++ ++a a k al+a+ ++++ar+ 422s CUFF.19.1.p1 467 AGDGDCGTTLVNGGEAITKAINDKsiRLDDGVNGIDDLAYIVEDSMGGTSGGLYSIYLSALAKGVHEsgDSELSVHTFAFASKYALDALFKYTRARK 563 422s 8***********************9****************************************8865777************************* PP 422s 422s TSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSGGGGGGGGGTT.......S--HHHHHHHHHHHHHH CS 422s Dak2 95 gdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgrAsylgerslg.......vvDpGAvglalileala 173 422s g +T++D+++p+ve+l++ k l++aakaa++g e+T+++ a++grAsy+++++l+ +DpGA +la+il+a++ 422s CUFF.19.1.p1 564 GFRTLIDAIQPFVETLNEGKG-------LDAAAKAATEGSEQTRKMDAVVGRASYVAKEELHkldseggLPDPGAFALAAILNAIV 642 422s ******************999.......*******************************9966999999**************997 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (174 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 803.81 422s // 422s Query: DJ-1_PfpI [M=165] 422s Accession: PF01965.23 422s Description: DJ-1/PfpI family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 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(-) 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 49.0 0.0 9.5e-17 3e-15 12 125 .. 30 168 .. 26 239 .. 0.74 422s 422s Alignments for each domain: 422s == domain 1 score: 49.0 bits; conditional E-value: 9.5e-17 422s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 422s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 422s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 422s CUFF.46.1.p1 30 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 126 422s 5579**************************955554433134444444444444666666667777******************************* PP 422s 422s HHHHHHTT-EEEEETTTHHHHHHTT...TTTTSEE--SGGGH CS 422s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag...vlkgrrvTsypavk 125 422s ++e++++g+++ a+C+gp+lLa+ + ++g++v ++ v+ 422s CUFF.46.1.p1 127 AREVFTNGGVLSAVCHGPVLLANVKnpqSVEGKTVVYHKHVT 168 422s **********************87512245555554444443 PP 422s 422s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 48.4 0.0 1.4e-16 4.5e-15 12 111 .. 51 172 .. 47 198 .. 0.78 422s 422s Alignments for each domain: 422s == domain 1 score: 48.4 bits; conditional E-value: 1.4e-16 422s EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS 422s DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 422s El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ 422s CUFF.47.1.p1 51 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 147 422s 5579**************************955554433134444444444444666666667777******************************* PP 422s 422s HHHHHHTT-EEEEETTTHHHHHHTT CS 422s DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag 111 422s ++e++++g+++ a+C+gp+lLa+ + 422s CUFF.47.1.p1 148 AREVFTNGGVLSAVCHGPVLLANVK 172 422s *********************9865 PP 422s 422s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 31.6 0.0 2.1e-11 6.7e-10 52 161 .. 75 215 .. 15 219 .. 0.78 422s 422s Alignments for each domain: 422s == domain 1 score: 31.6 bits; conditional E-value: 2.1e-11 422s EEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH......HHTTTTTTSEE--SGGGH.HHH............. CS 422s DJ-1_PfpI 52 aslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL......aaagvlkgrrvTsypavk.dkl............. 128 422s + +d++ ++y + GG+ ++ + + + + + ++ g+++aa+C+gp++L +++kg++vT++ + +++ 422s CUFF.42.1.p2 75 KNASDINFSDYSIFFAAGGHGTLFDFPSATNLHKGAAKIYSMGGVIAAVCHGPVILpcikdsTGFSIVKGKTVTAFNEIAeQQMnlmptfekyhfkt 171 422s 445699***************9999999999999999****************99955332223469***********995556999*9*9999999 PP 422s 422s .....HHTTSEE-SS......SEEEETTEEEESSGGGHHHHHHH CS 422s DJ-1_PfpI 129 .....ekagakyvdk......rvvvdgnlvTsrgpgaaiefale 161 422s ++ag+++vd v +dg+lvT ++p +a a++ 422s CUFF.42.1.p2 172 lnklfQEAGSNFVDPqepfddFVKTDGKLVTGANPASAASTAKA 215 422s 9999999999999999***977889*********9998776665 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (165 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 422s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 422s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 3 [number of targets reported over threshold] 422s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 422s # Mc/sec: 153.37 422s // 422s Query: DLH [M=217] 422s Accession: PF01738.17 422s Description: Dienelactone hydrolase family 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-771(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 35.2 0.0 5e-13 4.8e-11 3 215 .. 41 254 .. 39 256 .. 0.72 422s 422s Alignments for each domain: 422s == domain 1 score: 35.2 bits; conditional E-value: 5e-13 422s DLH 3 aylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa........ldpndeaeaaraldelvskvaeekvlddlkaavaylks 91 422s +y ++ ++ k v + + ++fG+ ++ik+ +++la+ + +Pd++ ++ + + e+++a ++ ++k ++ +l ++ ++ 422s CUFF.18.1.p1 41 TYFTGKRSS-KVVLIGFMDVFGLSKQIKEGADQLANHELAIYLPDFLNGETasiemidpK----TIEQKEARSKFMEKISSPLHWPKLTKVIEDIER 132 422s 555566666.4455559**********************************898863332....333344444555555555566677777888888 PP 422s 422s DLH 92 vpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188 422s ++ k+g+ GfC+G+++ + + ++ ++ + ++ s+ ++ +a+++ +p+ +l + + + d+ +k e+ + + ++ + H+ 422s CUFF.18.1.p1 133 IH-GQDVKIGAYGFCWGAKVLITYPNKE-RFLRIGCAHP-SLLDPV-DAKHVHCPVCFLCSKDEDPEEVDAWKKSFENS-PYFSESYFETFGKMHHG 224 422s 88.44589****************9999.5667777899.555555.578999***99998766665555544433333.46677778888888888 PP 422s 422s DLH 189 Fandsre...syneeaaedawervlelfkq 215 422s ++++++ +n + +++ +l++fk+ 422s CUFF.18.1.p1 225 WMAARANlsdPENRKYFDLGYQIFLKFFKE 254 422s 888888766677777777778888888776 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (217 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 959.55 422s // 422s Query: DsrD [M=64] 422s Accession: PF08679.10 422s Description: Dissimilatory sulfite reductase D (DsrD) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -4.1 0.0 1 95 21 33 .. 102 114 .. 97 116 .. 0.82 422s 2 ! 10.9 0.0 2.4e-05 0.0023 2 58 .. 132 188 .. 131 192 .. 0.80 422s 422s Alignments for each domain: 422s == domain 1 score: -4.1 bits; conditional E-value: 1 422s HHHHHH-TTS-HH CS 422s DsrD 21 kDlekalPdakpr 33 422s kDl k++ d ++r 422s CUFF.17.1.p1 102 KDLIKIFGDLSSR 114 422s 7999999888877 PP 422s 422s == domain 2 score: 10.9 bits; conditional E-value: 2.4e-05 422s HHHHHHHHSSCCCSS-EEHH..HHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETTEEE CS 422s DsrD 2 kkaiveflekkkkKskfYfk..DlekalPdakpreiKkvvneLVnegkLeywSsGSTtm 58 422s +k+i + +e + k+ Y+ +++ +P +++ e+ +++n+ V+ gk+ y G +tm 422s CUFF.17.1.p1 132 RKHIFDAVEDSVKRLGTYIDvlQIHRYDPHVSAEEVMRALNDVVESGKVRYI--GASTM 188 422s 578899999999877788762245567***********************95..66666 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (64 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 591.09 422s // 422s Query: DUF1129 [M=206] 422s Accession: PF06570.10 422s Description: Protein of unknown function (DUF1129) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 9.5 0.7 3.4e-05 0.0033 88 189 .. 128 229 .. 124 236 .. 0.73 422s 2 ? -1.5 0.0 0.083 7.9 119 133 .. 451 465 .. 423 478 .. 0.59 422s 422s Alignments for each domain: 422s == domain 1 score: 9.5 bits; conditional E-value: 3.4e-05 422s DUF1129 88 llalfallfgilalfskkkqtasiGlitl.llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvl 183 422s +la++++ ++ lfs ++++ Gli+ l+++l+ G+++ ++ +lt + +k++ + + +l+++++l ++ lf+ + + N ++++ 422s CUFF.45.1.p2 128 MLAFISFAWSMTVLFSG-FMSSYGGLIATrLILGLLEGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEQVHAGNKEGWQWIY 223 422s 67778888889999998.777787988543899****************997788877777777777777777666665544444555555555555 PP 422s 422s DUF1129 184 iiigvi 189 422s i+ g + 422s CUFF.45.1.p2 224 IVEGLV 229 422s 555555 PP 422s 422s == domain 2 score: -1.5 bits; conditional E-value: 0.083 422s DUF1129 119 valvgGlamvlvyrl 133 422s + +vgGla+v++ 422s CUFF.45.1.p2 451 CVIVGGLAYVVMFFS 465 422s 345555555554332 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (206 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 865.91 422s // 422s Query: DUF1989 [M=167] 422s Accession: PF09347.9 422s Description: Domain of unknown function (DUF1989) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 186.1 0.0 2.1e-59 2e-57 2 167 .] 58 231 .. 57 231 .. 0.98 422s 422s Alignments for each domain: 422s == domain 1 score: 186.1 bits; conditional E-value: 2.1e-59 422s DUF1989 2 tiparsgravevkaGqvlriidleGnqvvdllafnaddprerlsaadTrklqesahlttgdrlysnl..grplltiveDtv.........gvHDtlg 87 422s ++++r+g av++++ +++ i+ +eG+qv+dl+++n ++prer++aa+Tr+++ sah++t+drl+s+l rpl+ti+ D++ +vHDtlg 422s CUFF.34.1.p1 58 VCQPRTGLAVKIPQKSIFSIVVPEGPQVCDLNIWNFHNPRERFWAARTRQIH-SAHVSTYDRLWSTLpyLRPLVTIIGDSLqarhdewggRVHDTLG 153 422s 6899************************************************.************************************99****** PP 422s 422s DUF1989 88 gacdpevnellygegkeyhrnCrdnllralakyglterdvpdvlNlFmnvgvdedgrlfmeespskpGdyvelraemDll 167 422s ++cdp++ +l + gk+++ +C++nl+ra+ yglte+dv+dvlN+F+++g++e +++fme++p++ dy++++ae+Dll 422s CUFF.34.1.p1 154 TRCDPYIDKLIS--GKDNDLHCHSNLTRAIMPYGLTEFDVHDVLNVFQVTGLNEYDQYFMETCPATSKDYFQCFAEQDLL 231 422s *********999..678*************99**********************************************97 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (167 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 964.29 422s // 422s Query: DUF2157 [M=147] 422s Accession: PF09925.8 422s Description: Predicted membrane protein (DUF2157) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s ------ inclusion threshold ------ 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ? -0.5 0.2 0.055 5.2 109 109 .. 75 75 .. 10 128 .. 0.54 422s 2 ? 10.0 3.5 3.1e-05 0.0029 34 120 .. 156 243 .. 142 265 .. 0.89 422s 422s Alignments for each domain: 422s == domain 1 score: -0.5 bits; conditional E-value: 0.055 422s DUF2157 109 a 109 422s + 422s CUFF.14.1.p1 75 C 75 422s 1 PP 422s 422s == domain 2 score: 10.0 bits; conditional E-value: 3.1e-05 422s DUF2157 34 fleallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifqls 120 422s +++ll+l ++++ +G + A+ + +r + f l+++++++ l a++++ ++ + g + + + a+ll+ + ++ qi + + 422s CUFF.14.1.p1 156 VVRVLLLLLSICFFVGAAFYTAYTTNVTHRGIGFSLIFSPFAALTRLYlARFLNSPQYFIPYGTLCANVFATLLLSIMYMIPQITHCT 243 422s 489999999***********************************99999***99999999999999999999********99997766 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (147 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 422s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 410.65 422s // 422s Query: DUF2868 [M=328] 422s Accession: PF11067.7 422s Description: Protein of unknown function (DUF2868) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 11.1 0.3 1.1e-05 0.001 47 74 .. 97 123 .. 92 126 .. 0.94 422s 422s Alignments for each domain: 422s == domain 1 score: 11.1 bits; conditional E-value: 1.1e-05 422s DUF2868 47 fllGalltlllllatrdlaFgWetTLnl 74 422s +llGa++ l + ++r+l++gW+ TL l 422s CUFF.9.1.p1 97 LLLGAIFPLFAESLFRRLNYGWGCTL-L 123 422s 689***********************.6 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (328 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 422s # Mc/sec: 924.97 422s // 422s Query: DUF2976 [M=88] 422s Accession: PF11190.7 422s Description: Protein of unknown function (DUF2976) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 12.3 0.1 6.1e-06 0.00058 28 76 .. 120 168 .. 107 177 .. 0.90 422s 2 ! 2.3 0.1 0.0082 0.78 39 77 .. 307 348 .. 282 351 .. 0.68 422s 3 ? -1.6 0.1 0.13 13 58 75 .. 404 421 .. 371 425 .. 0.73 422s 422s Alignments for each domain: 422s == domain 1 score: 12.3 bits; conditional E-value: 6.1e-06 422s DUF2976 28 villgLvlaavaflaVakaalkkfnevregkaewgkfgltlvvGvvllv 76 422s ++ L +a++ + V+k +l kf+++ + +++ + l+ v+G++++ 422s CUFF.25.1.p1 120 SMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIGFIVVA 168 422s 678889999*************************************996 PP 422s 422s == domain 2 score: 2.3 bits; conditional E-value: 0.0082 422s DUF2976 39 aflaVaka.alkkfnevregkaewg..kfgltlvvGvvllvv 77 422s +l V ++ +l f+ + k+ w ++++++vvG v+l++ 422s CUFF.25.1.p1 307 ILLGVGWSiLLLPFSLTSYAKNGWKnpSMIAMMVVGGVILIA 348 422s 445555441345677777778888733588888999988876 PP 422s 422s == domain 3 score: -1.6 bits; conditional E-value: 0.13 422s DUF2976 58 kaewgkfgltlvvGvvll 75 422s +w+ f t+ ++ ++ 422s CUFF.25.1.p1 404 YRDWTYFNNTMTIALCVF 421 422s 567888888888888775 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (88 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 422s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 422s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 422s # Mc/sec: 486.94 422s // 422s Query: DUF2997 [M=47] 422s Accession: PF11211.7 422s Description: Protein of unknown function (DUF2997) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(+ 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 11.5 0.0 1.1e-05 0.0011 10 25 .. 83 98 .. 83 103 .. 0.91 422s 422s Alignments for each domain: 422s == domain 1 score: 11.5 bits; conditional E-value: 1.1e-05 422s DUF2997 10 rVeeeveGikGksCle 25 422s +V+ +ve+i+GksCl+ 422s CUFF.54.1.p1 83 KVKLRVEDIQGKSCLT 98 422s 79************96 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (47 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 578.20 422s // 422s Query: DUF3288 [M=89] 422s Accession: PF11691.7 422s Description: Protein of unknown function (DUF3288) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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(-) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 14.6 0.0 1.4e-06 0.00013 17 62 .. 72 117 .. 68 119 .. 0.90 422s 422s Alignments for each domain: 422s == domain 1 score: 14.6 bits; conditional E-value: 1.4e-06 422s DUF3288 17 LlaeepedenlaelArLliRYegFpGardiqkdldkvlkkWqltee 62 422s L++++++ +l e++r l+R +F G +++++ l+ l +W+++++ 422s CUFF.32.1.p3 72 LIEGSANLLSLEEISRTLLRILDFVGNKNMRTYLEVPLCRWHISQA 117 422s 55667777899********************************986 PP 422s 422s 422s 422s Internal pipeline statistics summary: 422s ------------------------------------- 422s Query model(s): 1 (89 nodes) 422s Target sequences: 95 (31269 residues searched) 422s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 422s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 422s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 422s Initial search space (Z): 95 [actual number of targets] 422s Domain search space (domZ): 1 [number of targets reported over threshold] 422s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 422s # Mc/sec: 894.38 422s // 422s Query: DUF4208 [M=96] 422s Accession: PF13907.5 422s Description: Domain of unknown function (DUF4208) 422s Scores for complete sequences (score includes all domains): 422s --- full sequence --- --- best 1 domain --- -#dom- 422s E-value score bias E-value score bias exp N Sequence Description 422s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 422s 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( 422s 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(+) 422s 422s 422s Domain annotation for each sequence (and alignments): 422s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 422s 422s Alignments for each domain: 422s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 422s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 422s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 422s CUFF.48.1.p3 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 422s 5567899**************99877***********999855576 PP 422s 422s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 422s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 422s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 422s 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 422s 422s Alignments for each domain: 422s == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 422s DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 422s ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp 422s CUFF.49.1.p2 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 422s 5567899**************99877***********999855576 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (96 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 678.65 423s // 423s Query: DUF705 [M=304] 423s Accession: PF05152.11 423s Description: Protein of unknown function (DUF705) 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.6 0.0 8e-06 0.00076 225 270 .. 70 116 .. 58 152 .. 0.73 423s 423s Alignments for each domain: 423s == domain 1 score: 11.6 bits; conditional E-value: 8e-06 423s DUF705 225 vlditnskrl..PksvkvvlkyLsdknleffksitLvDDladnninYD 270 423s + + n+++l Pks ++v+ sd n+ f+s L DD ++n i+Y 423s CUFF.52.1.p2 70 YTATVNHEDLnePKSHEIVMLLASDGNVGSFESN-LLDDCFKNRIEYA 116 423s 555566665333********************95.78*******9874 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (304 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 1244.64 423s // 423s Query: DUF999 [M=143] 423s Accession: PF06198.10 423s Description: Protein of unknown function (DUF999) 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+) 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 305.5 5.8 5e-96 2.4e-94 1 143 [] 21 163 .. 21 163 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 305.5 bits; conditional E-value: 5e-96 423s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 423s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyypdgristrs++rw+lliiwsiiiv 423s CUFF.5.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPDGRISTRSNFRWPLLIIWSIIIV 118 423s 9************************************************************************************************* PP 423s 423s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 423s +a+dkkfev++flsiwinenrfyseiw+piaiyvcllvl+ll+li 423s CUFF.5.1.p1 119 FAVDKKFEVQKFLSIWINENRFYSEIWVPIAIYVCLLVLMLLSLI 163 423s ******************************************996 PP 423s 423s >> CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 293.2 4.2 3.2e-92 1.5e-90 1 143 [] 21 163 .. 21 163 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 293.2 bits; conditional E-value: 3.2e-92 423s DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 423s mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyyp+grist++k+rwvlliiwsii++ 423s CUFF.3.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPNGRISTQDKSRWVLLIIWSIITI 118 423s 9************************************************************************************************* PP 423s 423s DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 423s l+idkkf++ke++++wi+en+++seiwgpi+iyv+l++lll+a++ 423s CUFF.3.1.p1 119 LTIDKKFKIKESYLEWIGENQSHSEIWGPIVIYVGLFILLLSAFN 163 423s ******************************************985 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (143 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 683.85 423s // 423s Query: FAD_syn [M=158] 423s Accession: PF06574.11 423s Description: FAD synthetase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 12.2 0.0 6.8e-06 0.00065 18 82 .. 33 92 .. 22 109 .. 0.84 423s 2 ? -1.4 0.0 0.1 9.9 112 145 .. 141 174 .. 125 188 .. 0.77 423s 423s Alignments for each domain: 423s == domain 1 score: 12.2 bits; conditional E-value: 6.8e-06 423s FAD_syn 18 vHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlv 82 423s +H GH +l+++a+++a+ ++vv +F + P+++ ++++ t+++ ++l++lgvd v+ 423s CUFF.50.1.p2 33 LHEGHFSLVREAKRHAE----KVVVSIFVN-PMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYA 92 423s 7*******999998884....577888865.99999988888888899999**********9986 PP 423s 423s == domain 2 score: -1.4 bits; conditional E-value: 0.1 423s FAD_syn 112 vvGfdfrfGkkregdvellkelgaklgfevevvp 145 423s v + +fG+k +v+ +k++ + l+f +e+++ 423s CUFF.50.1.p2 141 VNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQ 174 423s 5555568999999999999999999997776654 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (158 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 655.20 423s // 423s Query: Fe-ADH [M=364] 423s Accession: PF00465.18 423s Description: Iron-containing alcohol dehydrogenase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 415.6 1.9 8e-129 7.6e-127 1 364 [] 52 414 .. 52 414 .. 0.96 423s 423s Alignments for each domain: 423s == domain 1 score: 415.6 bits; conditional E-value: 8e-129 423s -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHH CS 423s Fe-ADH 1 PtrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtA 97 423s P+ +fgkg+l+e ++ +k g+k+ livtd+g++ k gl+dkv++ lee+ i+v+++dgv+pnpt+ +v+++++++++e++d +++GGGs++D+A 423s CUFF.50.1.p1 52 PSFNLFGKGCLAEAAKQIKMSGFKNTLIVTDPGII-KVGLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCA 147 423s 56678****************************99.************************************************************* PP 423s 423s HHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHH CS 423s Fe-ADH 98 Kaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahal 193 423s K+iall++n++ ++dy+g++k+ k++lpliai TtaGt+se+t++a+it e ++ k++i d++++P l++ Dpe +++lP+++taatg+Dal+ha+ 423s CUFF.50.1.p1 148 KGIALLATNGGkIADYEGVDKS-SKPQLPLIAINTTAGTASEMTRFAIITEETRHIKMAIIDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAV 243 423s *********956*****99987.8999***********************99999****************************************** PP 423s 423s HHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH........ CS 423s Fe-ADH 194 EayvskkanplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaa. 289 423s 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 ++ 423s CUFF.50.1.p1 244 EAYVSTAANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFYGIPHGVCNAVLLAHVQKFNSRDPr 340 423s ***********************************************************************99********************5554 PP 423s 423s ....HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHHH CS 423s Fe-ADH 290 p.erlaqlaralggesdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkdrslannpreltaedv 364 423s + +rl ++a lg +e ae++++++ +l+ e+++ +L +lgv+e+d+d l+++a+kd + a+np ++t+++v 423s CUFF.50.1.p1 341 AnARLGDIAFHLGC--EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKDFDVLVDHAMKDACGATNPIQPTHDEV 414 423s 44888888888864..699*****************************************************9986 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (364 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 423s # Mc/sec: 718.99 423s // 423s Query: Fe-ADH_2 [M=250] 423s Accession: PF13685.5 423s Description: Iron-containing alcohol dehydrogenase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 65.9 2.6 2.4e-22 2.3e-20 2 245 .. 57 320 .. 56 323 .. 0.89 423s 2 ? -3.6 0.0 0.4 38 27 60 .. 355 388 .. 350 399 .. 0.70 423s 423s Alignments for each domain: 423s == domain 1 score: 65.9 bits; conditional E-value: 2.4e-22 423s Fe-ADH_2 2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvs.. 95 423s +g+g l + ++ +k ++k+ l+v+d ++ k+ + +kv+ l+e+ i+v++++ v++++++ +v++ +e ++++++d +v++GgG+++D ak ++ 423s CUFF.50.1.p1 57 FGKGCLAEAAKQIKMSGFKNTLIVTDPGIIKVgLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCAKGIAll 153 423s 57899999********************9999899*********************************************************98622 PP 423s 423s Fe-ADH_2 96 ................aklnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkl 173 423s +k ++p++++ T+a + +a ++++ + k + k ++P+ + D + + P +l+a+ D+l + + + + 423s CUFF.50.1.p1 154 atnggkiadyegvdksSKPQLPLIAINTTAGTASEMTRFAIITEEtrHIKMAIiDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAVEAYVSTA 250 423s 222222222222222256689*********9999999999999887788888888999*************************************** PP 423s 423s Fe-ADH_2 174 anevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalH 245 423s an +++ a + ++ v + ++++v+++k++ea +++ a l+g+++ ++ G H ++H l + H 423s CUFF.50.1.p1 251 ANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFY--GIPH 320 423s ************************************************************997666..5555 PP 423s 423s == domain 2 score: -3.6 bits; conditional E-value: 0.4 423s Fe-ADH_2 27 dentkkaagekveeslkeagikvevveeveeead 60 423s +e+t +aa +++++ + e +i++++v+ +e+d 423s CUFF.50.1.p1 355 EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKD 388 423s 5778888888888888888888887765555554 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (250 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 423s # Mc/sec: 271.00 423s // 423s Query: Fig1 [M=188] 423s Accession: PF12351.7 423s Description: Ca2+ regulator and membrane fusion protein Fig1 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.4 0.1 1.2e-05 0.0012 73 147 .. 7 79 .. 2 95 .. 0.75 423s 423s Alignments for each domain: 423s == domain 1 score: 11.4 bits; conditional E-value: 1.2e-05 423s Fig1 73 sdnvvhpyllmvaiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalwqhvassaastl 147 423s ++++ +l+m a+++++ f + lyf +ei ++ fk a++ ++v+s ++l+ + ++l++ ++ + l 423s CUFF.52.1.p2 7 KNTLTKRKLIMLALAIVFTFFAFGLYFIPHDEISVFDFKLPALQYETTVTSLDNFLIGGSTTLYTATVN--HEDL 79 423s 5566677899999999999999999998899**********7777777777777888777777765543..3555 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (188 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 1130.09 423s // 423s Query: Flavodoxin_2 [M=198] 423s Accession: PF02525.16 423s Description: Flavodoxin-like fold 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 423s 423s Alignments for each domain: 423s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 423s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 423s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 423s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 423s CUFF.48.1.p3 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 423s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 423s 423s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 423s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 423s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 423s CUFF.48.1.p3 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 423s **************999999****97777778878888899******************999999****************************9644 PP 423s 423s CCCHHHHHHHHHH CS 423s Flavodoxin_2 180 gaedeealaeale 192 423s +++ ++ a+ 423s CUFF.48.1.p3 173 NPK----VDIAVC 181 423s 443....444444 PP 423s 423s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 423s 423s Alignments for each domain: 423s == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 423s -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS 423s Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 423s mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ 423s CUFF.49.1.p2 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 423s 9***********6.666999999999999988777899999999995....................8899***.********************** PP 423s 423s HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS 423s Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 423s +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v 423s CUFF.49.1.p2 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 423s **************999999****97777778878888899******************999999****************************9644 PP 423s 423s CCCHHHHHHHHHH CS 423s Flavodoxin_2 180 gaedeealaeale 192 423s +++ ++ a+ 423s CUFF.49.1.p2 173 NPK----VDIAVC 181 423s 443....444444 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (198 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 703.85 423s // 423s Query: FMN_red [M=155] 423s Accession: PF03358.14 423s Description: NADPH-dependent FMN reductase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 423s 423s Alignments for each domain: 423s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 423s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 423s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 423s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 423s CUFF.48.1.p3 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 423s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 423s 423s HCH CS 423s FMN_red 96 Drl 98 423s D + 423s CUFF.48.1.p3 82 DEV 84 423s 976 PP 423s 423s >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 423s 423s Alignments for each domain: 423s == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 423s -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS 423s FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 423s mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + 423s CUFF.49.1.p2 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 423s 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP 423s 423s HCH CS 423s FMN_red 96 Drl 98 423s D + 423s CUFF.49.1.p2 82 DEV 84 423s 976 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (155 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 423s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 423s # Mc/sec: 229.72 423s // 423s Query: FPP [M=866] 423s Accession: PF05911.10 423s Description: Filament-like plant protein, long coiled-coil 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 9.9 0.1 2.1e-05 0.00099 518 597 .. 171 250 .. 146 265 .. 0.76 423s 423s Alignments for each domain: 423s == domain 1 score: 9.9 bits; conditional E-value: 2.1e-05 423s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 423s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 423s CUFF.60.1.p2 171 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 250 423s 333333333333333334444455778999************************9*******************999985 PP 423s 423s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 9.6 0.1 2.7e-05 0.0013 518 597 .. 222 301 .. 197 316 .. 0.76 423s 423s Alignments for each domain: 423s == domain 1 score: 9.6 bits; conditional E-value: 2.7e-05 423s FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 423s + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ 423s CUFF.60.2.p2 222 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 301 423s 333333333333333334444455778999************************9*******************999985 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (866 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 423s # Mc/sec: 724.18 423s // 423s Query: FR47 [M=86] 423s Accession: PF08445.9 423s Description: FR47-like protein 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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- 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 18.3 0.0 1.9e-07 9e-06 18 81 .. 70 133 .. 53 137 .. 0.85 423s 423s Alignments for each domain: 423s == domain 1 score: 18.3 bits; conditional E-value: 1.9e-07 423s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 423s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 423s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 423s CUFF.34.1.p2 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 423s 455578********************999999899999999999999*************9975 PP 423s 423s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 18.2 0.0 2.1e-07 9.8e-06 18 81 .. 70 133 .. 53 137 .. 0.85 423s 423s Alignments for each domain: 423s == domain 1 score: 18.2 bits; conditional E-value: 2.1e-07 423s E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS 423s FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 423s +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k 423s CUFF.35.1.p1 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 423s 455578********************999999899999999999999*************9975 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (86 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 784.03 423s // 423s Query: Fungal_trans [M=267] 423s Accession: PF04082.17 423s Description: Fungal specific transcription factor domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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(+ 423s 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( 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 423s 423s Alignments for each domain: 423s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 423s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 423s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 423s CUFF.40.1.p2 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 423s 799*********************.*****************************9998444444....66....******..*************** PP 423s 423s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 423s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 423s CUFF.40.1.p2 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 423s ****************************************999**********************************99********9999997776 PP 423s 423s Fungal_trans 191 dlwesddase 200 423s ++e +++ 423s CUFF.40.1.p2 303 -VNEYRVNNA 311 423s .777766665 PP 423s 423s >> CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 423s 423s Alignments for each domain: 423s == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 423s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 423s l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L 423s CUFF.41.1.p1 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 423s 799*********************.*****************************9998444444....66....******..*************** PP 423s 423s Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 423s l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d 423s CUFF.41.1.p1 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 423s ****************************************999**********************************99********9999997776 PP 423s 423s Fungal_trans 191 dlwesddase 200 423s ++e +++ 423s CUFF.41.1.p1 303 -VNEYRVNNA 311 423s .777766665 PP 423s 423s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 87.3 5.9 1.9e-28 4.5e-27 3 234 .. 203 429 .. 201 459 .. 0.81 423s 2 ? 1.2 0.0 0.035 0.82 1 23 [. 471 492 .. 471 504 .. 0.87 423s 423s Alignments for each domain: 423s == domain 1 score: 87.3 bits; conditional E-value: 1.9e-28 423s Fungal_trans 3 rffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLll 99 423s ++f++++ ++p + +++f+++++ ++++ l+ +l+ ++ +++ + s++ ++s ++ ++ df+ +s + +q+L 423s CUFF.38.1.p1 203 SYFQHVNWWWPTFVYNDFMYEFERLYAFGFHSNNAWLISFYSILALSSIRKRLGNSKTLAESLF------STAWVFVQKSDFFLTPS-IDKVQALIV 292 423s 8999999999999999999999666666666677777766777777778888887766666643......34777666667777777.********* PP 423s 423s Fungal_trans 100 lelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddlwesd 196 423s + y +s+ +l+ ++g a+ +a++l Lhr++s +e+ aes++R++w++++lDk i+l++G p+ ++d +i+++LP++ +l + 423s CUFF.38.1.p1 293 MTQYAAYLSSSSLCRTLCGQACLMAQQLNLHRKQSTDV------EPEK-AESWKRIFWMCYILDKNISLIFGTPSVFNDKDIDCNLPDSKYELLFGV 382 423s **********************************9988......7777.**************************99**********9998887777 PP 423s 423s Fungal_trans 197 daseetlvetk.........lsneeksrkiasfllaLkkilskiags 234 423s + + + n+ s+k ++++ a ki+ i+ + 423s CUFF.38.1.p1 383 QSGGDLIFVPTvsltiiqseIRNRLYSVKSPTQMAAREKIIIPIHQK 429 423s 77666666544667777777777777777777777766666666554 PP 423s 423s == domain 2 score: 1.2 bits; conditional E-value: 0.035 423s Fungal_trans 1 ldrffsnfhpqfpilhkpsflpk 23 423s ++++fs+++ ++ ilh+ps +++ 423s CUFF.38.1.p1 471 MEVYFSYLNTLI-ILHRPSSSTE 492 423s 679******998.****997665 PP 423s 423s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 36.9 4.7 4.3e-13 1e-11 4 197 .. 151 329 .. 148 351 .. 0.75 423s 423s Alignments for each domain: 423s == domain 1 score: 36.9 bits; conditional E-value: 4.3e-13 423s Fungal_trans 4 ffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLlll 100 423s +f++fhp fp++h+ sf+++ + +l+++a+l++G + s + + s ++ + l + +++ w+ qs ll+ 423s CUFF.45.1.p1 151 YFEWFHPVFPFIHQASFNSEN-----VAASFLRSLVVIACLCTGIESDFSMALLFWDSGFHVL---------QLYL--QGDPERVKKAWVFQSRLLF 231 423s *********************.....4444444444555555555555555555544444433.........3333..3566667779********* PP 423s 423s Fungal_trans 101 elyektssdralher.....hhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddl 192 423s ++ ++ + ++ ++ v+ +r+ g + +v+ ++ + ++ e+ rR ++ ++l+ ++al+++ pp l+ ++++pLP ++ l 423s CUFF.45.1.p1 232 CTASLFEKT--ACFSgighvLLKDLVHESRTFGWTKLNWSVEGDTDISNLID-LECIRRSVFCLYILEWFLALIFNKPPSLSVLELQMPLPISSA-L 324 423s *99988775..55555445666666676777777666666676668888899.**************************99**************.9 PP 423s 423s Fungal_trans 193 wesdd 197 423s w+s + 423s CUFF.45.1.p1 325 WSSKE 329 423s 99875 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (267 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 423s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 4 [number of targets reported over threshold] 423s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 423s # Mc/sec: 220.12 423s // 423s Query: GalKase_gal_bdg [M=49] 423s Accession: PF10509.8 423s Description: Galactokinase galactose-binding signature 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 13.3 0.0 2.6e-06 0.00024 12 44 .. 5 37 .. 2 41 .. 0.90 423s 423s Alignments for each domain: 423s == domain 1 score: 13.3 bits; conditional E-value: 2.6e-06 423s EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEE CS 423s GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieldiy 44 423s +++s+PG + L GEH g l++A+ l+ y 423s CUFF.60.2.p2 5 LIVSSPGKTILFGEHAVVYGATALAAAVSLRSY 37 423s 799************************998866 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (49 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 510.57 423s // 423s Query: GDC-P [M=430] 423s Accession: PF02347.15 423s Description: Glycine cleavage system P-protein 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 665.5 0.0 1.7e-204 1.6e-202 2 430 .] 66 504 .. 65 504 .. 0.99 423s 2 ! 36.7 0.0 1.2e-13 1.2e-11 22 285 .. 529 810 .. 525 822 .. 0.77 423s 3 ? 0.7 0.0 0.01 0.96 332 373 .. 840 881 .. 836 926 .. 0.78 423s 423s Alignments for each domain: 423s == domain 1 score: 665.5 bits; conditional E-value: 1.7e-204 423s HH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S-------............--HHHHHHHHHHHHTTB---EE--BTTB------HHHHHH CS 423s GDC-P 2 rhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleap............ksEeellaelekiasknkvvksfiGaGyydtilPaviqrn 86 423s rhigps++dq+++Le+lG+k++d+++++ +P+++++++++ ++ + +sE+e+++ +++a++nk++ksfiG+Gyy+++lPa+iqrn 423s CUFF.57.1.p1 66 RHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGsvnpneknppvnYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRN 162 423s 9******************************************9999************************************************** PP 423s 423s TTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEE CS 423s GDC-P 87 ilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqtlevlktrakglgieiv 183 423s +lenpewyt+YtPYqaEisqGrLe+++n+qt++adltGl+i+nasllDegtAa+EA++++++++kkk+k+++vdk+++p+tl+vl+tra+g+gi+i+ 423s CUFF.57.1.p1 163 VLENPEWYTQYTPYQAEISQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIYPNTLSVLRTRASGFGIKIE 259 423s ************************************************************************************************* PP 423s 423s EE-GGG--S-...S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGG CS 423s GDC-P 184 evdlteekvtdkekevagvlvqypnteGriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkekl 280 423s ++++t e +t+++k+v+g++vqyp+++G+i d+ +l+++a++ +++vv+a+dllaLt+lk+Pge+gaD++vGs+qrfG+P+gyGGPhagffA++e++ 423s CUFF.57.1.p1 260 LDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATARSFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEF 356 423s ************************************************************************************************* PP 423s 423s GGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSS CS 423s GDC-P 281 kRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffd 377 423s kRkiPGRl+G+skD+ +++a+rlalqtREqHirR+kAtsniCtaqaLlAn++a+ya+yhG++gl+eia+ri+++t++l+++l+++ ++ ++k++ffd 423s CUFF.57.1.p1 357 KRKIPGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGLQEIANRIYASTSFLKSALESSGYKIVNKSHFFD 453 423s ************************************************************************************************* PP 423s 423s EEEEE--TTTHHHHHHHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS 423s GDC-P 378 tllieveekaaekvlkkaekeglnlrkvelktvgialdEtvtkedieallkvl 430 423s tl+ieve +a+kvl+ka+++g+nlrkv++++vg++ldEtv+++di+al++++ 423s CUFF.57.1.p1 454 TLTIEVE--SADKVLAKALDHGYNLRKVDDSHVGLSLDETVCDKDIQALFSIF 504 423s ****999..889**************************************987 PP 423s 423s == domain 2 score: 36.7 bits; conditional E-value: 1.2e-13 423s SHHHHHHHHS-GGGB--S-------.....--HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG.G-HHHHHH CS 423s GDC-P 22 slddliekavPkeiklkkelkleap.....ksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE.isqGrLea 111 423s ++d+l ++P++ + +++l l++p +sE+el++ ++++ sk+ ++ + G ++l av + + np + ++ PY +E ++G + 423s CUFF.57.1.p1 529 TVDNLSICSLPENFR-RTTLYLQHPvfnryHSETELMRYIHHLQSKDLSlAHAMTPLGSCTMKLNAVTEMMPITNPLF-ANIHPYVPEeQAKGYRHV 623 423s 677888888899985.456667777777779****************987899999************9988999976.5678999963789***** PP 423s 423s HHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHH.HH-SSS.....--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-......... CS 423s GDC-P 112 llnfqtlvadltGldianasllDegtAaaEAvllaa.raskkk.....akkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd........ 194 423s + + q +++ +tG+d a + ++ Aa+E l++ ra ++ ++ ++ + h + a g+ ++ v++ +++ d 423s CUFF.57.1.p1 624 IEDLQLMLTTITGFDAA--CFQPNSGAAGEYTGLSViRAYQRSigqghRNICLIPVSAHGTN----PASAAMAGFTVIPVKCLNNGYLDmqdlkeka 714 423s **************975..6778888888877665412222221111134444444444333....3445566666666666666666666677777 PP 423s 423s ....S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG-- CS 423s GDC-P 195 ..kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiP 285 423s +++++a+ +v yp+t+G e+ +ke e ++++ v a++ a++ l g++gaD+ + + f +P g GGP +g + vk++l+ +P 423s CUFF.57.1.p1 715 skHADKLAAFMVTYPSTFGIFEPdVKEALEVIHEHGGQVYFdGANMNAMVGLCKAGDIGADVChLNLHKTFCIPHGGGGPGVGPICVKKHLADFLP 810 423s 768899**************99669*********99888763689999999***********84667889******************99988777 PP 423s 423s == domain 3 score: 0.7 bits; conditional E-value: 0.01 423s HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--S CS 423s GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkkleeelkkk 373 423s + y+ + G gl++ ++ + +++++ak l ++ + + ++k 423s CUFF.57.1.p1 840 SWAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNK 881 423s 567999*************************98755444443 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (430 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 423s # Mc/sec: 284.39 423s // 423s Query: GHMP_kinases_C [M=85] 423s Accession: PF08544.12 423s Description: GHMP kinases C terminal 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 25.9 0.0 1.1e-09 5e-08 8 66 .. 233 287 .. 221 298 .. 0.90 423s 423s Alignments for each domain: 423s == domain 1 score: 25.9 bits; conditional E-value: 1.1e-09 423s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 423s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 423s CUFF.60.1.p2 233 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 287 423s 6678999********..899********************..*************9997 PP 423s 423s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 25.6 0.0 1.3e-09 6.2e-08 8 66 .. 284 338 .. 272 349 .. 0.90 423s 423s Alignments for each domain: 423s == domain 1 score: 25.6 bits; conditional E-value: 1.3e-09 423s GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 423s +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l 423s CUFF.60.2.p2 284 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 338 423s 6678999********..899********************..*************9997 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (85 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 423s # Mc/sec: 174.77 423s // 423s Query: GHMP_kinases_N [M=66] 423s Accession: PF00288.25 423s Description: GHMP kinases N terminal domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 57.0 1.6 1.8e-19 8.7e-18 2 66 .] 75 152 .. 74 152 .. 0.87 423s 423s Alignments for each domain: 423s == domain 1 score: 57.0 bits; conditional E-value: 1.8e-19 423s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 423s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 423s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 423s CUFF.60.1.p2 75 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 152 423s 799****************************877765543352257899999***********.************998 PP 423s 423s >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? 0.1 0.1 0.11 5.2 19 40 .. 25 47 .. 22 57 .. 0.68 423s 2 ! 56.7 1.6 2.3e-19 1.1e-17 2 66 .] 126 203 .. 125 203 .. 0.87 423s 423s Alignments for each domain: 423s == domain 1 score: 0.1 bits; conditional E-value: 0.11 423s HHHHHHHHHHHHHTTEHH.HHHH CS 423s GHMP_kinases_N 19 AlavalvaAlaallglsl.eeak 40 423s A a+a+++ l +++ l+ ++++ 423s CUFF.60.2.p2 25 ATALAAAVSLRSYCKLQTtNNNE 47 423s 77888888888999655323344 PP 423s 423s == domain 2 score: 56.7 bits; conditional E-value: 2.3e-19 423s EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS 423s GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 423s ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg 423s CUFF.60.2.p2 126 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 203 423s 799****************************877765543352257899999***********.************998 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (66 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 429.05 423s // 423s Query: GLEYA [M=91] 423s Accession: PF10528.8 423s Description: GLEYA domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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 423s 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 423s 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- 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 65.9 1.8 7.1e-22 1.7e-20 2 89 .. 256 345 .. 255 347 .. 0.95 423s 423s Alignments for each domain: 423s == domain 1 score: 65.9 bits; conditional E-value: 7.1e-22 423s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEE CS 423s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyangggagslnfsv 89 423s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang g+++f + 423s CUFF.31.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANGAYIGGFDFAF 345 423s 789***********************************************9666899999999************************987 PP 423s 423s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -3.6 0.0 3.6 85 70 84 .. 13 27 .. 3 33 .. 0.60 423s 2 ! 65.2 2.1 1.2e-21 2.9e-20 2 90 .. 157 253 .. 156 254 .. 0.92 423s 423s Alignments for each domain: 423s == domain 1 score: -3.6 bits; conditional E-value: 3.6 423s EEEEEEEEE-S-.EE CS 423s GLEYA 70 yPiRivyangggags 84 423s +P+ +a++ g+ s 423s CUFF.11.1.p1 13 LPFTTTLAQASGTVS 27 423s 577777777766555 PP 423s 423s == domain 2 score: 65.2 bits; conditional E-value: 1.2e-21 423s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.......TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEEE CS 423s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.......sgssesktvt.vtltaGtyyPiRivyangggagslnfsvt 90 423s +++++ +++ p+t tYt+ ++n+Dd+++ w+GdkA+s+w+++n d+++ + g+ + +++t + +G+++P+R+v+ang g+++f +t 423s CUFF.11.1.p1 157 VIVYQFFLRIPETDTYTLVVNNVDDVFFGWFGDKAISGWSNNNFDAYSYWhespnmgLGTVGMGNFTvGNYPEGYFLPVRFVVANGAYIGGFDFYFT 253 423s 689***********************************************9999888444677777757899**********************998 PP 423s 423s >> CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007-3(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 59.6 0.7 6.9e-20 1.6e-18 2 79 .. 256 335 .] 255 335 .] 0.95 423s 423s Alignments for each domain: 423s == domain 1 score: 59.6 bits; conditional E-value: 6.9e-20 423s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 423s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 423s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 423s CUFF.30.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 335 423s 789***********************************************9666899999999***************96 PP 423s 423s >> CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749-3(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -3.0 0.0 2.3 55 59 86 .. 20 45 .. 14 50 .. 0.50 423s 2 ? -2.0 0.1 1.1 26 75 75 .. 66 66 .. 31 96 .. 0.59 423s 3 ! 60.3 0.7 4e-20 9.4e-19 2 79 .. 170 249 .] 169 249 .] 0.95 423s 423s Alignments for each domain: 423s == domain 1 score: -3.0 bits; conditional E-value: 2.3 423s EEEEEE-TT-BEEEEEEEEE-S-.EEEE CS 423s GLEYA 59 tvtvtltaGtyyPiRivyangggagsln 86 423s + +v+++ G+ + +y g ++++ 423s CUFF.30.2.p1 20 SSSVSVETGSCVRYTTIYSSGS--SEFT 45 423s 4455666666554444444433..3444 PP 423s 423s == domain 2 score: -2.0 bits; conditional E-value: 1.1 423s E CS 423s GLEYA 75 v 75 423s 423s CUFF.30.2.p1 66 H 66 423s 1 PP 423s 423s == domain 3 score: 60.3 bits; conditional E-value: 4e-20 423s EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS 423s GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 423s +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang 423s CUFF.30.2.p1 170 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 249 423s 789***********************************************9666899999999***************96 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (91 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 423s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 4 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 286.51 423s // 423s Query: Glyco_hydro_cc [M=239] 423s Accession: PF11790.7 423s Description: Glycosyl hydrolase catalytic core 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 199.1 0.0 4.5e-63 4.3e-61 1 239 [] 298 528 .. 298 528 .. 0.92 423s 423s Alignments for each domain: 423s == domain 1 score: 199.1 bits; conditional E-value: 4.5e-63 423s Glyco_hydro_cc 1 GlaynadasddkllsaksskisWyYnwsskpsselssaalefvPmlwgaksadtdalanvksaakenskylLgFNePDlks.qsnmspeeAaklw 94 423s Gla++ +++ ++ + ++ i+WyYnw+s++s+ +ss e+v ++a+s + +++s+ ++ +++gFNePDl+ + +++++Aa+++ 423s CUFF.59.1.p1 298 GLAWIPGTDLGYSDNFVNKGINWYYNWGSYSSGLSSSF--EYVLNQHDANSLS-----SASSV-FTGGATVIGFNEPDLSAaGNPIDAATAASYY 384 423s 78999888888888999**************9988885..********99865.....44444.55579**********8889************ PP 423s 423s Glyco_hydro_cc 95 kqliqplre..kgvklvsPavaatnseegleWldeFleacskdckvdflavHwYkgdfeelkehieelheaynkpiWvTEfalqs..esgdasqe 185 423s q+++plre +l+sPa+++ g +Wl+eF++acs dck+df+a+HwY+ df++l+++i++l ++y++piW+TEfa+++ +s+ s + 423s CUFF.59.1.p1 385 LQYLTPLREsgAIGYLGSPAISN--V--GEDWLSEFMSACS-DCKIDFIACHWYGIDFSNLQDYINSL-ANYGLPIWLTEFACTNwdDSNLPSLD 473 423s ********6355669******33..3..669**********.************999***********.9***************999999**** PP 423s 423s Glyco_hydro_cc 186 etkeflnevlawldsqeyVeryawfg.frsevsnvgannaLldenGeltelgsaY 239 423s e+k++++++l +ld + +Very+wf+ +++ ++vg+nnaL++++G+l+e+g++Y 423s CUFF.59.1.p1 474 EVKTLMTSALGFLDGHGSVERYSWFApATELGAGVGNNNALISSSGGLSEVGEIY 528 423s *****************************************************99 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (239 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 724.20 423s // 423s Query: Glyco_tranf_2_3 [M=230] 423s Accession: PF13641.5 423s Description: Glycosyltransferase like family 2 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 423s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 423s 423s Alignments for each domain: 423s == domain 1 score: -1.4 bits; conditional E-value: 0.19 423s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 423s + ++ D+ t ++P+tl++l++ 423s CUFF.60.1.p1 237 VCIISDGRTKIHPRTLAYLAA 257 423s 45688999*******999876 PP 423s 423s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 423s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 423s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 423s CUFF.60.1.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 423s 5667889999********************9999999999999888766666666668888********************8566779****** PP 423s 423s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 423s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 423s CUFF.60.1.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 423s ******999****************9984466699************9988899*****************************86 PP 423s 423s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 423s 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 423s 423s Alignments for each domain: 423s == domain 1 score: -1.4 bits; conditional E-value: 0.19 423s Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 423s + ++ D+ t ++P+tl++l++ 423s CUFF.60.2.p1 237 VCIISDGRTKIHPRTLAYLAA 257 423s 45688999*******999876 PP 423s 423s == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 423s Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 423s +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r 423s CUFF.60.2.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 423s 5667889999********************9999999999999888766666666668888********************8566779****** PP 423s 423s Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 423s e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ 423s CUFF.60.2.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 423s ******999****************9984466699************9988899*****************************86 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (230 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 423s # Mc/sec: 396.63 423s // 423s Query: Glyco_transf_34 [M=239] 423s Accession: PF05637.11 423s Description: galactosyl transferase GMA12/MNN10 family 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 283.8 0.3 1.4e-88 6.5e-87 2 238 .. 98 334 .. 97 335 .. 0.97 423s 423s Alignments for each domain: 423s == domain 1 score: 283.8 bits; conditional E-value: 1.4e-88 423s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 423s +++ivlllvs+ ++++ ++ +++++++i+NrvdY++k++y+++y++v+ l ++vW+k+pa+ ++mkkyP+aewiW+lDqdA+i+n++ls 423s CUFF.51.1.p2 98 SQNIVLLLVSDGHTSY--NNGANTFEEAIQNRVDYSTKQNYNFEYVNVTGLPI---PAVWSKMPAVLQTMKKYPKAEWIWLLDQDAIITNTHLS 186 423s 789***********97..455559***************************99...************************************** PP 423s 423s Glyco_transf_34 96 leehvlkperLeelllkntpv........vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesd 181 423s l++++lkpe+L+++l++nt + +lr+++++++ +d+e+ +viisqd+nglnags+l+rns +++l+lD+w+dp+++e++ka ++ 423s CUFF.51.1.p2 187 LQDSFLKPENLQKTLITNTILtkrpinanGDLRYTPSNYSLKDIENLMVIISQDHNGLNAGSILFRNSPATALFLDIWTDPVVAECAKA---NN 277 423s *******************999*****9999**********************************************************...** PP 423s 423s Glyco_transf_34 182 eqsaleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankc 238 423s eq++l+yl++kh++++s vgl++q+ in+++eg++++++++gdlv+hfagC+v+n+c 423s CUFF.51.1.p2 278 EQDMLGYLISKHSQLASLVGLIPQRKINAFHEGPENMEWQKGDLVIHFAGCWVENRC 334 423s ********************************************************9 PP 423s 423s >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 281.4 0.0 7.1e-88 3.4e-86 2 239 .] 84 318 .. 83 318 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 281.4 bits; conditional E-value: 7.1e-88 423s Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 423s ++eiv+ll+s+ + s +++ll++++kNr++Ya++++y++++++vs+l + vW k+pai ++m+kyP+a+wiWwlDqdAlimn++ls 423s CUFF.52.1.p2 84 SHEIVMLLASDGNVG---SFESNLLDDCFKNRIEYAKLQNYNFEFVNVSSLVV---PPVWGKMPAILQTMRKYPSAKWIWWLDQDALIMNKNLS 171 423s 79**********997...58999***************************999...************************************** PP 423s 423s Glyco_transf_34 96 leehvlkperLeelllkntpv......vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesdeq 183 423s l+e +l+p +L+++ll+++p+ ++ r ++ +++e++e+++++isqd+nglnagsfl+rns+ +ll+Dl++dp+l++++++ ++eq 423s CUFF.52.1.p2 172 LQELFLSPAMLQKSLLREQPIinsfgeDNFRITPAAYSKEMIEQIQFLISQDHNGLNAGSFLVRNSRSIALLMDLLTDPSLADAGVV---RHEQ 262 423s **************************999**********************************************************...**** PP 423s 423s Glyco_transf_34 184 saleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankca 239 423s ++++y+++kh++v+s+vg+++q++in+++eg+++++++egdl++hfagC+v+nkca 423s CUFF.52.1.p2 263 DLIGYFIQKHSQVASMVGILPQRFINAFHEGPPTMQWQEGDLALHFAGCWVENKCA 318 423s ******************************************************96 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (239 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 423s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 578.41 423s // 423s Query: Glyco_transf_8 [M=256] 423s Accession: PF01501.19 423s Description: Glycosyl transferase family 8 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 37.5 1.6 1.1e-13 1e-11 9 221 .. 84 321 .. 77 336 .. 0.81 423s 423s Alignments for each domain: 423s == domain 1 score: 37.5 bits; conditional E-value: 1.1e-13 423s Glyco_transf_8 9 nYllgasvviksllknakepawfalnfhiltaeievenleklnklassykevlellesdkksledfesklklrspkylsllnylRlylpelfpkl 103 423s Y ++ v+i+ l + +++ +++ + ++++ ++e+++k + s++ ++++ sd+ ++++++++ ++ + ++ +l+++e ++ 423s CUFF.51.1.p1 84 YYFNATRVLIHRLKYHPTTKSKYPIHIL-ALRGVDEWKIERFRKDGASVIVIDPIASSDIVY----DTSSFSQEISARYEQMFSKLRIFEQ-IQF 172 423s 5677778888888888886556666666.7899*******************9999998843....3578899999999999*********.9** PP 423s 423s Glyco_transf_8 104 dkilylDaDvvvqgdlseLwdldlk.gkvlaaved............................krfkkylnksepliaenfkp..eacyFnaGvl 167 423s dki +D+D+++ +++++++d++ ++++ + + + + l + + +++p + yFnaG++ 423s CUFF.51.1.p1 173 DKICVIDSDILIMKNIDDIFDTPYMyQQINTLNYTrlpsytkpdddtvyhfnedfkeygasrsEFYPYLLAAVSDRGEHHSIPpeDTPYFNAGLM 267 423s **********************9997888888888*************************8863333333444444444444411567******* PP 423s 423s Glyco_transf_8 168 lfdldewrkenitetlikwlnlnekrtllklgdqdilnivfk....gkvkeldkkynv 221 423s l+ + e + + i + + ++e+ k ++q +ln++f + +ld++yn 423s CUFF.51.1.p1 268 LIRPSELHFNRILKI-GRFPYMYEN---AKMMEQSLLNLAFSldgwFPWTRLDPYYNG 321 423s *******99988764.455566666...89***********86655789999999995 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (256 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 423s # Mc/sec: 302.41 423s // 423s Query: Glyco_trans_2_3 [M=197] 423s Accession: PF13632.5 423s Description: Glycosyl transferase family group 2 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 423s 423s Alignments for each domain: 423s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 423s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 423s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 423s CUFF.60.1.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 423s 799**************999*988************97765333347788888888**********************************8888 PP 423s 423s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 423s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 423s CUFF.60.1.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 423s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 423s 423s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 423s +r++ +++++s ++ +++++f+++ + ++++l 423s CUFF.60.1.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 423s 3333313445555555555555566665544333321....22222 PP 423s 423s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 423s 423s Alignments for each domain: 423s == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 423s Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 423s +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq 423s CUFF.60.2.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 423s 799**************999*988************97765333347788888888**********************************8888 PP 423s 423s Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 423s + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ 423s CUFF.60.2.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 423s 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP 423s 423s Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 423s +r++ +++++s ++ +++++f+++ + ++++l 423s CUFF.60.2.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 423s 3333313445555555555555566665544333321....22222 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (197 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 423s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06 423s # Mc/sec: 102.49 423s // 423s Query: GNAT_acetyltr_2 [M=227] 423s Accession: PF13718.5 423s Description: GNAT acetyltransferase 2 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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- 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 12.4 0.0 8.6e-06 0.00041 94 131 .. 72 109 .. 67 128 .. 0.78 423s 423s Alignments for each domain: 423s == domain 1 score: 12.4 bits; conditional E-value: 8.6e-06 423s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 423s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 423s CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 423s 679******************98766666666665554 PP 423s 423s >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 12.3 0.0 9e-06 0.00043 94 131 .. 72 109 .. 67 130 .. 0.79 423s 423s Alignments for each domain: 423s == domain 1 score: 12.3 bits; conditional E-value: 9e-06 423s GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 423s + +Ri R+ v+p+ ++ GYG + + + + ++++ss 423s CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 423s 679******************98766666666665554 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (227 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 906.89 423s // 423s Query: His_Phos_1 [M=194] 423s Accession: PF00300.21 423s Description: Histidine phosphatase superfamily (branch 1) 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 77.3 0.0 7e-26 6.6e-24 1 181 [. 9 203 .. 9 215 .. 0.86 423s 423s Alignments for each domain: 423s == domain 1 score: 77.3 bits; conditional E-value: 7e-26 423s EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT.......--EEE-GGGS----GGGT. CS 423s His_Phos_1 1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg.......lpveldegLrEidfGdwe. 86 423s +yL+RHG+ ++n+ d+ Lt eG+eq eala+ l++ +pid i++Sp++R+ qT+e+++++ +pv + + ++E+ + ++ 423s CUFF.48.1.p2 9 VYLIRHGQAQHNVGPDeDHNIRDPVLTSEGIEQCEALAKELESkqIPIDGIVCSPMRRTLQTMEIALKKYLaeggpdkVPVYISPFFQEVGHLPCDi 105 423s 69*********99877778889999****************9988999999***************99876788999************99999999 PP 423s 423s T-B.HHHHHH..HSHHHHHHHHH-GGG-B....S-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH.T--GGGGG.GB---TT-EE CS 423s His_Phos_1 87 glttaeiaeeypeeleawlrdpadvrppg....gEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll.glpleelr.rleldnaslt 177 423s gl+ +++++ yp++ + +d p++ + a R ++ale laa +++ ++v++H ++ir ll++++ ++++l+ +l ++n++ 423s CUFF.48.1.p2 106 GLELDKLNKLYPKYNFQSCQDGIY--PEKrdiyASDVTISAIRSKEALEYLAALPQQQ-IAVITHSAFIRFLLKKMVkAADIDFLPpQLSFKNCEFR 199 423s **********99987777666653..3334587888888899***********99987.*****************966777766546777999887 PP 423s 423s EEEE CS 423s His_Phos_1 178 vley 181 423s + ++ 423s CUFF.48.1.p2 200 IYDL 203 423s 7765 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (194 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 1026.59 423s // 423s Query: Hpt [M=85] 423s Accession: PF01627.22 423s Description: Hpt domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.9 0.3 1.1e-05 0.0011 32 64 .. 217 248 .. 205 267 .. 0.74 423s 423s Alignments for each domain: 423s == domain 1 score: 11.9 bits; conditional E-value: 1.1e-05 423s HHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTS CS 423s Hpt 32 aaHtLKGsagmlGltelaelahelEdlldrage 64 423s ++H+++Gsa+ lGl+ l ++a+ ++++d a 423s CUFF.19.1.p1 217 LVHKIAGSAAALGLD-LHQVAQVAQSVIDNAAT 248 423s 79***********64.66666666666654444 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (85 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 689.25 423s // 423s Query: HTH_29 [M=63] 423s Accession: PF13551.5 423s Description: Winged helix-turn helix 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 5.3 0.0 0.0011 0.1 16 35 .. 122 141 .. 111 145 .. 0.88 423s 2 ! 4.0 0.0 0.0027 0.26 10 30 .. 278 298 .. 271 301 .. 0.83 423s 423s Alignments for each domain: 423s == domain 1 score: 5.3 bits; conditional E-value: 0.0011 423s HTH_29 16 sqiAkllglsrrtvyrwlkr 35 423s ++A ++glsr+++++++++ 423s CUFF.17.1.p1 122 PELANQCGLSRKHIFDAVED 141 423s 589************99986 PP 423s 423s == domain 2 score: 4.0 bits; conditional E-value: 0.0027 423s HTH_29 10 eGvstvsqiAkllglsrrtvy 30 423s +s+v ++Ak +++s+ t 423s CUFF.17.1.p1 278 AILSRVEELAKKYNVSMATLA 298 423s 456799************986 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (63 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 606.62 423s // 423s Query: HTH_psq [M=45] 423s Accession: PF05225.15 423s Description: helix-turn-helix, Psq domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 3.8 0.0 0.0026 0.25 24 33 .. 81 90 .. 80 93 .. 0.91 423s 2 ? -1.9 0.0 0.16 16 7 16 .. 169 179 .. 165 180 .. 0.80 423s 3 ! 4.1 0.0 0.0021 0.2 21 33 .. 285 297 .. 281 304 .. 0.87 423s 423s Alignments for each domain: 423s == domain 1 score: 3.8 bits; conditional E-value: 0.0026 423s HTH_psq 24 rkYgiPrsTL 33 423s rkY+iPrs++ 423s CUFF.17.1.p1 81 RKYEIPRSSI 90 423s 79******98 PP 423s 423s == domain 2 score: -1.9 bits; conditional E-value: 0.16 423s HTH_psq 7 aAleavv.nGk 16 423s +Al++vv +Gk 423s CUFF.17.1.p1 169 RALNDVVeSGK 179 423s 8******8887 PP 423s 423s == domain 3 score: 4.1 bits; conditional E-value: 0.0021 423s HTH_psq 21 kAArkYgiPrsTL 33 423s ++A+kY+++ TL 423s CUFF.17.1.p1 285 ELAKKYNVSMATL 297 423s 79********999 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (45 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 401.55 423s // 423s Query: Hydantoinase_A [M=291] 423s Accession: PF01968.17 423s Description: Hydantoinase/oxoprolinase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -3.5 0.2 0.54 26 82 95 .. 5 18 .. 4 22 .. 0.87 423s 2 ! 349.6 0.2 1.4e-108 6.5e-107 1 290 [. 239 540 .. 239 541 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: -3.5 bits; conditional E-value: 0.54 423s Hydantoinase_A 82 ItfDmGGTstDvsl 95 423s I +D GGT tD+++ 423s CUFF.44.1.p1 5 IHIDRGGTFTDAIA 18 423s 889********875 PP 423s 423s == domain 2 score: 349.6 bits; conditional E-value: 1.4e-108 423s Hydantoinase_A 1 rtetavvnAylspilreylesvekslekrgak......arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaat.sklagekkvItfDmGG 88 423s r+++a+ +Aylsp++r+yl ++++ + + ++ r+ +mqsdGglv+++++++ ++ilSGPa+Gvvg+a t ++++ + +vI+fDmGG 423s CUFF.44.1.p1 239 RATSATADAYLSPVVRRYLAGFQSGFLHGLKTkdnskgVRCEFMQSDGGLVDVNKFSGL--HAILSGPAGGVVGFALTsYDEDVKIPVIGFDMGG 331 423s 7889*********************9997776999999********************9..*****************77888888********* PP 423s 423s Hydantoinase_A 89 TstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls. 182 423s TstDvs++ g++e+++et++agv++++p+ldi+tv+agGgs+l ++++g + vgpesaga+pgp+cyrkGg ltvTDanl+LGrl pe+f++ 423s CUFF.44.1.p1 332 TSTDVSRYG-GSYEHVFETTTAGVTIQSPQLDINTVAAGGGSRL-FWKNGLFVVGPESAGAHPGPVCYRKGG-YLTVTDANLLLGRLLPESFPKi 423 423s *********.**********************************.***************************.********************** PP 423s 423s Hydantoinase_A 183 .gpdgdqkldvelarrafeelakelnlk........veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkv 268 423s gp++d++ldve +r++fe+l++e+n + ++evA g++++a+e+ma+++r l++++g+d++ + l++fGGaG+qh+aa+a++lg+++v 423s CUFF.44.1.p1 424 fGPNEDESLDVESTRKEFEKLTAEINSGlekerqmtADEVAFGFIKIANETMARPIRALTEAKGHDISIHRLTSFGGAGGQHCAAIAKSLGITQV 518 423s *********************************************************************************************** PP 423s 423s Hydantoinase_A 269 ivppyagvlsalGmalAdvree 290 423s +v++y+++lsa+GmalAdv +e 423s CUFF.44.1.p1 519 LVHKYSSILSAYGMALADVVSE 540 423s ******************9876 PP 423s 423s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 296.2 0.0 2.7e-92 1.3e-90 44 290 .. 1 252 [. 1 253 [. 0.97 423s 423s Alignments for each domain: 423s == domain 1 score: 296.2 bits; conditional E-value: 2.7e-92 423s Hydantoinase_A 44 lvsadearkkpvetilSGPaaGvvgaaat..sklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvde 136 423s lv++d+++ +i+SGPaaG vg+a+t + ++++++I+fDmGGTstDvs+++ g++e+ +e +i g+ +++p+ldi+tv+agGgs+l +++ 423s CUFF.42.1.p1 1 LVDIDNFTAI--SAIMSGPAAGTVGFAKTssLHADDKTPAIGFDMGGTSTDVSRYD-GKFEHIYEANIFGLYIQSPQLDIQTVAAGGGSRL-FWR 91 423s 6789999987..*****************5445567788*****************.**********************************.999 PP 423s 423s Hydantoinase_A 137 ggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvave 223 423s ++ ++vgpesaga pgpacy +Gg +ltvTDan++LGr+ p++f++ gp+++++++++++ ++f+el + +n + +ee+A+g+++va+e 423s CUFF.42.1.p1 92 NQLFSVGPESAGAFPGPACYLNGG-PLTVTDANVLLGRIIPDFFPKifGPKENESMNKDIVIEKFSELRDIINIDiekektIEEIAMGFIQVANE 185 423s ************************.********************************************************************** PP 423s 423s Hydantoinase_A 224 nmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290 423s +m++++rkl+++rgld + ++l+vfGGaG+qha+a+a l+++k+i+++y++vlsa+G+alA+v++e 423s CUFF.42.1.p1 186 TMCRPIRKLTESRGLDLSAHHLAVFGGAGGQHACAIASLLNIEKIIIHKYSSVLSAYGLALAHVTHE 252 423s ****************************************************************998 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (291 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 423s # Mc/sec: 366.75 423s // 423s Query: Hydantoinase_B [M=516] 423s Accession: PF02538.13 423s Description: Hydantoinase B/oxoprolinase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 708.2 0.1 5.6e-217 2.7e-215 1 516 [] 749 1285 .. 749 1285 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 708.2 bits; conditional E-value: 5.6e-217 423s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyagg 93 423s Dpi l+vf +r+m++ae+mgr+lq+t++S+n+kerlD+scalfda+g+lva+aph+pvhlgsms++v+++++ +eg+lkpGDvl+tN+P +gg 423s CUFF.44.1.p1 749 DPIYLSVFGSRFMAVAEQMGRALQKTSVSTNVKERLDYSCALFDAKGNLVANAPHMPVHLGSMSTCVRTQAKIHEGKLKPGDVLVTNHPSYGG 841 423s 9**********************************************************************99999***************** PP 423s 423s Hydantoinase_B 94 tHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........Rtpednl 176 423s tHlpDit+itP f +e++f+va+raHhaDiGGi pGsmp++++e+ eEG+ i++ klv +g+ +ee++++ll +++ R+++dnl 423s CUFF.44.1.p1 842 THLPDITTITPHFEGDEIMFYVAARAHHADIGGILPGSMPSSSKELSEEGATIKSEKLVVDGVfQEERMIDLLYNEPakveggsgsRCLRDNL 934 423s *************9889*********************************************************999**************** PP 423s 423s Hydantoinase_B 177 gDlkAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgts 263 423s +DlkAq++anq+g+++++ li+eyG++ v ++m++i++nae avr++l +++ +++ aed++ddg++i++++tid+++ a++Dftgt 423s CUFF.44.1.p1 935 NDLKAQVSANQKGINLITSLIKEYGKNSVLRYMKAIQENAESAVRQLLLGVRErflgEDLYAEDHMDDGSKICLRITIDEENgdAIFDFTGTT 1027 423s ************************************************7777777778899*******************9999********* PP 423s 423s Hydantoinase_B 264 pqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtm 356 423s ++++gniNap+avt+sa+iy+lr+l++e+iplN+Gcl pi+v++p++++l+pse+aavvggnv+tsqr++d++lka++ ++Aasqg++ 423s CUFF.44.1.p1 1028 EEIYGNINAPEAVTYSAIIYCLRVLISENIPLNQGCLLPIKVIIPDNCFLKPSETAAVVGGNVLTSQRITDTILKAFQ------ACAASQGDT 1114 423s ******************************************************************************......********* PP 423s 423s Hydantoinase_B 357 nnltf..ggvderg...geffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreief 444 423s nnltf gg+d+++ + fgyyeti+gGsGA g dG+s+vh+hmtntr+td E+lErryPv++++f +r++sgGaGky+GGdGv+r+ief 423s CUFF.44.1.p1 1115 NNLTFgiGGKDPETgevKPGFGYYETICGGSGAIDGLDGTSGVHTHMTNTRITDLEVLERRYPVILRKFIIRENSGGAGKYKGGDGVIRDIEF 1207 423s ****94446677669998889************************************************************************ PP 423s 423s Hydantoinase_B 445 lepevtvsilserrvfapwGlaGGepGargrvvlnllvr..........greenlggkatvelkagdvlvietpGGGGyGdp 516 423s + p vt+silserr ++p+G++GG+++++g+ n+++r r++n+ggk+t++++agd +vi+tpGGGGyG p 423s CUFF.44.1.p1 1208 RIP-VTLSILSERRAYHPYGMKGGKDAECGK---NIWIRkdilpsgeqrVRQINVGGKNTCHMQAGDHIVIMTPGGGGYGPP 1285 423s **9.***************************...88888899999998899*****************************86 PP 423s 423s >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 701.5 0.3 5.9e-215 2.8e-213 1 515 [. 459 986 .. 459 987 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 701.5 bits; conditional E-value: 5.9e-215 423s Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyaggtH 95 423s 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 423s CUFF.42.1.p1 459 DPITMTIFANRFMSISEQMGQVLQKTAVSVNVKERLDYSCALFSPDGGLVANAPHVPAMLGSMQTAVKWQHNYWKGKLVPGDVLLSNHPIAGGVH 553 423s 9********************************************************************************************** PP 423s 423s Hydantoinase_B 96 lpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........RtpednlgDl 179 423s lpD+tv+tPvf +++ ++f++a+r+H++D+GGitpGsmp++++ i+eEG++i+++k+v++g+ +e+++++ll +++ Rt++dn++D+ 423s CUFF.42.1.p1 554 LPDLTVVTPVFDNNKdIIFYCAARGHMVDVGGITPGSMPSNSKAIYEEGAAIKTFKVVKAGTfDEKGLTQLLFDEPakypdcsgsRTLRDNISDV 648 423s ***********98879******************************************************************************* PP 423s 423s Hydantoinase_B 180 kAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgtspqvkg 268 423s kA+++a+++g++ +++l+ eyGl+ v++ m i++ ae+avr++l++++ + ++a dy+ddg+p++++v+id+++ a++Df+gt+p+v+g 423s CUFF.42.1.p1 649 KAMLSACHRGRSMVEKLVVEYGLDIVQRSMYGIQAAAEKAVRDVLKAFSVqnsqKPLKAIDYMDDGTPLQLEVKIDPETgdAVFDFEGTGPEVYG 743 423s *********************************************9877766777899********************99*************** PP 423s 423s Hydantoinase_B 269 niNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfgg 363 423s n+Nap a+t+s viy+lr+++++diplNeGcl+pie+++p+ ++lnpse+aavvggnv+tsqr++dv+lka++ ++Aasqg+mnnltfg 423s CUFF.42.1.p1 744 NWNAPIAITYSSVIYCLRSIINQDIPLNEGCLKPIEIRIPPSCFLNPSETAAVVGGNVLTSQRITDVILKAFS------ICAASQGCMNNLTFGY 832 423s *************************************************************************......***************7 PP 423s 423s Hydantoinase_B 364 vderggeffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserr 458 423s e+g+e f++yetiagG+GA+p+++G+s+vh+hmtntr+td+E++Err Pv+++rf lr++sgG+G+y+GGdGv+r++ef+++ +++silserr 423s CUFF.42.1.p1 833 DGENGEEGFAMYETIAGGAGAGPTWNGTSGVHTHMTNTRITDPEVVERRAPVILRRFCLRENSGGKGEYHGGDGVIRHFEFRRS-MHCSILSERR 926 423s 777779999**************************************************************************7.********** PP 423s 423s Hydantoinase_B 459 vfapwGlaGGepGargrvvlnllvr......greenlggkatvelkagdvlvietpGGGGyGd 515 423s + ap+G++GGe+Ga+g n+++ r +nlggk++v + +gd +vietpGGGGyG 423s CUFF.42.1.p1 927 SRAPYGMNGGEDGAMGV---NTWIDcsnpdfPRYVNLGGKNHVLMGKGDHIVIETPGGGGYGA 986 423s *****************...99999999999*******************************6 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (516 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06 423s # Mc/sec: 233.41 423s // 423s Query: Hydant_A_N [M=178] 423s Accession: PF05378.12 423s Description: Hydantoinase/oxoprolinase N-terminal region 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 210.0 0.0 1.1e-66 1.1e-64 1 178 [] 4 220 .. 4 220 .. 0.98 423s 2 ! 2.4 0.6 0.0062 0.59 2 14 .. 325 337 .. 324 355 .. 0.82 423s 423s Alignments for each domain: 423s == domain 1 score: 210.0 bits; conditional E-value: 1.1e-66 423s Hydant_A_N 1 rigIDvGGTfTDavaldeke.eevavlKllst.....pdavaegirealeevleesipr.....tskidvvrmGTTvatNallerkgervaLittkg 86 423s +i+ID+GGTfTDa+a+ ++e + +v+Klls+ +da +e++r++le v+++sipr ts+i+++r+GTTvatNallerkger+a+ittkg 423s CUFF.44.1.p1 4 KIHIDRGGTFTDAIATFADEsRPPIVIKLLSEdpsnyKDASIEAVRRILEIVQGKSIPRtekldTSCINHLRCGTTVATNALLERKGERCAFITTKG 100 423s 699************998777999************************************************************************* PP 423s 423s Hydant_A_N 87 frdlleigrqnrpdlfelrikkplvlyeevvevdervead............................gevlkpldeeevrealkalkaagvesiav 155 423s f+d l ig+q+rp++fel i++p+vly++v+evderv+++ ++++k++d++++r++l+al+++g++siav 423s CUFF.44.1.p1 101 FKDGLLIGNQSRPNIFELGIRRPEVLYSKVIEVDERVTLEdyvedpmkvkttidgsdpslvvgrsgevVRIMKKVDCDALRKDLQALYDEGFTSIAV 197 423s ***************************************99******************************************************** PP 423s 423s Hydant_A_N 156 vllhSylnpehElrvaeiareig 178 423s +l+hS+++p+hEl v++ia+e+g 423s CUFF.44.1.p1 198 CLAHSFTFPDHELLVGKIAEEVG 220 423s ********************975 PP 423s 423s == domain 2 score: 2.4 bits; conditional E-value: 0.0062 423s Hydant_A_N 2 igIDvGGTfTDav 14 423s ig D+GGT TD+ 423s CUFF.44.1.p1 325 IGFDMGGTSTDVS 337 423s 899********96 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (178 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 423.51 423s // 423s Query: IBR [M=62] 423s Accession: PF01485.20 423s Description: IBR domain, a half RING-finger domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.8 2.4 1.2e-05 0.0012 10 51 .. 569 611 .. 561 613 .. 0.71 423s 423s Alignments for each domain: 423s == domain 1 score: 11.8 bits; conditional E-value: 1.2e-05 423s IBR 10 kslesdpnlkwCprpdCeaiiekseg...cksvtCskCgfefCfn 51 423s ++ ++++++ C C i ++ e ++ +Cs+C +e+C++ 423s CUFF.12.1.p1 569 TTQNNNESFAVCL--ACAIIQRSLERkklSTPTQCSSCFQEYCWD 611 423s 33455777999*9..9997776555544445578**********6 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (62 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 570.12 423s // 423s Query: Lung_7-TM_R [M=295] 423s Accession: PF06814.12 423s Description: Lung seven transmembrane receptor 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 24.4 18.7 8.4e-10 8e-08 59 258 .. 80 270 .. 26 288 .. 0.83 423s 423s Alignments for each domain: 423s == domain 1 score: 24.4 bits; conditional E-value: 8.4e-10 423s Lung_7-TM_R 59 vllgilWlfilakykkdilkiqkliaavivlkmlelaf.vyieYatinskGssievlavlasilsalkktlsrlliliislGygivkpkLgdllkkvl 155 423s +l+ W++ ++ + k i++ qk+i + i+l +l++ + ie ++++s+ + ++ +++i+ l+ + rl ++ +lG+gi ++ + k l 423s CUFF.6.1.p1 80 LLFLSYWIWTCLHFSKIIFPAQKVICLYIFLFALNQTLqECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRT-----VPKYL 172 423s 466778*******************9999887776655167899999**************************************865.....66666 PP 423s 423s Lung_7-TM_R 156 llglllfvla.evlelvresseesessakllkvllfliplalldlffvvwifrsLqktlrdlklkrnlvklklYrkftvvlvisvvasviivlvekil 252 423s ++ ++ +v+a + + + ++ ++++ +i+ + ++ v+++ +L k + + n k++ +r+ +++ ++ + as + ++++i+ 423s CUFF.6.1.p1 173 MIKGISIVIAlCSVYWISLYKDVYVV-----SEIFDMIQYEVS-PAIWVYSICHLLKQCTSVTTYENASKARFFRRMLNAFIFIFCASPMLHYLSNII 264 423s 66555544441455555555444444.....689999999666.578888999********************************************9 PP 423s 423s Lung_7-TM_R 253 lktvds 258 423s + ++d+ 423s CUFF.6.1.p1 265 FGNFDY 270 423s 988775 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (295 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 423s # Mc/sec: 377.00 423s // 423s Query: malic [M=182] 423s Accession: PF00390.18 423s Description: Malic enzyme, N-terminal domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 65.7 0.0 2.5e-22 2.4e-20 3 76 .. 32 108 .. 30 110 .. 0.95 423s 423s Alignments for each domain: 423s == domain 1 score: 65.7 bits; conditional E-value: 2.5e-22 423s TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGET..CHHHHHTTSS..SS..EEEEE-SS CS 423s malic 3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdke..kikeilknlp.eedvkvivvtdge 76 423s +n+tlfy+l++++l e++pi+YtPt g+a++++s++yr+++g+yl+i++++ ik++l+++ +++v++i++td+e 423s CUFF.1.1.p1 32 TNQTLFYALISQHLIEMIPIIYTPTEGDAIKQFSDIYRYPEGCYLDIDHSDlsYIKQQLSEFGkSDSVEYIIITDSE 108 423s 799*******************************************99988779********97899********97 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (182 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 1209.88 423s // 423s Query: Mannosyl_trans3 [M=275] 423s Accession: PF11051.7 423s Description: Mannosyltransferase putative 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 12.4 1.2 4.1e-06 0.00039 92 143 .. 171 223 .. 85 298 .. 0.70 423s 423s Alignments for each domain: 423s == domain 1 score: 12.4 bits; conditional E-value: 4.1e-06 423s Mannosyl_trans3 92 sFeevllLDaDnvplknpdklFese.eYkktglllw.kdrdlwkrstspkfyei 143 423s F+++ ++D+D +++kn+d++F+++ Y++ ++l + + ++++k +++ y++ 423s CUFF.51.1.p1 171 QFDKICVIDSDILIMKNIDDIFDTPyMYQQINTLNYtRLPSYTKPD-DDTVYHF 223 423s 69*********************97358888888882224443333.4444444 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (275 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 423s # Mc/sec: 402.51 423s // 423s Query: MatE [M=161] 423s Accession: PF01554.17 423s Description: MatE 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 423s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 423s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 423s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 423s CUFF.38.1.p3 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 423s 99****************************************************************************************.****** PP 423s 423s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 423s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 423s CUFF.38.1.p3 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 423s ***************************************************************86 PP 423s 423s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 423s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 423s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 423s CUFF.38.1.p3 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 423s 667789******************************************************************************************* PP 423s 423s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 423s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 423s CUFF.38.1.p3 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 423s *******************************************************99997 PP 423s 423s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 423s 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 423s MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 423s P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ 423s CUFF.39.1.p1 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 423s 99****************************************************************************************.****** PP 423s 423s MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 423s il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l 423s CUFF.39.1.p1 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 423s ***************************************************************86 PP 423s 423s == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 423s MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 423s +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ 423s CUFF.39.1.p1 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 423s 667789******************************************************************************************* PP 423s 423s MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 423s ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ 423s CUFF.39.1.p1 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 423s *******************************************************99997 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (161 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 22 (0.231579); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 380.46 423s // 423s Query: MDM31_MDM32 [M=525] 423s Accession: PF08118.10 423s Description: Yeast mitochondrial distribution and morphology (MDM) proteins 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 9.7 0.1 1.7e-05 0.0016 365 448 .. 134 218 .. 124 228 .. 0.68 423s 423s Alignments for each domain: 423s == domain 1 score: 9.7 bits; conditional E-value: 1.7e-05 423s MDM31_MDM32 365 eeevtskkaleeeekseelakeaks.aeeseeekeeeeekeeeeeekyvvvdlklklndvkAavPlftkdlsyvnnaliRpivay 448 423s e++++k+++ ++ +++++++a+s a++s + + + + + +++ k v ++klnd A++P ++ +s ++a Rp v++ 423s CUFF.20.1.p1 134 VEKISQKNQEARSRANSRVNSRANSrANSSVSLAGMDGSPNWKRKMKSAVFGSRVKLNDEEAQLPRNKSSVSIAEQAASRPKVSF 218 423s 33344443333333333444333330333444444555666678889999*********************************99 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (525 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 1075.20 423s // 423s Query: MFS_1 [M=353] 423s Accession: PF07690.15 423s Description: Major Facilitator Superfamily 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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( 423s 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(+) 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 135.1 27.5 5.9e-43 1.4e-41 2 349 .. 113 492 .. 112 497 .. 0.82 423s 2 ? -1.5 0.1 0.2 4.8 230 256 .. 500 529 .. 493 543 .. 0.53 423s 423s Alignments for each domain: 423s == domain 1 score: 135.1 bits; conditional E-value: 5.9e-43 423s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGl 97 423s +++++++++a+s++++ + +a++l++s +++l ++ + +g++v+slp+++lsd +Gr +++++ll+f ++ + + a+++w+l+++r++qG+ 423s CUFF.37.1.p1 113 SVITIVVTFASSVYSSGII-DIASELHSSIP-VSTLGSCtFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGV 207 423s 56889999**********9.9******5555.56666664888********************************6666645*************** PP 423s 423s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeee..... 188 423s ++++ +++++ i+d+f++ +r+ ++ + ++ lG+i+gp++g +++ s+l Wr++f+i+ i ++ ++v++++++pe++ + + +++ + 423s CUFF.37.1.p1 208 FGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFITqSYLEWRWTFWINMIWAAAVIVFVFIFFPETHEDTILDYKAKYLrkttg 304 423s ************************************************99999*********************************999999***** PP 423s 423s MFS_1 189 ..........kgtgpaplvp....awkallkdpvlwillialllfffgfsglltllplylqevlgls.glllaglllallalvgail....allagr 266 423s +++ + ++++ a +++++ p + +++ l++ +++++ + ++ +g++ g +++ +++++ +++++ ++ + + 423s CUFF.37.1.p1 305 ntayytiherERDPKNAMIQaatqAVSLIFTEPIVV-CFTLYLTVVYIINYINFEGYPIVFAKYGFNkG-EQGLSFIGVGVGIVCAGlctpFIYWHY 399 423s ******9999777777777789999********554.44444444444444444444446888899984.555555555555544444444888888 PP 423s 423s MFS_1 267 ls.dr.....lgrrrrlllallllllaalglallavt...ssavllll..vlvliGf.glgfvfpsllalasdlappeeagtasglfntagslgg 349 423s l ++ + ++ rl+ +++++l+ ++++++a+t ++ ++++ +++++Gf l ++f+s++++++++ ++a +a+++++++++ ++ 423s CUFF.37.1.p1 400 LKvNKkrngvICPEDRLYPLFIGCFLLPISMFWFAWTcypHHIHWIVPiiASAFFGFsLLIVFFVSYNYIIDSYQ--HMAPSALAAATLVRYSAS 492 423s 8766666666555************************98855555544558888***888888899888888888..999999999998877443 PP 423s 423s == domain 2 score: -1.5 bits; conditional E-value: 0.2 423s MFS_1 230 lplylqevlgls....glllaglllallalv 256 423s p+yl+ +++ g +++++++++++++ 423s CUFF.37.1.p1 500 RPMYLNLGDHWAtsvlG-FISVAMVPIPFIF 529 423s 57777777777744443.3333333333333 PP 423s 423s >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 128.6 21.0 5.6e-41 1.3e-39 2 352 .. 66 429 .. 65 430 .. 0.87 423s 2 ? -2.4 0.0 0.39 9.4 282 296 .. 450 464 .. 440 476 .. 0.44 423s 423s Alignments for each domain: 423s == domain 1 score: 128.6 bits; conditional E-value: 5.6e-41 423s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlg 98 423s +++++++l+rs++g a+ ++e+l + + ++ +++++++++++ p +l+ r+ + r+l + ++++ ++l+ f ss+ l++ r++ Gl 423s CUFF.45.1.p2 66 GFLYLMAFLDRSNIGNAAVAGMTEALSLYGERLNVAVSIFYVLYILVETPSVVLVKRIKASRMLAFISFAWSMTVLFSGFMSSYGGLIATRLILGLL 162 423s 6899******************************************************999988888888888834444536666************ PP 423s 423s MFS_1 99 agalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg....Wravfyilaivsllafvlfllllpeepperkrkspkeee.. 188 423s +g+lfpa + +++ ++++e+ + +++l a+++l+ ++g l++ +l ++g W++++++ ++vs++++ l l+ lp++ + + + +e+e 423s CUFF.45.1.p2 163 EGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEqVHAGnkegWQWIYIVEGLVSFIGVPLCLFALPDKMENAWFLTREEREva 259 423s ********************************************999666669******************776555555555555555555555** PP 423s 423s MFS_1 189 ..........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275 423s +g +++++++ ++ +kdp +++ ++ +++ ++++g++++lp++ + lg+ g l++ ++ ++++g+i++l++++lsdr++ 423s CUFF.45.1.p2 260 iirrdinaryHGEQHFEWSE-VRKAFKDPKVYVSATSQFCADMVLYGFSSFLPVI-IKGLGFVG-LQTNYMTIPVYIAGVISFLFVAWLSDRTQL-- 351 423s ********************.888888888878*********************7.*******8.888889999999999************776.. PP 423s 423s MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntagslggalg 352 423s r + +++ +++a+g++++ +++s+++ + + ++i +g + ++ l ++++++ + +++ta+g+ +t+ + +g+++ 423s CUFF.45.1.p2 352 RAVYLISASTVVAVGYIIMLASDSNAAKYTATYIIAIGCYIGPGLNLGWLNNNVaGHYKRATAIGIQQTLANSSGIVA 429 423s 88889999999999999999998999999988887775555566666666665546689*********9999999987 PP 423s 423s == domain 2 score: -2.4 bits; conditional E-value: 0.39 423s MFS_1 282 lllllaalglallav 296 423s ++++++ l+++++ + 423s CUFF.45.1.p2 450 GCVIVGGLAYVVMFF 464 423s 222222222222222 PP 423s 423s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 54.9 16.8 1.5e-18 3.5e-17 2 263 .. 92 349 .. 85 361 .. 0.77 423s 2 ! 26.7 12.4 5.4e-10 1.3e-08 212 353 .] 370 516 .. 357 516 .. 0.76 423s 423s Alignments for each domain: 423s == domain 1 score: 54.9 bits; conditional E-value: 1.5e-18 423s MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGl 97 423s l + + sa+++s++++ + + +++ s i++l + a+ ++v ++lG +sd +r ++ l ll++++g ++ + + s++ + +++ v+ ++ 423s CUFF.25.1.p1 92 LACSWASAIQSSTTYSYQV-YATASFN-RTSMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIG-FIVVASsSTISAYVIGSVFISI 185 423s 5677778888888777777.8999999.88889999999******************96666************.55552446677*********** PP 423s 423s MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyilaivsllafv.lfllllpeepperkrkspkeee.... 188 423s g+++l + ++ d+++ + rg++++lls+ + + + g ++ g++ +Wr+ + ++ai++ ++ +++l++ e+ ++k ++ k+ 423s CUFF.25.1.p1 186 GSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVwFTGFIVQGIID--SNWRWGYGMFAIIMPAVMTpAVIILMYLERQANKDENIKKIInyqt 280 423s *************************************666677777777..45*****999999999955533444444444444444333335577 PP 423s 423s MFS_1 189 ...kgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailall 263 423s ++ +++++ ++wka+l l+ +ll+ +g+s+ l + l++y g+++ +++ +++++ v++i+ 423s CUFF.25.1.p1 281 eekNKNKQSKWQKLWKAVLEVD----LFGLILLG-VGWSIllLPFSLTSY--AKNGWKNPSMIA--MMVVGGVILIA--Y 349 423s 77788999999999*****999....44444444.366665588888887..777777335555..77777776666..4 PP 423s 423s == domain 2 score: 26.7 bits; conditional E-value: 5.4e-10 423s MFS_1 212 llialllfffgfsg....lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallll.llaalglallavt.ssavl 302 423s +i+++++ f++++ ++++++y+ +++s + +++ + ++ ++++++ag++++ + r ++l +++l++ ++++ +l+ +++ + +v 423s CUFF.25.1.p1 370 TFITAVIIDFFYYLagylQSMYFTTYTWILYDWS-YRDWTYFNNTMTIALCVFGVFAGAMHRVFHRYKYLQIIGLVIkIVGYGILIRPNFAaTGKVD 465 423s 3444444444444445558889999999******.55555556666666666689999999998887766655555505555555555555999999 PP 423s 423s MFS_1 303 lllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353 423s l+++l+liG+g++f ++ +++ ++ ++p + + as+l ++ ++gga+g+ 423s CUFF.25.1.p1 466 LAWSLILIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGA 516 423s 999**********************************************96 PP 423s 423s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 53.0 19.0 5.4e-18 1.3e-16 23 293 .. 47 347 .. 6 350 .. 0.71 423s 2 ! 26.7 11.5 5.6e-10 1.3e-08 3 201 .. 267 475 .. 266 507 .. 0.74 423s 423s Alignments for each domain: 423s == domain 1 score: 53.0 bits; conditional E-value: 5.4e-18 423s MFS_1 23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpke 117 423s +++++ +s+ + ll+++ +g+++++++ +++++r+G + +++ +++++ lll + a ++w +lv+ +l+G+g gal ++ + ++++p++ 423s CUFF.24.1.p1 47 ISNSYSYSAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAeLLLVT-AVPSWiQVLVGKILAGVGIGALSVLSPGYQSEVAPPQ 142 423s 24444466666888999999*********************************666666.567787******************************* PP 423s 423s MFS_1 118 ergraigllsagfslGailgpllgg...llasslgWravfyilaivsllafvlfllllpeepperkrkspkeee....................... 188 423s rg +++ +++++ +a++++ + l ++Wr +f i+ + ++l++v ++l+lpe+p+ k ee 423s CUFF.24.1.p1 143 IRGAVVATYQIFSTGAALVAACINMgthKLRKTASWRTSFGINMLWGILLMV-GVLFLPESPRYLIYKGRDEEAlrimcnmaelspeseiiqtnfnt 238 423s ***********999999999888772323335555***************88.558888888888887777776*******9888887777666666 PP 423s 423s MFS_1 189 ........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrl 277 423s g+a w +++ + + +++l++ f + + + y+ +v++ +g + l +l++++++ + a + +d lgrr++l 423s CUFF.24.1.p1 239 iksdieieMAGGKA----RWIEIFGKDIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGMTDIFLPAVILGAINFGTTFGALYTIDNLGRRNPL 331 423s 65555444344444....4444555553322333333333333334444444455555555533444446777777777676666667********* PP 423s 423s MFS_1 278 llallllllaalglal 293 423s +++ ++ +++++++a 423s CUFF.24.1.p1 332 IFGAAFQSICFFIYAA 347 423s ************9986 PP 423s 423s == domain 2 score: 26.7 bits; conditional E-value: 5.6e-10 423s MFS_1 3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrl..sdrfGrrrvlllglllfalglllll.fa............s 83 423s +++fl++l r ++g ++ + ++ + ++ + +l + + lga+ + +G+l +d++Grr l++g+++ ++++++ + ++ + 423s CUFF.24.1.p1 267 CLGFLVMLFRELIGNNYYFyYATQVFKGTGMTDIFLPA-VILGAINFGTTFGALytIDNLGRRNPLIFGAAFQSICFFIYAaVGdrkliykngtsdH 362 423s 67889999999999999987888888855555555444.556666666666655569*******************555552314444455555664 PP 423s 423s MFS_1 84 slw.lllvlrvlqGlgagalf.pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178 423s +++v+ +l + +++++ p+g +++ + fp + r++ +++++g+ lG + + +++ ++g+ + ++ ++i ++ +f+ +++++++++ 423s CUFF.24.1.p1 363 RAGsVMIVFSCLFLFSYCCSWgPMGWVIVGETFPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIGFKLGYIYACINLFSSFM---IFFLAKETK 456 423s 45556777777777777666537777999*****************************************998888888888877...677677766 PP 423s 423s MFS_1 179 rkrkspkeeekgtgpaplvpawk 201 423s + +++ ++ ++++p w+ 423s CUFF.24.1.p1 457 GLTLEEVNDL---YMSNIKP-WE 475 423s 6666666663...4444444.44 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (353 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 27 (0.284211); expected 1.9 (0.02) 423s Passed bias filter: 9 (0.0947368); expected 1.9 (0.02) 423s Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) 423s Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 4 [number of targets reported over threshold] 423s # CPU time: 0.13u 0.01s 00:00:00.14 Elapsed: 00:00:00.14 423s # Mc/sec: 75.29 423s // 423s Query: MFS_3 [M=522] 423s Accession: PF05977.12 423s Description: Transmembrane secretion effector 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 8.4 5.5 3.5e-05 0.0033 258 364 .. 60 168 .. 49 202 .. 0.73 423s 423s Alignments for each domain: 423s == domain 1 score: 8.4 bits; conditional E-value: 3.5e-05 423s MFS_3 258 illgalGvGAilgalllsrLRerlsser.lvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavql.avPrWvvgRalavYltvl 352 423s +l g++ +G ++ga+l+s er++++ + + v + + ll ++ ++s ++++ +l+G i als l q + P ++g ++a Y+ + 423s CUFF.24.1.p1 60 LLTGTINAGCLFGAMLSSPFTERIGKKYsICFFSGVYIIAELLLVTAVPSWIQVLVGKILAG-VGIGALSVLSPGYQSeVAPPQIRGAVVATYQIFS 155 423s 688999******************98861555666665555555555555555555555555.56********9999735699************** PP 423s 423s MFS_3 353 aGg.laaGsllWG 364 423s +G+ l a + G 423s CUFF.24.1.p1 156 TGAaLVAACINMG 168 423s 9972455555555 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (522 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 423s # Mc/sec: 692.61 423s // 423s Query: MFS_4 [M=363] 423s Accession: PF06779.13 423s Description: Uncharacterised MFS-type transporter YbfB 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -1.2 0.2 0.053 5.1 146 206 .. 101 156 .. 98 157 .. 0.65 423s 2 ! 16.9 0.5 1.7e-07 1.6e-05 38 175 .. 152 288 .. 132 311 .. 0.84 423s 3 ! 4.3 0.1 0.0012 0.11 119 144 .. 374 399 .. 365 405 .. 0.85 423s 423s Alignments for each domain: 423s == domain 1 score: -1.2 bits; conditional E-value: 0.053 423s MFS_4 146 sasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfG 206 423s s s W+++ +s++ +++ ++ + + ++++s+p+ l +l+GfG 423s CUFF.37.1.p1 101 SHSYKWWIVIQVSVITIVVTFASSV---YSSGIIDIA--SELHSSIPVSTLGSCTFLVGFG 156 423s 5566699999999998888877665...333333333..3677777777777777777776 PP 423s 423s == domain 2 score: 16.9 bits; conditional E-value: 1.7e-07 423s MFS_4 38 ylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavs 133 423s ++G+ vG+l + ls R + ll ++ + ++++++++++++Rf Gv + + l ++ ++ ++ +r v+ + + lG +++ 423s CUFF.37.1.p1 152 LVGFGVGSLPF-APLSDIYGRFIiYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGVFGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIG 247 423s 57999999988.677888888884567778888899999*********************************************99999******** PP 423s 423s MFS_4 134 gllvllllqlglsasslWlalavlsavllllvalllpraalr 175 423s ++ ++ q l++ ++ ++ + +a++++ v++ p + ++ 423s CUFF.37.1.p1 248 PIIGDFITQSYLEWRWTFWINMIWAAAVIVFVFIFFP-ETHE 288 423s ****************977777889999999999999.3333 PP 423s 423s == domain 3 score: 4.3 bits; conditional E-value: 0.0012 423s MFS_4 119 gallfaGvGlGiavsgllvllllqlg 144 423s ++l f GvG+Gi+ +gl+ +++ + 423s CUFF.37.1.p1 374 QGLSFIGVGVGIVCAGLCTPFIYWHY 399 423s 6899*************999887665 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (363 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 423s # Mc/sec: 406.75 423s // 423s Query: MIP [M=227] 423s Accession: PF00230.19 423s Description: Major intrinsic protein 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 167.2 6.0 2.4e-53 2.3e-51 6 227 .] 308 548 .. 303 548 .. 0.91 423s 423s Alignments for each domain: 423s == domain 1 score: 167.2 bits; conditional E-value: 2.4e-53 423s HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS 423s MIP 6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllG 102 423s +f r+ +AEfl+tl+lv++gvgs+l+ +v++ + +++e+ ++a+g++ + +vy+a+giSG+H+NPavT++l+++rk++ ++++Yi Q+ G 423s CUFF.20.1.p1 308 HFFREGFAEFLGTLVLVVFGVGSNLQA--TVTN---GAGGSFESLSFAWGFGCMLGVYIAGGISGGHVNPAVTISLAIFRKFPWYKVPIYIFFQIWG 399 423s 6899******************99844..3433...34579******************************************************** PP 423s 423s HHHHHHHHHHHCHHH............HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHH CS 423s MIP 103 aivaaallklltkgl............esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgiplt 187 423s a+ + al ++ + + g + +kp+++ +a++ E+i t+vLv ++fa+ dd+++ + +++ +gll+a+i ++ +++t 423s CUFF.20.1.p1 400 AFFGGALAYGYHWSSitefeggkdirtPATGGCLYTNPKPYVTWRNAFFDEFIGTAVLVGCLFAILDDTNSPPTQGMTAFIVGLLIAAIGMALGYQT 496 423s *********99988889******9976556666678899*********************************99899******************** PP 423s 423s ST-SSHHHHHHHHHHHTH............STTTTHHHHHHHHHHHHHHHHH CS 423s MIP 188 GaamNpArslgpavvlnk............fedhwvylvGPliGailgalvY 227 423s +++NpAr+lgp+++++ + w + G + G+i+g+l+Y 423s CUFF.20.1.p1 497 SFTLNPARDLGPRMFAWWigygphsfhlyhWWWTWGAWGGTIGGGIAGGLIY 548 423s *************************98855555566788999999999**99 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (227 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 423s # Mc/sec: 739.55 423s // 423s Query: MVP_shoulder [M=118] 423s Accession: PF11978.7 423s Description: Shoulder domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 423s 423s Alignments for each domain: 423s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 423s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 423s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 423s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 423s CUFF.60.1.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 423s 57799999**************************************9.5555555554444 PP 423s 423s >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 423s 423s Alignments for each domain: 423s == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 423s HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS 423s MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 423s +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ 423s CUFF.60.2.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 423s 57799999**************************************9.5555555554444 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (118 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 458.67 423s // 423s Query: Na_H_Exchanger [M=381] 423s Accession: PF00999.20 423s Description: Sodium/hydrogen exchanger family 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+) 423s 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 423s 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 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 138.5 8.5 4.2e-44 1.3e-42 1 198 [. 83 291 .] 83 291 .] 0.97 423s 423s Alignments for each domain: 423s == domain 1 score: 138.5 bits; conditional E-value: 4.2e-44 423s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 423s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 423s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 423s CUFF.13.2.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 423s 6889999******997799999********************99999************************************************ PP 423s 423s HHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSX CS 423s Na_H_Exchanger 87 vlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeaggetslll 178 423s ++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++++ ++ 423s CUFF.13.2.p1 178 MAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRNAGRDW 271 423s **********9**8.69***************************988889**********************************99********* PP 423s 423s HHHHHHHHHHHHHHHHHHHH CS 423s Na_H_Exchanger 179 llliflvvavgglllglvig 198 423s +ll++l+++++g+++g+vig 423s CUFF.13.2.p1 272 VLLVVLYECAFGIFFGCVIG 291 423s ******************97 PP 423s 423s >> CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414-1770(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 87.5 2.1 1.3e-28 4.1e-27 82 198 .. 1 119 [] 1 119 [] 0.97 423s 423s Alignments for each domain: 423s == domain 1 score: 87.5 bits; conditional E-value: 1.3e-28 423s HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTS CS 423s Na_H_Exchanger 82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeagge 173 423s ++l++++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++ 423s CUFF.13.1.p2 1 MLLPVMAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRN 94 423s 67999*******9999998.79***************************988889**********************************99**** PP 423s 423s SSTSXHHHHHHHHHHHHHHHHHHHH CS 423s Na_H_Exchanger 174 tslllllliflvvavgglllglvig 198 423s ++ +++ll++l+++++g+++g+vig 423s CUFF.13.1.p2 95 AGRDWVLLVVLYECAFGIFFGCVIG 119 423s ***********************97 PP 423s 423s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 49.8 1.9 3.6e-17 1.1e-15 1 93 [. 83 184 .. 83 185 .. 0.96 423s 423s Alignments for each domain: 423s == domain 1 score: 49.8 bits; conditional E-value: 3.6e-17 423s XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS 423s Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 423s iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ 423s CUFF.13.3.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 423s 6889999******997799999********************99999************************************************ PP 423s 423s HHHHHHH CS 423s Na_H_Exchanger 87 vlitvvl 93 423s ++ +++ 423s CUFF.13.3.p1 178 MAYGWIF 184 423s ****987 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (381 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) 423s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 423s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 3 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 687.62 423s // 423s Query: NEMO [M=68] 423s Accession: PF11577.7 423s Description: NF-kappa-B essential modulator NEMO 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 11.3 0.0 1.5e-05 0.0014 22 55 .. 54 87 .. 50 98 .. 0.93 423s 423s Alignments for each domain: 423s == domain 1 score: 11.3 bits; conditional E-value: 1.5e-05 423s NEMO 22 lkqsNqalkeRlEeLsawqekqkeerefleeklr 55 423s lk N++lk+R+ e s ++ ee f + klr 423s CUFF.54.1.p1 54 LKNANDSLKGRILEVSLADLQKDEEHSFRKVKLR 87 423s 89**************************999998 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (68 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 527.80 423s // 423s Query: Nucleotid_trans [M=212] 423s Accession: PF03407.15 423s Description: Nucleotide-diphospho-sugar transferase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 15.0 0.0 1e-06 9.9e-05 106 189 .. 238 318 .. 210 333 .. 0.81 423s 423s Alignments for each domain: 423s == domain 1 score: 15.0 bits; conditional E-value: 1e-06 423s Nucleotid_trans 106 desknliNsGfffvrateatkallkkwaeelase.sglw.DqdvfnlllregaakesglkvrvLdtalfvngkgyfvq.vrdeeevk 189 423s ++++n +N G + +r+++at +l+ w + + +e +++ +qd++ +l + + + v++++++++ + f + ++ e+ k 423s CUFF.51.1.p2 238 SQDHNGLNAGSILFRNSPATALFLDIWTDPVVAEcAKANnEQDMLGYLISKHSQ--LASLVGLIPQRKI----NAFHEgPENMEWQK 318 423s 4567888************************999855556*********99664..8888999999999....77777655555554 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (212 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 1062.18 423s // 423s Query: Oleosin [M=113] 423s Accession: PF01277.16 423s Description: Oleosin 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s ------ inclusion threshold ------ 423s 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(+) 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ? -2.3 0.0 0.21 20 87 107 .. 57 77 .. 47 82 .. 0.60 423s 2 ? -0.2 0.1 0.045 4.3 35 46 .. 107 118 .. 104 127 .. 0.85 423s 3 ? 8.8 1.0 7.4e-05 0.007 41 63 .. 141 163 .. 140 167 .. 0.86 423s 423s Alignments for each domain: 423s == domain 1 score: -2.3 bits; conditional E-value: 0.21 423s Oleosin 87 gadqldqakrrlaekasevke 107 423s +++++ k++++ k++++ke 423s CUFF.5.1.p1 57 FTNTIKPQKDKMNIKTNKIKE 77 423s 455555666666666666655 PP 423s 423s == domain 2 score: -0.2 bits; conditional E-value: 0.045 423s Oleosin 35 tPllvlfSPvlv 46 423s Pll++ S ++v 423s CUFF.5.1.p1 107 WPLLIIWSIIIV 118 423s 69*****99998 PP 423s 423s == domain 3 score: 8.8 bits; conditional E-value: 7.4e-05 423s Oleosin 41 fSPvlvPaaivialavagflasg 63 423s +S ++vP+ai + l+v ++l+ 423s CUFF.5.1.p1 141 YSEIWVPIAIYVCLLVLMLLSLI 163 423s 688*************9999864 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (113 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 423s # Mc/sec: 763.09 423s // 423s Query: Orthopox_A5L [M=271] 423s Accession: PF06193.10 423s Description: Orthopoxvirus A5L protein-like 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 8.2 4.9 8.4e-05 0.008 146 192 .. 3 49 .. 1 92 [. 0.77 423s 423s Alignments for each domain: 423s == domain 1 score: 8.2 bits; conditional E-value: 8.4e-05 423s Orthopox_A5L 146 ttpstqpsqtlPtttcvrqsdasistttdivtppqppivatvctptP 192 423s t t s tlP tt q+ +++s t +iv+p + p t + 423s CUFF.11.1.p1 3 TVTETITSGTLPFTTTLAQASGTVSGTVEIVSPKNNPTTVYSGTVAT 49 423s 56678899*************************98886543322222 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (271 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 423s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 423s # Mc/sec: 1137.93 423s // 423s Query: Oxidored_FMN [M=341] 423s Accession: PF00724.19 423s Description: NADH:flavin oxidoreductase / NADH oxidase family 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 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( 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 453.0 0.0 1.1e-139 3.6e-138 1 341 [] 12 360 .. 12 360 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 453.0 bits; conditional E-value: 1.1e-139 423s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 423s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 423s 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++ 423s CUFF.52.1.p1 12 KLFQPIKVGNMQLQHRMVHAPATRLRCLDNGLVMTDLVKEYYKQRSSIPGTLLITESLFSGAKSGGFSNIPCLYNDEHVEAWKPIVQAIHDNDCFVF 108 423s 7************************************************************************************************ PP 423s 423s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 423s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 423s +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+ 423s CUFF.52.1.p1 109 IQFWNLPGELKVDYLEDQErlekvtqGECPMDPTGLPAALGsaysICGEELyvdKFMTKQDIQEHITTYTEAAKRAVFgCGADGVEVHQVNGFLLDK 205 423s *************************99************99999999999999******************************************** PP 423s 423s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 423s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 423s F+ +++++++D+++ Gs+enRarF+le++++v++a+g+ervgyR+Sp+++++k++d++e+ +++++k++++r++ +la++h++epr++++g+v+ 423s CUFF.52.1.p1 206 FVLNGYGDKCDPEYcGSLENRARFCLELLESVVNAIGQERVGYRISPFSDIWKDKDSFEA--HVFMIKKIKERFP---NLAYLHAIEPRQYWNGHVH 297 423s ************************************************************..*************...******************* PP 423s 423s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 423s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 423s ++q+ kn+ ++k++w +p+it+G++d+++ a+++a++e+tlvafgR+fl++pdl+++lk+++pln 423s CUFF.52.1.p1 298 ITQE-KNTLIYKNLWGDPFITAGGHDRDS--AIQMAEQENTLVAFGRYFLSNPDLPFRLKYNLPLN 360 423s **66.************************..********************************997 PP 423s 423s >> CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 423s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 423s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 423s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 423s CUFF.48.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 423s 69*****************************.9999************************************************************* PP 423s 423s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 423s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 423s +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+ 423s CUFF.48.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 423s *************************9***************9999888888999******************************************* PP 423s 423s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 423s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 423s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 423s CUFF.48.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 423s ************************************************************..*************...******************* PP 423s 423s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 423s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 423s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 423s CUFF.48.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 423s **66.9**********************9..********************************987 PP 423s 423s >> CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 423s CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS 423s Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 423s +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ 423s CUFF.49.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 423s 69*****************************.9999************************************************************* PP 423s 423s EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS 423s Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 423s +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+ 423s CUFF.49.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 423s *************************9***************9999888888999******************************************* PP 423s 423s HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS 423s Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 423s F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ 423s CUFF.49.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 423s ************************************************************..*************...******************* PP 423s 423s CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS 423s Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 423s ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln 423s CUFF.49.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 423s **66.9**********************9..********************************987 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (341 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 423s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 3 [number of targets reported over threshold] 423s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 423s # Mc/sec: 359.89 423s // 423s Query: Pantoate_ligase [M=266] 423s Accession: PF02569.14 423s Description: Pantoate-beta-alanine ligase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 341.6 0.0 1.5e-106 1.4e-104 4 265 .. 5 278 .. 2 279 .. 0.91 423s 423s Alignments for each domain: 423s == domain 1 score: 341.6 bits; conditional E-value: 1.5e-106 423s -SHHHHHHHHHHHHHTT-EEEEEEE-SS--HHHHHHHHHHHHHSSEEEEEE---GGGSSTTSCTTTS---HHHHHHHHHHTT-SEEE---HHHH CS 423s Pantoate_ligase 4 ktvaelrellkelrkegkkvglVpTmGaLHeGHlsLvkaakeendvvvvSiFvNplqFgpkedlekYPrtleaDlelleeagvdlvFaPsveem 97 423s k+ ++++++++rk+g+++++VpTmG+LHeGH sLv++ak+++++vvvSiFvNp+qF++ +dl YPrt+++D+++l+++gvdlv+aP+vee+ 423s CUFF.50.1.p2 5 KEKLLIHQQVDNWRKDGNRIAFVPTMGNLHEGHFSLVREAKRHAEKVVVSIFVNPMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYAPTVEEL 98 423s 55566788999***9999**************************************************************************** PP 423s 423s ST......EEEEECSGGCSTHHHHSTTHHHHHHHHHHHHHHHH--SEEEEEGGGHHHHHHHHHHHHHTT-SSEEEEE-XXBXTTSXBXXGGGGG CS 423s Pantoate_ligase 98 yp......tevevkelsevlegasrpghFrGVatvvtkLfnivqpdrayfGqKDaqqlavirrlvkdlnlpveivavpivReedgLAlSSRNky 185 423s yp t v+v++ls++legasrpghFrGV+tvv+kLf+iv+pd+a+fG+KD+qq+a+i+++v+dln+ +ei++vpivR++dgLAlSSRN y 423s CUFF.50.1.p2 99 YPegsqdiTFVDVPKLSTMLEGASRPGHFRGVTTVVSKLFHIVNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQVPIVRADDGLALSSRNGY 192 423s ********99************************************************************************************ PP 423s 423s SXHHHHHHTTHHHHHHHHHH........BHHHHHHHHHHHHHTHTTEEEEEEEEEETTTSSX.BSSBXSEEEEEEEEEETTEEEEEEE CS 423s Pantoate_ligase 186 LseeerkaAlvlykaLkaak........eaealkeaakeeleeeelekadyveivdaetleeleleeekkavllvaakvgkvrLiDni 265 423s L++eerk A++lyk+Lk+++ + e+l +++++el++ ++ d +ei+d++tle+++ + +k++v+l+aa++gk+rLiDni 423s CUFF.50.1.p2 193 LTSEERKIAPNLYKILKKLAqelsngngDLEKLIAETNTELSRCRFI-PDQLEICDSTTLEPFT-AGTKNVVILAAAWLGKARLIDNI 278 423s *******************9555555444444445555555544433.5***********9964.55588*****************8 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (266 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 423s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 831.41 423s // 423s Query: Pantoate_transf [M=259] 423s Accession: PF02548.14 423s Description: Ketopantoate hydroxymethyltransferase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+) 423s 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- 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 341.7 0.0 2.8e-106 1.3e-104 2 258 .. 6 261 .. 5 262 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 341.7 bits; conditional E-value: 2.8e-106 423s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 423s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 423s CUFF.50.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 423s 79*************************************************************************************.99**** PP 423s 423s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 423s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 423s CUFF.50.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 423s *********9.********99866********************************************************************** PP 423s 423s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPa 258 423s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ a +i++a+++Y+ ev++g +Pa 423s CUFF.50.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLSGAGDIRTAIQRYIYEVEQGLYPA 261 423s *********************************************************************8 PP 423s 423s >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 319.5 0.0 1.7e-99 8.1e-98 2 235 .. 6 238 .. 5 240 .] 0.98 423s 423s Alignments for each domain: 423s == domain 1 score: 319.5 bits; conditional E-value: 1.7e-99 423s Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 423s +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a 423s CUFF.52.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 423s 79*************************************************************************************.99**** PP 423s 423s Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 423s ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la 423s CUFF.52.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 423s *********9.********99866********************************************************************** PP 423s 423s Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyae 235 423s ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ 423s CUFF.52.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLS 238 423s ********************************************986 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (259 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 2 [number of targets reported over threshold] 423s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 423s # Mc/sec: 654.62 423s // 423s Query: Phosphodiest [M=357] 423s Accession: PF01663.21 423s Description: Type I phosphodiesterase / nucleotide pyrophosphatase 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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( 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 13.6 0.3 2e-06 0.00019 1 59 [. 48 108 .. 48 116 .. 0.87 423s 2 ! 40.3 0.1 1.6e-14 1.5e-12 143 237 .. 166 261 .. 117 275 .. 0.77 423s 423s Alignments for each domain: 423s == domain 1 score: 13.6 bits; conditional E-value: 2e-06 423s EEEEEETT-BCCHHHHCGGTSHHHHHHHHHSEEESE..EE-SSS-SHHHHHHHHHHSS-HH CS 423s Phosphodiest 1 vlvislDGlradlldrlaellpnlaaLakegvsapn..lrpvfPtlTfpnhaslvTGlyPg 59 423s v+++ +D lrad ++ ++ +p+ ++L+ +++++ + Pt+T+p + +l TG+ Pg 423s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGfsAFARSPTVTMPRLKALTTGTIPG 108 423s 7999***********9448*********977666643488889***************997 PP 423s 423s == domain 2 score: 40.3 bits; conditional E-value: 1.6e-14 423s THHHHHHHHHHCHHHHCHTHCHHHHHTT.TSECEEEEEEEHHHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEE....EEEEES--- CS 423s Phosphodiest 143 pledkvdkavlqtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetn....iilvSDHGm 234 423s ++ ++v + ++++f +++l+ +l +d l++++ ++D++gH +Gp sp ++ +l ++D i +++++l+e +++tn i+l +DHGm 423s CUFF.53.1.p1 166 SFFVSDYTEVD-NNVTRNF-DHALPSSLsHSWDALILHYLGVDHIGHLYGPSSPLLNIKLLEIDTIISRIYKYLQEY--DEKTNthslIVLCGDHGM 258 423s 33332223344.4478888.568888889**********************************************98..444444466********* PP 423s 423s EE- CS 423s Phosphodiest 235 adv 237 423s ++v 423s CUFF.53.1.p1 259 NEV 261 423s 998 PP 423s 423s 423s 423s Internal pipeline statistics summary: 423s ------------------------------------- 423s Query model(s): 1 (357 nodes) 423s Target sequences: 95 (31269 residues searched) 423s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 423s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 423s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 423s Initial search space (Z): 95 [actual number of targets] 423s Domain search space (domZ): 1 [number of targets reported over threshold] 423s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 423s # Mc/sec: 365.59 423s // 423s Query: PLA2_B [M=491] 423s Accession: PF01735.17 423s Description: Lysophospholipase catalytic domain 423s Scores for complete sequences (score includes all domains): 423s --- full sequence --- --- best 1 domain --- -#dom- 423s E-value score bias E-value score bias exp N Sequence Description 423s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 423s 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(+ 423s 423s 423s Domain annotation for each sequence (and alignments): 423s >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) 423s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 423s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 423s 1 ! 677.6 1.8 4.4e-208 4.2e-206 1 490 [. 132 614 .. 132 615 .. 0.99 423s 423s Alignments for each domain: 423s == domain 1 score: 677.6 bits; conditional E-value: 4.4e-208 423s PLA2_B 1 iaiavSGGGyramltgaGvlkAldsRtdnatglgGlLqsatYlaGlsGgsWlvgslavNnftsvqellkkkeedsvwdlensivnpeglnlvknikr 97 423s ++ia+SGGG+ram++g+G+ +A+dsR + + l+GlLqsa+Y++GlsGgsWlvgs+a+Nnft+++ l++ +vw+le+s+++p+g n+++n+++ 423s CUFF.12.1.p1 132 LGIAFSGGGLRAMVNGGGAFNAFDSRFESDSPLSGLLQSAMYISGLSGGSWLVGSVAINNFTNITYLRD-----NVWNLEHSVFAPHGDNVIENLNY 223 423s 69*******************************************************************.....8********************** PP 423s 423s PLA2_B 98 yeeivdevekKksagfnvsltDiwGralseklveleegganltlsslkdaekfqnaemplPiivadgrkpgesvinlNatvfEfsPyelgswdakln 194 423s y+++ +e+++Kk+agf+ sltD+wGrals+klv++e+gg+ +t+ss++++++fqna++p+Piivad+r ++e++i +N+++fEf+ ye+g+wd++++ 423s CUFF.12.1.p1 224 YNDLRKEIDQKKHAGFDCSLTDLWGRALSRKLVDAERGGPGITYSSMRNQSWFQNADYPYPIIVADSRLEEETAIPANTSIFEFTAYEFGTWDNGIK 320 423s ************************************************************************************************* PP 423s 423s PLA2_B 195 sFvdvkylGtklsnGtvvkkgkcvagfdnaGflmgtsstlFnevlleinstsmlesllkellkkllkdlsedsediaqyapnpfkdaeeenqnatqs 291 423s +F++++y+Gt+l +G+++ +++c++++dnaGf+mgts+tlFn++ll++n++ +++ +++l+ +l+dls+ ++dia y+ np++++++ n+ + ++ 423s CUFF.12.1.p1 321 AFIPMEYVGTHLLDGVPP-DKSCIHNYDNAGFVMGTSATLFNSFLLDWNENVKKNDTYYDILHAILEDLSKHQDDIAPYP-NPYQNYTTSNTSVVNA 415 423s ******************.*********************************9**************************9.**************** PP 423s 423s PLA2_B 292 ivesktLdlvdggedgqniplvpllqkerkvdvifaldssadteeswpdgsslvktyeRvle...ssqvkgkkfpyvpdqntfvnlgLnkrptffGc 385 423s ++ +t+dlvdgged +nipl+pll+++r vdv+fa+ds+++ + wp gss+v+tyeRv++ +++v++++fpy+pd+nt+++lgLn+rptffGc 423s CUFF.12.1.p1 416 FEPYDTIDLVDGGEDRENIPLWPLLHPQRFVDVVFAIDSTYNDPYGWPLGSSIVATYERVVTfnaNKSVDVRGFPYIPDENTIISLGLNTRPTFFGC 512 423s ************************************************************999889999**************************** PP 423s 423s PLA2_B 386 DarnltdlsatvdestpPlvvylpnekytylsnlstfklsykdseregliengfeaatqdnekdddefaacvacaiirRklerknittpseckkcFe 482 423s 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+ 423s CUFF.12.1.p1 513 DGKNTTAGNHDVDNNTPPLLVYFPNYPWTYYSNISTFTMSMDDKMANGILENAFMSTTQNN---NESFAVCLACAIIQRSLERKKLSTPTQCSSCFQ 606 423s ************************************************************9...9******************************** PP 423s 423s PLA2_B 483 nycwngtv 490 423s +ycw+gt+ 423s CUFF.12.1.p1 607 EYCWDGTL 614 423s ******97 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (491 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 424s # Mc/sec: 600.45 424s // 424s Query: Polysacc_synt_C [M=142] 424s Accession: PF14667.5 424s Description: Polysaccharide biosynthesis C-terminal domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 424s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 424s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 424s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 424s 424s Alignments for each domain: 424s == domain 1 score: -1.8 bits; conditional E-value: 0.34 424s Polysacc_synt_C 13 slstvlssiLqglg 26 424s +++ ++++ L++lg 424s CUFF.38.1.p3 51 YMFAMSTGWLIALG 64 424s 33333333333332 PP 424s 424s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 424s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 424s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 424s CUFF.38.1.p3 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 424s 7899999999999999*********************************8883357******************99999999999889955555 PP 424s 424s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 424s l p++ ++giv++ ++ +++ 424s CUFF.38.1.p3 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 424s 4444666666666666555555555543 PP 424s 424s == domain 3 score: -0.6 bits; conditional E-value: 0.14 424s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 424s +l gl+ +a +a +++v+vg ++ + + 424s CUFF.38.1.p3 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 424s 33333333331111335555555555555544 PP 424s 424s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 424s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 424s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 424s CUFF.38.1.p3 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 424s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 424s 424s >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 424s 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 424s 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 424s 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 424s 424s Alignments for each domain: 424s == domain 1 score: -1.8 bits; conditional E-value: 0.34 424s Polysacc_synt_C 13 slstvlssiLqglg 26 424s +++ ++++ L++lg 424s CUFF.39.1.p1 51 YMFAMSTGWLIALG 64 424s 33333333333332 PP 424s 424s == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 424s Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 424s L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ 424s CUFF.39.1.p1 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 424s 7899999999999999*********************************8883357******************99999999999889955555 PP 424s 424s Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 424s l p++ ++giv++ ++ +++ 424s CUFF.39.1.p1 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 424s 4444666666666666555555555543 PP 424s 424s == domain 3 score: -0.6 bits; conditional E-value: 0.14 424s Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 424s +l gl+ +a +a +++v+vg ++ + + 424s CUFF.39.1.p1 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 424s 33333333331111335555555555555544 PP 424s 424s == domain 4 score: 6.0 bits; conditional E-value: 0.0013 424s Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 424s ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ 424s CUFF.39.1.p1 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 424s 566666777899999999999999998555440455668888888888344488**************9999888775 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (142 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 18 (0.189474); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 2 [number of targets reported over threshold] 424s # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 424s # Mc/sec: 90.94 424s // 424s Query: Pombe_5TM [M=256] 424s Accession: PF09437.9 424s Description: Pombe specific 5TM protein 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 516.1 19.2 9.6e-160 9.1e-158 15 256 .] 1 242 [. 1 242 [. 1.00 424s 424s Alignments for each domain: 424s == domain 1 score: 516.1 bits; conditional E-value: 9.6e-160 424s Pombe_5TM 15 sfaysgnsesvlvgenitsirktllinetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 112 424s sfaysgnsesv++genitsi+kt+linetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 424s CUFF.6.1.p1 1 SFAYSGNSESVWTGENITSIWKTILINETGSYCVAARPMTMDGAEFNLDLMGYSVSEDQINNDEIGIWNYISVAEMGGVLLFLSYWIWTCLHFSKIIF 98 424s 8************************************************************************************************* PP 424s 424s Pombe_5TM 113 paqkviclyiflfalnqtlqekieeyvfssevikyrkfysvyeiidflrtnfyrlfviycalgigiirtvskylvikgisivialesvyrislkkdvy 210 424s paqkviclyiflfalnqtlqe+ieeyvfsse+ikyr+fysvyeiidflrtnfyrlfviycalg+gi+rtv+kyl+ikgisivial+svy+isl+kdvy 424s CUFF.6.1.p1 99 PAQKVICLYIFLFALNQTLQECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRTVPKYLMIKGISIVIALCSVYWISLYKDVY 196 424s ************************************************************************************************** PP 424s 424s Pombe_5TM 211 vvseifdliqyevfpaiwvysichllkqctsvttyenaskarfirr 256 424s vvseifd+iqyev paiwvysichllkqctsvttyenaskarf+rr 424s CUFF.6.1.p1 197 VVSEIFDMIQYEVSPAIWVYSICHLLKQCTSVTTYENASKARFFRR 242 424s *********************************************8 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (256 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 801.60 424s // 424s Query: PsbN [M=43] 424s Accession: PF02468.14 424s Description: Photosystem II reaction centre N protein (psbN) 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 12.8 0.0 9e-06 0.00043 27 43 .] 118 136 .. 106 136 .. 0.85 424s 424s Alignments for each domain: 424s == domain 1 score: 12.8 bits; conditional E-value: 9e-06 424s PsbN 27 FGPPskeLaDPF..edHED 43 424s FGP +++L DPF dH D 424s CUFF.13.3.p1 118 FGPHAAKLVDPFswGDHGD 136 424s ***********84469988 PP 424s 424s >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 12.0 0.0 1.6e-05 0.00075 27 43 .] 118 136 .. 107 136 .. 0.84 424s 424s Alignments for each domain: 424s == domain 1 score: 12.0 bits; conditional E-value: 1.6e-05 424s PsbN 27 FGPPskeLaDPF..edHED 43 424s FGP +++L DPF dH D 424s CUFF.13.2.p1 118 FGPHAAKLVDPFswGDHGD 136 424s ***********84469988 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (43 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 2 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 474.59 424s // 424s Query: REPA_OB_2 [M=98] 424s Accession: PF16900.4 424s Description: Replication protein A OB domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 424s 424s Alignments for each domain: 424s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 424s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 424s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 424s CUFF.40.1.p3 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 424s 689999****555554444444367789**********************9875 PP 424s 424s >> CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 424s 424s Alignments for each domain: 424s == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 424s REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 424s +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l 424s CUFF.41.1.p2 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 424s 689999****555554444444367789**********************9875 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (98 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 2 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 816.77 424s // 424s Query: Ribosomal_S3Ae [M=205] 424s Accession: PF01015.17 424s Description: Ribosomal S3Ae family 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 303.1 3.9 5e-95 4.7e-93 2 205 .] 16 221 .. 15 221 .. 0.99 424s 424s Alignments for each domain: 424s == domain 1 score: 303.1 bits; conditional E-value: 5e-95 424s S----S-TTSSEEEEEEE--TTSSSSEECEEEEE--BTTC-SCCCHCC-EEEEESHCCCTTCCCSS-EEEEEEEEEETT.EEEEEEEEE--HHHH CS 424s Ribosomal_S3Ae 2 kkkkvvDkfkkKeWydvkaPalfgkreiGktlvtrtqgtkiaseglkgrvvevslaDLtndeeqafrklklkiedvqgk.altnFhgmeltrDkl 95 424s kk+vvD+f++K+Wyd+kaPa+f+ +++Gktlv+rt+g k+a+++lkgr++evslaDL++dee++frk+kl++ed+qgk +lt+F+g ++t+Dkl 424s CUFF.54.1.p1 16 IKKRVVDPFSRKDWYDIKAPAFFEVKNVGKTLVNRTAGLKNANDSLKGRILEVSLADLQKDEEHSFRKVKLRVEDIQGKsCLTSFNGFDMTSDKL 110 424s 599***********************************************************99******************************* PP 424s 424s HHC--CTB-EEEEEEEEEETTTEEEEEEEEEEE--TGCGS.S-B---HHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHCTTHHHHHHHHHHTTTS CS 424s Ribosomal_S3Ae 96 rslvrkwsslIeaivdvkttDgyllrvfvvafTkkrenqk.ktsyakssqvkaIrkkmveilteeaseldlkelvkklipesigkeiekeakkIy 189 424s rslvrkw+s+Iea+ ++kttDgyl r+fv++fT +r nq+ kt+ya+ssq++aI++km+++++++a+ +++kelv+klipe ig+ iek++++Iy 424s CUFF.54.1.p1 111 RSLVRKWQSTIEANQTIKTTDGYLCRIFVIGFTSRRVNQVkKTTYAQSSQIRAIHQKMFQVIQNQANGCSMKELVQKLIPEVIGRAIEKATNNIY 205 424s *********************************************************************************************** PP 424s 424s -EEEEEEEEEEEEE-- CS 424s Ribosomal_S3Ae 190 plrnveirKvkvlkkP 205 424s pl+nv++rKvk+lk+P 424s CUFF.54.1.p1 206 PLQNVFVRKVKILKAP 221 424s **************98 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (205 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 930.68 424s // 424s Query: Ribosomal_S6e [M=126] 424s Accession: PF01092.18 424s Description: Ribosomal protein S6e 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 199.8 0.0 6.5e-64 6.2e-62 1 126 [] 11 136 .. 11 136 .. 1.00 424s 424s Alignments for each domain: 424s == domain 1 score: 199.8 bits; conditional E-value: 6.5e-64 424s -EEEEEETTTTEEEEEE---HHHHTTCTT-BSSEEEESTTT-SSS-S-EEEEEEEEESCC-BB-TT--SSSEEEEEE-TTSSS---SSSS--EEEE CS 424s Ribosomal_S6e 1 mklnisdpatgkqklievddekklrtfiekrigeevdgdalgeelkgyvlkitggsdkqGfpmkqgvlthgrvrlLlskggsgyrprrkGerkrks 96 424s mklnis+pa+g+qklie+dd+++lr f+ekr+g+ev gd++g+e++gyv+kitgg+dkqGfpm qgvl ++rvrlLl+ g+++yrprr+Gerkrks 424s CUFF.58.1.p1 11 MKLNISYPANGTQKLIEIDDDRRLRVFMEKRMGQEVPGDSVGPEFAGYVFKITGGNDKQGFPMFQGVLLPHRVRLLLRAGHPCYRPRRDGERKRKS 106 424s 9*********************************************************************************************** PP 424s 424s EE-SB--SSEEEEEEEEEE--SS--TTSSS CS 424s Ribosomal_S6e 97 vrgcivsadlsvlnlvivkkgekdiegLtd 126 424s vrgciv +dl+vl l i+k+ge+di+gLtd 424s CUFF.58.1.p1 107 VRGCIVGQDLAVLALAIIKQGEQDIPGLTD 136 424s *****************************8 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (126 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 1040.86 424s // 424s Query: RNA_POL_M_15KD [M=36] 424s Accession: PF02150.15 424s Description: RNA polymerases M/15 Kd subunit 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 9.6 0.0 4.5e-05 0.0043 19 33 .. 56 70 .. 53 72 .. 0.78 424s 2 ! 4.0 0.0 0.0026 0.24 8 24 .. 112 128 .. 109 130 .. 0.87 424s 424s Alignments for each domain: 424s == domain 1 score: 9.6 bits; conditional E-value: 4.5e-05 424s STEEEETTSS-EEES CS 424s RNA_POL_M_15KD 19 gknfeCrqCgYeepa 33 424s +k++ C+qC+ +epa 424s CUFF.7.1.p1 56 NKVLRCSQCDWHEPA 70 424s 33466*********8 PP 424s 424s == domain 2 score: 4.0 bits; conditional E-value: 0.0026 424s TSBEEEEECSSSTEEEE CS 424s RNA_POL_M_15KD 8 gNlLlpkedkegknfeC 24 424s Nl l+k+++eg++f C 424s CUFF.7.1.p1 112 QNLFLSKSKEEGVIFLC 128 424s 59**********99988 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (36 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 624.98 424s // 424s Query: SAUGI [M=111] 424s Accession: PF06106.10 424s Description: S. aureus uracil DNA glycosylase inhibitor 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(-) 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 424s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 424s 424s Alignments for each domain: 424s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 424s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 424s y ++ n ++i g +nhf ++++ 424s CUFF.26.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 424s 4666788999***********998754 PP 424s 424s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 424s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 424s +n + + i+ lm+an l s+ +l h+ + + 424s CUFF.26.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 424s 555566667764269**************997654 PP 424s 424s >> CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 424s 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 424s 424s Alignments for each domain: 424s == domain 1 score: 5.5 bits; conditional E-value: 0.0021 424s SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 424s y ++ n ++i g +nhf ++++ 424s CUFF.27.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 424s 4666788999***********998754 PP 424s 424s == domain 2 score: 6.1 bits; conditional E-value: 0.0013 424s SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 424s +n + + i+ lm+an l s+ +l h+ + + 424s CUFF.27.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 424s 555566667764269**************997654 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (111 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 2 [number of targets reported over threshold] 424s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 424s # Mc/sec: 201.47 424s // 424s Query: Smim3 [M=60] 424s Accession: PF17307.1 424s Description: Small integral membrane protein 3 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 3.5 0.0 0.0027 0.26 12 33 .. 11 32 .. 2 35 .. 0.70 424s 2 ! 5.4 0.1 0.00072 0.068 42 56 .. 88 102 .. 85 106 .. 0.89 424s 424s Alignments for each domain: 424s == domain 1 score: 3.5 bits; conditional E-value: 0.0027 424s Smim3 12 vLPkhiLDiWvivLiiLativi 33 424s LP++ ++ +vLii+ t ++ 424s CUFF.51.1.p1 11 SLPRYKFLLFSVVLIIVMTTLV 32 424s 5677777777788877766555 PP 424s 424s == domain 2 score: 5.4 bits; conditional E-value: 0.00072 424s Smim3 42 ataviiYRvrthPvl 56 424s at v+i+R++ hP+ 424s CUFF.51.1.p1 88 ATRVLIHRLKYHPTT 102 424s 9************85 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (60 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 563.66 424s // 424s Query: SnoaL [M=126] 424s Accession: PF07366.11 424s Description: SnoaL-like polyketide cyclase 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 5.8 0.0 0.00065 0.062 45 64 .. 7 26 .. 3 28 .. 0.89 424s 2 ! 22.5 0.1 4.3e-09 4.1e-07 5 110 .. 14 107 .. 9 114 .. 0.90 424s 424s Alignments for each domain: 424s == domain 1 score: 5.8 bits; conditional E-value: 0.00065 424s HHHHHHHHHCTTCEEEEEEE CS 424s SnoaL 45 afveelfkafPDlkvevedl 64 424s f+++lfkaf D++++ve+l 424s CUFF.36.1.p1 7 SFIRQLFKAFTDFSTDVESL 26 424s 5889*************986 PP 424s 424s == domain 2 score: 22.5 bits; conditional E-value: 4.3e-09 424s HHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE-TT-EEEEEEEE CS 424s SnoaL 5 rfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGipptGkkvkfeeit 101 424s ++++++ s d++ l+ ++++d+ + ++++ l++f ++++l++ + l ++v+++v++g k+a+ + + i +G + +++ i 424s CUFF.36.1.p1 14 KAFTDF--STDVESLRGFLTPDYRQL--VDGRELTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIA--------HAIRSSGESSRIKVIA 98 424s 556666..779***********9988..559**********************************99998885........56999*********** PP 424s 424s EEEEETTEE CS 424s SnoaL 102 llrvedGkI 110 424s ++ ++dG+I 424s CUFF.36.1.p1 99 FYSFKDGRI 107 424s ********9 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (126 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 424s # Mc/sec: 327.01 424s // 424s Query: SnoaL_2 [M=102] 424s Accession: PF12680.6 424s Description: SnoaL-like domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 38.4 0.0 8.5e-14 8.1e-12 2 100 .. 10 108 .. 9 110 .. 0.92 424s 424s Alignments for each domain: 424s == domain 1 score: 38.4 bits; conditional E-value: 8.5e-14 424s HHHHHHHH..TTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEET CS 424s SnoaL_2 2 rrflaaln..agdldalaalfapdvvwedpggelrGreairaffraafaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrved 96 424s r+++ a++ + d++ l+ +++pd+++ g e ++++ + +a++ ++ l++ ++++v++g+++a+ +++ i+ +g+ ++++++++ ++d 424s CUFF.36.1.p1 10 RQLFKAFTdfSTDVESLRGFLTPDYRQLVDGRE-LTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIAHA-IRSSGESSRIKVIAFYSFKD 104 424s 789999998899***************999865.5889999999999999*******************9888877.9******************* PP 424s 424s TEEE CS 424s SnoaL_2 97 GkIv 100 424s G+I 424s CUFF.36.1.p1 105 GRIS 108 424s ***6 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (102 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 949.75 424s // 424s Query: Sugar_tr [M=452] 424s Accession: PF00083.23 424s Description: Sugar (and other) transporter 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+ 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 370.4 24.1 1.4e-114 6.7e-113 2 451 .. 10 466 .. 9 467 .. 0.95 424s 424s Alignments for each domain: 424s == domain 1 score: 370.4 bits; conditional E-value: 1.4e-114 424s HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTST.T--SHHHHHH....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-T CS 424s Sugar_tr 2 alvaalggllfgYdtgvigafltllkfaknfg.lsksksskee.ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaa 96 424s +++++++g l+g dtg i+++l + +f+++f ++ s+ ++ s+ ++ l+++ ++G+++G+++++++++r+G+k+s+ +++ +++i+ +l ++a 424s CUFF.24.1.p1 10 VVFISMSGWLQGADTGSISGILGMRDFQSRFAdRYNPISNSYSySAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAELLLVTA 106 424s 67899**********************99987534433333334899************************************************** PP 424s 424s TTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS 424s Sugar_tr 97 kgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193 424s s+ +++vg++l+G+g+G+ svl+P y+sE+Ap+++Rga+v yq + t lvaa++++g+ k +++ wr +g+++++ +ll++++lflPE 424s CUFF.24.1.p1 107 V--PSWIQVLVGKILAGVGIGALSVLSPGYQSEVAPPQIRGAVVATYQIFSTGAALVAACINMGTHKLRKTASWRTSFGINMLWGILLMVGVLFLPE 201 424s *..89******************************************************************************************** PP 424s 424s -HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS- CS 424s Sugar_tr 194 SPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeee....kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgl 286 424s SPryl+ kg++eea +++ ++ + +++++ ++ +++++ e e ka w e++++ ++r+r+ +g+++++f l G+n+ +yy++++f+ +g+ 424s CUFF.24.1.p1 202 SPRYLIYKGRDEEALRIMCNMAELSPESEIIQTNFNTIKSDIEIEmaggKARWIEIFGK-DIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGM 297 424s ********************99999999988888888888888888888*********9.99*********************************** PP 424s 424s THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH.....HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH CS 424s Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg...ivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsEl 378 424s ++ +l +i+g++nf +tf a++++d +GRR+ l++Gaa+++icf+i++ l++++++ a+ v+ivf +lf++ + ++wgp+ wv+v E+ 424s CUFF.24.1.p1 298 TDIFLPAVILGAINFGTTFGALYTIDNLGRRNPLIFGAAFQSICFFIYAavgDRKLIYKNGTsdHRAGSVMIVFSCLFLFSYCCSWGPMGWVIVGET 394 424s *************************************************87655667777768899******************************* PP 424s 424s SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS 424s Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieel 451 424s fp + Rsk++++a+ nwl nf is+++p+i +aig ++ ++++a++++++ +++ff etkg+tlee++ l 424s CUFF.24.1.p1 395 FPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIG-FKLGYIYACINLFSSFMIFFLAKETKGLTLEEVNDL 466 424s ************************************.********************************9976 PP 424s 424s >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 30.0 30.1 2.7e-11 1.3e-09 25 437 .. 121 530 .. 105 534 .. 0.75 424s 424s Alignments for each domain: 424s == domain 1 score: 30.0 bits; conditional E-value: 2.7e-11 424s HHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS 424s Sugar_tr 25 llkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121 424s + + ++ g s+ +s s+l + flvG +Gsl + +l+d++GR ++ ++ ++f i +v ++a+ +v+ l++ R++ G++ + + 424s CUFF.37.1.p1 121 FASSVYSSGIIDIASELHSSIPVSTLGSCTFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAH---NVWTLAIVRFFQGVFGSTPLA 214 424s 5555555555555555555677899999*********************************************...********************* PP 424s 424s HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS---HHHHHHTT-HHHHHHHHHHHHH CS 424s Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill.lflPESPrylvekgkeeeakevlaklrg 216 424s + +is + ++ R ++ + ++ +G +++ i+g ++ + + + wr+++++++++a ++++++ +f+PE+ e + + + l+k g 424s CUFF.37.1.p1 215 NAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFItQSYLE---WRWTFWINMIWAAAVIVFVfIFFPET----HEDTILDYKAKYLRKTTG 304 424s *********999999999999999999********99888455555...**************99998689****....333333333334444333 PP 424s 424s C....HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHT.TTHHHHSS-THH.....HHHHHHHHHH.HHH CS 424s Sugar_tr 217 e....edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyys.ptifenlglsks.....llvtiivgvv.nfv 302 424s + + +re + + ++++a+ ++ ++ ++++ ++++ + ++ + in+i + + p +f + g++k + + ++vg+v + 424s CUFF.37.1.p1 305 NtayyTIHERERDPKNAMIQAA----TQAVSLIFTE------PIVVCFTLYLTVVYIINYINFEGyPIVFAKYGFNKGeqglsF-IGVGVGIVcAGL 390 424s 3123333333333333333333....3344444444......455555666666777787777654889********9988844.444444440445 PP 424s 424s HHHHHHHHHHHS-SHHHHHHH........HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH..SHTTTHHHHHH CS 424s Sugar_tr 303 atfvaiflvdrfGRRtllllG........aagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsEl..fpqsvRskala 389 424s t + + ++ +++ +++ ++g++++ + + ++++ i iv ++ a+f++++ v++v + + q++ ++ala 424s CUFF.37.1.p1 391 CTPFIYWHYLKVNKKRNGVICpedrlyplFIGCFLLPISMF--WFAWTCYP--HHIHWIVP-IIASAFFGFSLLIVFFVSYNYIidSYQHMAPSALA 482 424s 56666688999999999****9***7765555555555554..44444443..23444444.455699999******999999844469******** PP 424s 424s HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS CS 424s Sugar_tr 390 iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffv 437 424s a+ v a+ is++ + ++g + v +++ v+++ + f+f+ 424s CUFF.37.1.p1 483 AATLVRYSASGGISMVARPMYLNLGDHWATSVLGFISVAMVPIPFIFY 530 424s *************************99999999999999999998886 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (452 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 2 [number of targets reported over threshold] 424s # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.07 424s # Mc/sec: 191.57 424s // 424s Query: SUI1 [M=76] 424s Accession: PF01253.21 424s Description: Translation initiation factor SUI1 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+ 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 16.5 0.2 5e-07 4.8e-05 3 52 .. 82 132 .. 80 177 .. 0.88 424s 2 ? -1.8 0.0 0.26 25 16 38 .. 167 188 .. 158 189 .. 0.69 424s 424s Alignments for each domain: 424s == domain 1 score: 16.5 bits; conditional E-value: 5e-07 424s SUI1 3 pkihirveqrggrKkvTtvsglepfgidlkklakelkkkfacsgsvvk.dg 52 424s +k+++rve +g+ ++T +g+++ +l +l+++++++ ++ ++ dg 424s CUFF.54.1.p1 82 RKVKLRVEDIQGKSCLTSFNGFDMTSDKLRSLVRKWQSTIEANQTIKTtDG 132 424s 69*******************************************944444 PP 424s 424s == domain 2 score: -1.8 bits; conditional E-value: 0.26 424s SUI1 16 KkvTtvsglepfgidlkklakel 38 424s K ++++ ++g +k+l+++l 424s CUFF.54.1.p1 167 KMFQVIQNQ-ANGCSMKELVQKL 188 424s 444455555.8888888888876 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (76 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 424s # Mc/sec: 233.98 424s // 424s Query: Sulfatase [M=309] 424s Accession: PF00884.22 424s Description: Sulfatase 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 11.6 0.1 7.3e-06 0.00069 3 61 .. 48 106 .. 46 125 .. 0.91 424s 2 ! 11.6 0.0 7.7e-06 0.00073 218 309 .] 223 321 .. 221 321 .. 0.71 424s 424s Alignments for each domain: 424s == domain 1 score: 11.6 bits; conditional E-value: 7.3e-06 424s EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS- CS 424s Sulfatase 3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgry 61 424s vv++++d l+a+ + + ++ ++ t+ l + ++g+ f+ f + +++ p + al tg 424s CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGFSAFARSPTVTMPRLKALTTGTI 106 424s 9***********9999999999999999999**********999************975 PP 424s 424s == domain 2 score: 11.6 bits; conditional E-value: 7.7e-06 424s HHHHHHHHHHHHHHHHHTTTGGGE..EEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC......EEECSEEE......GGGHH CS 424s Sulfatase 218 veyvDdligrvlaaLeenglldnt..lvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap......rvseelvs......hiDlf 300 424s + ++D i+r++++L+e ++ nt l+v +Dhg + +gg + + + t l+ ++e+++ ++++++s ++D++ 424s CUFF.53.1.p1 223 LLEIDTIISRIYKYLQEYDEKTNThsLIVLCGDHGMNEVG----NHGGSS---SGETTAALSLLFPSNELSHinkpilNMDDNPYSilerveQVDVV 312 424s 6799************999999987789999****94322....222222...33444444455555555556666776888888888888899999 PP 424s 424s HHHHHHTTE CS 424s Sulfatase 301 ptildlagi 309 424s pti l+gi 424s CUFF.53.1.p1 313 PTICLLLGI 321 424s 999888875 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (309 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 424s # Mc/sec: 805.54 424s // 424s Query: ThiJ_like [M=196] 424s Accession: PF17124.4 424s Description: ThiJ/PfpI family-like 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(-) 424s 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( 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 29.3 0.3 1.1e-10 3.3e-09 3 155 .. 47 185 .. 46 198 .. 0.78 424s 424s Alignments for each domain: 424s == domain 1 score: 29.3 bits; conditional E-value: 1.1e-10 424s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 424s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 424s CUFF.47.1.p1 47 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 134 424s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 424s 424s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlw 155 424s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + 424s CUFF.47.1.p1 135 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYH 185 424s 99.9999999999988888.......4568*****************999998887655 PP 424s 424s >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 29.1 0.2 1.2e-10 3.9e-09 3 160 .. 26 169 .. 25 185 .. 0.78 424s 424s Alignments for each domain: 424s == domain 1 score: 29.1 bits; conditional E-value: 1.2e-10 424s ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 424s ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ 424s CUFF.46.1.p1 26 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 113 424s 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP 424s 424s ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmerts 160 424s + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + t+ 424s CUFF.46.1.p1 114 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYHKHVTA 169 424s 99.9999999999988888.......4568*****************99999998866655555 PP 424s 424s >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 10.9 0.2 4.5e-05 0.0014 77 169 .. 77 164 .. 16 190 .. 0.77 424s 424s Alignments for each domain: 424s == domain 1 score: 10.9 bits; conditional E-value: 4.5e-05 424s ThiJ_like 77 sesFsleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpe...ldlktttlPlwmertsillgstaek 169 424s ++ ++ +y++ + GG++ ++ lh+ ++ + v++a+c+g + l + k+ +k t+ ++ e + ++ +++ 424s CUFF.42.1.p2 77 ASDINFSDYSIFFAAGGHGTLF-DFPSATNLHKGAAKIY-------SMGGVIAAVCHGPVILPCIKDStgfSIVKGKTVTAFNEIAEQQMNLMPTF 164 424s 3345889************999.9999999999988877.......5568********99998887775554456666666666555555555555 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (196 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 424s Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) 424s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 424s Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 3 [number of targets reported over threshold] 424s # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 424s # Mc/sec: 149.48 424s // 424s Query: TPP_enzyme_C [M=153] 424s Accession: PF02775.20 424s Description: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 2.2 0.0 0.0076 0.72 115 153 .] 132 172 .. 107 172 .. 0.80 424s 2 ? -3.6 0.1 0.47 45 112 124 .. 234 246 .. 227 252 .. 0.76 424s 3 ! 81.8 0.0 2.3e-27 2.2e-25 24 153 .] 415 539 .. 395 539 .. 0.85 424s 424s Alignments for each domain: 424s == domain 1 score: 2.2 bits; conditional E-value: 0.0076 424s HHHHHTTSE.EE..EESSH.HHHHHHHHHHHHCSSSEEEEEE CS 424s TPP_enzyme_C 115 klaealGak.ga..rvekadveeleealkealekkgpaliev 153 424s ++a+ l + +a r e+a + ++ a+++a+ +++p++ie+ 424s CUFF.32.1.p1 132 EIAKKLTCAaVAikRAEDA-PVMIDHAIRQAILQHKPVYIEI 172 424s 6788887775667665555.78899*******999****996 PP 424s 424s == domain 2 score: -3.6 bits; conditional E-value: 0.47 424s -HHHHHHHTTSEE CS 424s TPP_enzyme_C 112 dfaklaealGakg 124 424s f+klaeal + + 424s CUFF.32.1.p1 234 AFVKLAEALNCAA 246 424s 6999999998874 PP 424s 424s == domain 3 score: 81.8 bits; conditional E-value: 2.3e-27 424s ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHT CS 424s TPP_enzyme_C 24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaeal 120 424s + +g++G+++p A+G ++a+p+r+ +++vGDG+f+ ++qe+++++r++lp+++++lnN+gy + ++ ++ r ++ dfa+++e+l 424s CUFF.32.1.p1 415 EMQWGHIGWSVPSAMGYAVAAPERRTIVMVGDGSFQLTGQEISQMIRHKLPVLIFLLNNRGYTIEIQIHDGPYN-R--------IQNWDFAAFCESL 502 424s 56789*********************************************************766666666664.2........6799********* PP 424s 424s TSE.EE....EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS 424s TPP_enzyme_C 121 Gak.ga....rvekadveeleealkeal.ekkgpaliev 153 424s + g ++ eel a+k al +k+gp+lie+ 424s CUFF.32.1.p1 503 NGEtGKakglHAKTG--EELTSAIKVALqNKEGPTLIEC 539 424s 666555674455555..***********99*******97 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (153 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 740.49 424s // 424s Query: TPP_enzyme_M [M=137] 424s Accession: PF00205.21 424s Description: Thiamine pyrophosphate enzyme, central domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 76.8 0.0 7.2e-26 6.9e-24 3 113 .. 207 316 .. 205 325 .. 0.90 424s 424s Alignments for each domain: 424s == domain 1 score: 76.8 bits; conditional E-value: 7.2e-26 424s HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHH.HH-SEEEEES-SSSTCCCTTTT CS 424s TPP_enzyme_M 3 raaellkkakrpvilvGggvsrsgaskelrelaeklgiPvvttlmgkgaipedhplylG.mlgllgspaaneal.eeaDlvlllGarlsdirttgss 97 424s aael++k+++p++l+G + + +ga+ ++++lae+l++ + ++++kg+++e+h++y+G ++g ++s++ +a+ e++Dlv+ G+ ++d++t g 424s CUFF.32.1.p1 207 IAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMPAAKGFYSEEHKNYAGvYWGEVSSSETTKAVyESSDLVIGAGVLFNDYSTVGWR 303 424s 599***************************************************************99999999899****************9966 PP 424s 424s TTTTTT-EEEEEESSC CS 424s TPP_enzyme_M 98 pefapeakiihididp 113 424s + +p+ i +++d 424s CUFF.32.1.p1 304 AAPNPN---ILLNSDY 316 424s 666666...5555554 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (137 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 740.64 424s // 424s Query: TPP_enzyme_N [M=172] 424s Accession: PF02776.17 424s Description: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 121.7 0.1 1.3e-39 1.3e-37 1 170 [. 9 183 .. 9 185 .. 0.94 424s 2 ! 2.6 0.0 0.005 0.48 136 161 .. 516 541 .. 428 545 .. 0.91 424s 424s Alignments for each domain: 424s == domain 1 score: 121.7 bits; conditional E-value: 1.3e-39 424s EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEE CS 424s TPP_enzyme_N 1 ltvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvls 97 424s +tv+++l+++L + g++ f vpG+ +l lld l+ +g++ + + +E ++afaA+gyar+ g +++++vt+ +Ga+ a+ ++ +A+ +++P++++s 424s CUFF.32.1.p1 9 MTVGTYLAQRLVEIGIKNHFVVPGDYNLRLLDFLEYYPGLSEIGCCNELNCAFAAEGYARSNG-IACAVVTYSVGALTAFDGIGGAYAENLPVILVS 104 424s 89**********************************************************976.********************************* PP 424s 424s EE--CCCHH.....S--TC.-T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EEEH CS 424s TPP_enzyme_N 98 gdrptslrg.....qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleevde 170 424s g+++t + + +++l q+++++++t +a+ ++++e++p++++ Air+a ++ Pvy+e+p ++ +++++ 424s CUFF.32.1.p1 105 GSPNTNDLSsghllHHTLGTHDfeYQMEIAKKLTCAAVAIKRAEDAPVMIDHAIRQA-ILQHKPVYIEIPTNMANQPCPV 183 424s *********9888755555333657********************************.99****************9986 PP 424s 424s == domain 2 score: 2.6 bits; conditional E-value: 0.005 424s HHHHHHHHHHHHHSSS--EEEEEEEH CS 424s TPP_enzyme_N 136 lpealrrAirtalsgrpgPvylelpk 161 424s + e+l Ai++al+++ gP ++e + 424s CUFF.32.1.p1 516 TGEELTSAIKVALQNKEGPTLIECAI 541 424s 568999***************99665 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (172 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 707.06 424s // 424s Query: Transferase [M=434] 424s Accession: PF02458.14 424s Description: Transferase family 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 12.1 0.0 3.1e-06 0.0003 348 403 .. 49 107 .. 37 111 .. 0.76 424s 424s Alignments for each domain: 424s == domain 1 score: 12.1 bits; conditional E-value: 3.1e-06 424s Transferase 348 nstlkaelv..skgkkdgeevtvsswlklplyevdFGwgkP..vyvvpvvsskkdnkill 403 424s n tl+a+++ ++g ++ + +v +wlk++l v FG g P v++ +++s+ + ++i++ 424s CUFF.2.1.p1 49 N-TLMAHCFetYNGVEKSGTQCVADWLKVGLLAVTFGAGGPrlVNTLGGSSPTTKRVIYI 107 424s 4.5666664226777777*********************995566777888888877554 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (434 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 1807.69 424s // 424s Query: TRAPP [M=146] 424s Accession: PF04051.15 424s Description: Transport protein particle (TRAPP) component 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-505(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 83.1 0.2 8.5e-28 8e-26 1 99 [. 34 142 .. 34 163 .. 0.88 424s 424s Alignments for each domain: 424s == domain 1 score: 83.1 bits; conditional E-value: 8.5e-28 424s TRAPP 1 fefllgelvsylirdskdveeve..........krLekmGyrvGlrllelllarerpretdilevlkfickdlWkalfgkqidnlktnhrgeyvltd 87 424s ++fll+elv+++ r ++d ++ + + Le++G++vG +++e +l+ +r+r t++ +v+ f+c++lW ++f+k+ dnlktn+rg +vltd 424s CUFF.55.1.p1 34 LDFLLIELVHTAKRLAEDRKKKSsseksiesdfQMLESIGFQVGRKITE-RLLLNRNRITETTDVMRFLCRELWPIVFRKPLDNLKTNRRGIFVLTD 129 424s 58************9999888889999**********************.888888***************************************** PP 424s 424s TRAPP 88 nef.pltrfvelp 99 424s + f ++t+++ + 424s CUFF.55.1.p1 130 TYFyWFTKMTAMT 142 424s *********6433 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (146 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 1022.78 424s // 424s Query: TRI12 [M=599] 424s Accession: PF06609.12 424s Description: Fungal trichothecene efflux pump (TRI12) 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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(+) 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 29.7 27.0 1.3e-11 1.2e-09 31 494 .. 69 553 .. 49 575 .. 0.69 424s 424s Alignments for each domain: 424s == domain 1 score: 29.7 bits; conditional E-value: 1.3e-11 424s TRI12 31 elpegyyrsprvvasfaafslnvvatyfvlqasasa.lpnilqdvgqsensslfstlwttgqavsil...vmgrltdrfgrrpfvilthilglvgai 123 424s + + y+ r + af + ++a + +s+ + + +s++stl +s + ++g+++d r l ++ ++g i 424s CUFF.25.1.p1 69 AVRDSIYQNKRGMYLAYAFGIAILACSWASAIQSSTtYSYQVYATASFNRTSMISTLEIATAIISSVckpILGKFSDITSRPMTYTLVLLFYVIGFI 165 424s 4567777777777666778877777766543333330333334445556679999998776665544233899999987765555666677788889 PP 424s 424s TRI12 124 vgctatkfntllaamtllgv.aagpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiy.iitsaiav.llivvwy 217 424s v ++++ + + + ++ + ++g l+vg+l s k + + ++s p ++t + ++ q + i+ +wrw + ++ ii+ a+ +i++ y 424s CUFF.25.1.p1 166 VVASSSTISAYVIGSVFISIgSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVWFTGFIVQGI-IDSNWRWGYGMFaIIMPAVMTpAVIILMY 261 424s 888888888877777776662457777899*********9987777889********9999999986.9******9987646777765514555555 PP 424s 424s TRI12 218 ypps......fa.....qlhgk...kvrkreelak....ldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkp 296 424s ++ q k k +k ++l k +d g+il+ vg s++ll s ++ w+ +i ++ g l+ ++ ye++ p 424s CUFF.25.1.p1 262 LERQankdenIKkiinyQTEEKnknKQSKWQKLWKavleVDLFGLILLGVGWSILLLPFSLTSYAKNGWKNPSMIAMMVVGGVILIAYSGYEMFIAP 358 424s 4332111111221111122223111444555554444448*******************************************************99 PP 424s 424s TRI12 297 vrpivppalfkdtrgfvcillissimgamnlslviiypqq.vvnifgsslknwee..tawmsatasfgtgagvvvlgslfhlvrhirwqilvgalwl 390 424s p p +++ r f+ ++i + l +y ++ s ++w + a + fg +ag + +fh ++++ lv + 424s CUFF.25.1.p1 359 Y-PSCPRRVMN--RTFITAVIIDFFYY-LAGYLQSMYFTTyTWILYDWSYRDWTYfnNTMTIALCVFGVFAGAM--HRVFHRYKYLQIIGLVIKI-- 447 424s 6.888998875..77999888876554.44455556655504556889*****8521334457789******87..6899977776544444333.. PP 424s 424s TRI12 391 taflgamssvnrd.nknaaialsv.lsgfvvawaqditmllvqfittdedlgvafavvaaarpfagsiftaafislysnrypkelashlssalrgtd 485 424s g + n + +a s+ l g+ +++ + + q +dl +a +++ + g+i +a ++sn+ pk l +l s++ t+ 424s CUFF.25.1.p1 448 -VGYGILIRPNFAaTGKVDLAWSLiLIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGAAIASPIFSNKVPKYLREYLPSSINDTQ 543 424s .33344433332202233344443144555555555566778999999***************999999999999*******************999 PP 424s 424s TRI12 486 ipq.asfssl 494 424s + + s ssl 424s CUFF.25.1.p1 544 VYNfYSDSSL 553 424s 7651455555 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (599 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.07 424s # Mc/sec: 245.93 424s // 424s Query: UPF0489 [M=178] 424s Accession: PF12640.6 424s Description: UPF0489 domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 12.0 0.0 1e-05 0.00099 7 43 .. 186 229 .. 183 270 .. 0.67 424s 424s Alignments for each domain: 424s == domain 1 score: 12.0 bits; conditional E-value: 1e-05 424s UPF0489 7 HheaLeaiyraigskklpsdlslvHlDaHpDllipk..........k 43 424s H+ +L+ i r +++ + ++s++H+D+H D pk 424s CUFF.38.1.p4 186 HTIVLP-ILRSVSRAY--GPVSIIHFDSHLDSWKPKvfgggkssvgS 229 424s 444444.555566666..99***********8777666555554440 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (178 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 1137.86 424s // 424s Query: Usher [M=551] 424s Accession: PF00577.19 424s Description: Outer membrane usher protein 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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- 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 11.1 0.0 7.2e-06 0.00069 35 132 .. 17 114 .. 2 116 .. 0.77 424s 424s Alignments for each domain: 424s == domain 1 score: 11.1 bits; conditional E-value: 7.2e-06 424s EEEEEEEEEETTTTEEEEEEEEE--SSSS---EEEEEEEEE-GGGS-CCCCCEEEEEEEEESSSEEEEEECTTEEEEEEEE-SEEEEE-S---TTTT CS 424s Usher 35 ssrtylqraipqlkskLtlGesytssdiFdsvsfrGvsLasddnmlPdslrgyaPevrGiArtnAkVtirqnGyviYqtlVppGpFeiqdlnptsss 131 424s +s + r + +l+++ G s+++++i + + + +L+ + + + ++ +P G Ar+n +t+ + +viY+t+ +pG + + s++ 424s CUFF.20.1.p2 17 WSARRVCRIFANLRTHRARGSSNVKNEIKKQEGNVSFQLKMSVKQFVSDGHIVRPYLLGLARSNPGLTVIEHDRVIYRTASAPGSGDLPKVTLVSGG 113 424s 5555566667777777777777777777777777777777776666667777889999**************************9888888777766 PP 424s 424s C CS 424s Usher 132 g 132 424s g 424s CUFF.20.1.p2 114 G 114 424s 5 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (551 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 424s Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 424s # Mc/sec: 919.60 424s // 424s Query: zf-C2H2 [M=23] 424s Accession: PF00096.25 424s Description: Zinc finger, C2H2 type 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 16.2 1.0 5.9e-07 5.6e-05 1 20 [. 31 50 .. 31 51 .. 0.95 424s 2 ! 19.7 1.9 4.7e-08 4.4e-06 2 23 .] 60 82 .. 59 82 .. 0.96 424s 424s Alignments for each domain: 424s == domain 1 score: 16.2 bits; conditional E-value: 5.9e-07 424s EEETTTTEEESSHHHHHHHH CS 424s zf-C2H2 1 ykCpdCgksFkrksnLkrHi 20 424s ++C+ C k+F+r +nL+rH 424s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 424s 89*****************5 PP 424s 424s == domain 2 score: 19.7 bits; conditional E-value: 4.7e-08 424s EETTTTEEESSHHHHHHHHHC.C CS 424s zf-C2H2 2 kCpdCgksFkrksnLkrHirt.H 23 424s +Cp+C ++krk++LkrHi++ H 424s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRfH 82 424s 6********************99 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (23 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 340.88 424s // 424s Query: zf-C2H2_4 [M=24] 424s Accession: PF13894.5 424s Description: C2H2-type zinc finger 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 10.0 4.0 7.8e-05 0.0074 1 20 [. 31 50 .. 31 53 .. 0.89 424s 2 ! 12.9 1.6 8.8e-06 0.00084 2 24 .] 60 82 .. 59 82 .. 0.93 424s 424s Alignments for each domain: 424s == domain 1 score: 10.0 bits; conditional E-value: 7.8e-05 424s zf-C2H2_4 1 fkCpiCgksFsskkaLlrHl 20 424s f+C++C k+F+++++L rH 424s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 424s 89********99999****4 PP 424s 424s == domain 2 score: 12.9 bits; conditional E-value: 8.8e-06 424s zf-C2H2_4 2 kCpiCgksFsskkaLlrHlkthH 24 424s +Cp+C +++k+ L+rH+++ H 424s CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRFH 82 424s 7********99999*****9988 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (24 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) 424s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 316.54 424s // 424s Query: zf-C2H2_6 [M=27] 424s Accession: PF13912.5 424s Description: C2H2-type zinc finger 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 20.0 3.1 2.7e-08 2.6e-06 1 26 [. 30 55 .. 30 56 .. 0.96 424s 2 ? -3.5 0.6 0.62 59 4 7 .. 61 64 .. 60 65 .. 0.86 424s 424s Alignments for each domain: 424s == domain 1 score: 20.0 bits; conditional E-value: 2.7e-08 424s zf-C2H2_6 1 vfeCdeCsksFpslqaLggHkksHrk 26 424s vf Cd+C k+F + +L+ Hk++H k 424s CUFF.45.1.p1 30 VFPCDQCAKRFTRHENLTRHKACHSK 55 424s 79**********************97 PP 424s 424s == domain 2 score: -3.5 bits; conditional E-value: 0.62 424s zf-C2H2_6 4 CdeC 7 424s C++C 424s CUFF.45.1.p1 61 CPYC 64 424s **** PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (27 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 424s Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 323.13 424s // 424s Query: zf-C2H2_jaz [M=27] 424s Accession: PF12171.7 424s Description: Zinc-finger double-stranded RNA-binding 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 8.2 0.2 0.00018 0.017 2 21 .. 31 50 .. 30 51 .. 0.92 424s 2 ! 5.3 0.1 0.0014 0.13 4 21 .. 61 78 .. 58 79 .. 0.93 424s 3 ? -3.8 0.1 1 95 10 16 .. 166 172 .. 165 172 .. 0.83 424s 424s Alignments for each domain: 424s == domain 1 score: 8.2 bits; conditional E-value: 0.00018 424s CBBTTTTBBBSSHHHHHCCT CS 424s zf-C2H2_jaz 2 fYCvlCdKyFksenaldnHl 21 424s f C C+K F +++l H+ 424s CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 424s 77*****************6 PP 424s 424s == domain 2 score: 5.3 bits; conditional E-value: 0.0014 424s BTTTTBBBSSHHHHHCCT CS 424s zf-C2H2_jaz 4 CvlCdKyFksenaldnHl 21 424s C++C+ +k l+ H+ 424s CUFF.45.1.p1 61 CPYCEIKCKRKDLLKRHI 78 424s *****************8 PP 424s 424s == domain 3 score: -3.8 bits; conditional E-value: 1 424s BBSSHHH CS 424s zf-C2H2_jaz 10 yFksena 16 424s F+sen+ 424s CUFF.45.1.p1 166 SFNSENV 172 424s 59***96 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (27 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 383.98 424s // 424s Query: zf-Di19 [M=54] 424s Accession: PF05605.11 424s Description: Drought induced 19 protein (Di19), zinc-binding 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s ------ inclusion threshold ------ 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ? 11.2 1.0 2e-05 0.0019 3 28 .. 59 85 .. 57 88 .. 0.79 424s 424s Alignments for each domain: 424s == domain 1 score: 11.2 bits; conditional E-value: 2e-05 424s zf-Di19 3 ftCPyCgkeltvkeLv.eHvedeHrve 28 424s ++CPyC+ + + k L+ +H++ H ++ 424s CUFF.45.1.p1 59 IPCPYCEIKCKRKDLLkRHIQRFHNDK 85 424s 68*****99877776527***999876 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (54 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) 424s Passed bias filter: 10 (0.105263); expected 1.9 (0.02) 424s Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 211.80 424s // 424s Query: zf-H2C2_2 [M=26] 424s Accession: PF13465.5 424s Description: Zinc-finger double domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 7.6 0.4 0.0003 0.028 12 26 .] 28 42 .. 26 42 .. 0.83 424s 2 ! 10.1 4.9 4.9e-05 0.0047 1 21 [. 45 65 .. 45 70 .. 0.90 424s 3 ? 0.9 0.1 0.042 4 2 10 .. 74 83 .. 74 89 .. 0.70 424s 424s Alignments for each domain: 424s == domain 1 score: 7.6 bits; conditional E-value: 0.0003 424s zf-H2C2_2 12 ekpyeCplCdkaFkt 26 424s ++ + C+ C+k+F++ 424s CUFF.45.1.p1 28 KRVFPCDQCAKRFTR 42 424s 4559*********85 PP 424s 424s == domain 2 score: 10.1 bits; conditional E-value: 4.9e-05 424s zf-H2C2_2 1 nLrrHlrkHtgekpyeCplCd 21 424s nL+rH + H + p Cp+C 424s CUFF.45.1.p1 45 NLTRHKACHSKAEPIPCPYCE 65 424s 8*******************7 PP 424s 424s == domain 3 score: 0.9 bits; conditional E-value: 0.042 424s zf-H2C2_2 2 LrrHlr.kHt 10 424s L+rH+ +H 424s CUFF.45.1.p1 74 LKRHIQrFHN 83 424s 89**962586 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (26 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 424s Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 428.55 424s // 424s Query: zf-TRAF [M=60] 424s Accession: PF02176.17 424s Description: TRAF-type zinc finger 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s ------ inclusion threshold ------ 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ? 7.3 8.4 0.00042 0.04 9 56 .. 30 72 .. 27 80 .. 0.77 424s 2 ? -2.0 0.0 0.33 31 26 43 .. 276 293 .. 274 294 .. 0.77 424s 424s Alignments for each domain: 424s == domain 1 score: 7.3 bits; conditional E-value: 0.00042 424s EEE-TT--S-BEEETTTCCCCCCTTSTTS--XXSSXXXXSXXXXXHHH CS 424s zf-TRAF 9 pvpCpnecckkkilRkdlkdHlekdCkkaevkCkfkevGCkekvkrea 56 424s pC ++c+k ++l H + k +++C++ C+ k+kr++ 424s CUFF.45.1.p1 30 VFPC-DQCAKRFTRHENLTRHKACHSKAEPIPCPY----CEIKCKRKD 72 424s 5689.88**9999999*****997777889*****....555555554 PP 424s 424s == domain 2 score: -2.0 bits; conditional E-value: 0.33 424s CCCCCCTTSTTS--XXSS CS 424s zf-TRAF 26 lkdHlekdCkkaevkCkf 43 424s + + ++ +C + v C + 424s CUFF.45.1.p1 276 ISNLIDLECIRRSVFCLY 293 424s 666678889999999988 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (60 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) 424s Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) 424s Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 424s # Mc/sec: 459.67 424s // 424s Query: Zn_clus [M=40] 424s Accession: PF00172.17 424s Description: Fungal Zn(2)-Cys(6) binuclear cluster domain 424s Scores for complete sequences (score includes all domains): 424s --- full sequence --- --- best 1 domain --- -#dom- 424s E-value score bias E-value score bias exp N Sequence Description 424s ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 424s 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( 424s 424s 424s Domain annotation for each sequence (and alignments): 424s >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) 424s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 424s --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 424s 1 ! 30.8 13.0 1.3e-11 1.2e-09 1 39 [. 5 42 .. 5 44 .. 0.91 424s 424s Alignments for each domain: 424s == domain 1 score: 30.8 bits; conditional E-value: 1.3e-11 424s -S-HHHHHCT---STSSSS-HHHHHCT---ECCCTCCCE CS 424s Zn_clus 1 haCdnCrkkKvKCdakkPaCsnCkklnleCtfysesskr 39 424s +aCd Cr kK+KC++++P C+ C +++C ys++ +r 424s CUFF.38.1.p1 5 KACDLCRLKKIKCSRGQPRCQTCTLFQADCH-YSNRARR 42 424s 59*****************************.7777665 PP 424s 424s 424s 424s Internal pipeline statistics summary: 424s ------------------------------------- 424s Query model(s): 1 (40 nodes) 424s Target sequences: 95 (31269 residues searched) 424s Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) 424s Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) 424s Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) 424s Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) 424s Initial search space (Z): 95 [actual number of targets] 424s Domain search space (domZ): 1 [number of targets reported over threshold] 424s # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 424s # Mc/sec: 445.79 424s // 424s [ok] 424s 424s eval $cmd 424s ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v 424s * [Sat Mar 16 21:11:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 424s * [Sat Mar 16 21:11:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 424s -skipping training candidate: CUFF.60.1.p1, not unique enough 424s -skipping training candidate: CUFF.26.1.p1, not unique enough 424s -skipping training candidate: CUFF.38.1.p3, not unique enough 424s -skipping training candidate: CUFF.48.1.p1, not unique enough 424s -skipping training candidate: CUFF.60.1.p2, not unique enough 424s -skipping training candidate: CUFF.30.1.p1, not unique enough 424s -skipping training candidate: CUFF.41.1.p1, not unique enough 424s -skipping training candidate: CUFF.41.1.p2, not unique enough 424s -skipping training candidate: CUFF.30.2.p1, not unique enough 424s -skipping training candidate: CUFF.52.1.p3, not unique enough 424s -skipping training candidate: CUFF.20.1.p2, not unique enough 424s -skipping training candidate: CUFF.47.1.p1, not unique enough 424s -skipping training candidate: CUFF.48.1.p3, not unique enough 424s -skipping training candidate: CUFF.13.3.p1, not unique enough 424s -skipping training candidate: CUFF.28.1.p1, not unique enough 425s -skipping training candidate: CUFF.34.1.p2, not unique enough 425s -skipping training candidate: CUFF.13.1.p1, not unique enough 425s -skipping training candidate: CUFF.38.1.p5, not unique enough 425s -skipping training candidate: CUFF.27.1.p2, not unique enough 425s -skipping training candidate: CUFF.41.1.p3, not unique enough 425s -skipping training candidate: CUFF.13.1.p2, not unique enough 425s -skipping training candidate: CUFF.27.1.p3, not unique enough 425s -skipping training candidate: CUFF.41.1.p4, not unique enough 425s 425s -redundancy-minimized set includes 72 / 95 = 75.79% 425s 425s * [Sat Mar 16 21:11:13 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 425s PCT_GC: 37 425s * [Sat Mar 16 21:11:13 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores 426s * [Sat Mar 16 21:11:14 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 428s * [Sat Mar 16 21:11:16 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 428s Selecting best orfsblastp output found (blastp.outfmt6) and processing... 428s PFAM output found (pfam.domtblout) and processing... 428s 428s * [Sat Mar 16 21:11:16 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement 428s Training start codon pattern recognition* [Sat Mar 16 21:11:16 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 429s * [Sat Mar 16 21:11:17 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 429s -round: 1 440s -round: 2 452s -round: 3 464s -round: 4 475s -round: 5 487s * [Sat Mar 16 21:12:15 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 487s -parsing scores 501s * [Sat Mar 16 21:12:29 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 502s Error in library(ggplot2) : there is no package called ‘ggplot2’ 502s Execution halted 502s * [Sat Mar 16 21:12:30 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 503s Error in library(ggplot2) : there is no package called ‘ggplot2’ 503s Execution halted 503s * [Sat Mar 16 21:12:31 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 503s Error in library(seqLogo) : there is no package called ‘seqLogo’ 503s Execution halted 503s * [Sat Mar 16 21:12:31 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 504s Error in library(seqLogo) : there is no package called ‘seqLogo’ 504s Execution halted 504s * [Sat Mar 16 21:12:32 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 504s num features: 62 num_incorporate: 18 504s -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 504s -feature swap of score: 1.94858034627835 instead of -0.884029553505083 504s -feature swap of score: 2.12188175995298 instead of -0.685343860113718 504s -feature swap of score: 2.31823471239686 instead of 1.3320086516586 504s -feature swap of score: 3.37895288616016 instead of 1.93080159572592 504s -feature swap of score: 3.63482432490867 instead of 3.22946119764082 504s -feature swap of score: 5.41689919345157 instead of 3.20580366781557 504s -num feature swaps: 7 504s * [Sat Mar 16 21:12:32 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 504s -round: 1 516s -round: 2 527s -round: 3 539s -round: 4 550s -round: 5 562s * [Sat Mar 16 21:13:30 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 562s -parsing scores 576s * [Sat Mar 16 21:13:44 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 577s Error in library(ggplot2) : there is no package called ‘ggplot2’ 577s Execution halted 577s * [Sat Mar 16 21:13:45 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 577s Error in library(ggplot2) : there is no package called ‘ggplot2’ 577s Execution halted 577s * [Sat Mar 16 21:13:45 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 578s Error in library(seqLogo) : there is no package called ‘seqLogo’ 578s Execution halted 578s * [Sat Mar 16 21:13:46 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 578s Refining start codon selections. 578s -number of revised start positions: 1 578s * [Sat Mar 16 21:13:46 2024] Running CMD: cp /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 578s copying output to final output file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Sat Mar 16 21:13:46 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 578s Making bed file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed 578s * [Sat Mar 16 21:13:46 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 579s Making pep file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep 579s * [Sat Mar 16 21:13:47 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 579s Making cds file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds 579s transdecoder is finished. See output files /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* 579s 579s 579s 579s 579s ## convert to genome coordinates 579s ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3 579s 579s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1, 612 579s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [3], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1471, 2862 579s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CUFF.30.2.p1. 579s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1164, 2072 579s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 3, 440 579s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1899, 2783 579s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 2759, 3736 579s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1142, 4111 579s -Warning [16], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 3280, 4776 579s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 1, 534 579s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 4115, 4705 579s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 579s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 579s CDS coords: 3, 722 579s 579s 579s Done. 81 / 82 transcript orfs could be propagated to the genome 579s 579s 579s 579s ## make bed files for viewing with GenomeView 579s 579s # covert cufflinks gtf to bed 579s ../../util/gtf_to_bed.pl transcripts.gtf > transcripts.bed 579s 579s # convert the genome-based gene-gff3 file to bed 579s ../../util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.genome.gff3 > transcripts.fasta.transdecoder.genome.bed 580s 580s 580s 580s # ensure no fatal problems w/ pep file 580s ../../util/fasta_prot_checker.pl transcripts.fasta.transdecoder.pep 580s 580s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 580s 580s 580s exit 0 580s make[1]: Leaving directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/cufflinks_example' 580s Running example in $... 580s make[1]: Entering directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 580s ./runMe.sh 580s #!/bin/bash -ve 580s 580s if [ ! -e genome.fasta ]; then 580s gunzip -c genome.fasta.gz > genome.fasta 580s fi 580s 580s if [ ! -e pasa_assemblies.fasta ]; then 580s gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta 580s fi 580s 580s if [ ! -e pasa_assemblies.gff3 ]; then 580s gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3 580s fi 580s 580s if [ ! -e pasa_assemblies_described.txt ]; then 580s gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt 580s fi 580s 580s 580s # get the gene-to-transcript relationships 580s cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt 580s 580s ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir 580s CMD: mkdir -p /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir 580s * [Sat Mar 16 21:13:48 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat 580s 580s 580s -first extracting base frequencies, we'll need them later. 581s 581s 581s - extracting ORFs from transcripts. 581s -total transcripts to examine: 858 586s [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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 586s 586s 586s ################################# 586s ### Done preparing long ORFs. ### 586s ################################## 586s 586s Use file: /tmp/autopkgtest.x2gTgS/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. 586s 586s Then, run TransDecoder.Predict for your final coding region predictions. 586s 586s 586s 586s 586s 586s ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir 587s * [Sat Mar 16 21:13:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 587s * [Sat Mar 16 21:13:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 587s -skipping training candidate: asmbl_804.p1, not unique enough 587s -skipping training candidate: asmbl_395.p1, not unique enough 587s -skipping training candidate: asmbl_805.p1, not unique enough 587s -skipping training candidate: asmbl_446.p1, not unique enough 587s -skipping training candidate: asmbl_745.p1, not unique enough 587s -skipping training candidate: asmbl_692.p1, not unique enough 587s -skipping training candidate: asmbl_570.p1, not unique enough 587s -skipping training candidate: asmbl_558.p1, not unique enough 587s -skipping training candidate: asmbl_694.p1, not unique enough 587s -skipping training candidate: asmbl_434.p1, not unique enough 587s -skipping training candidate: asmbl_688.p1, not unique enough 587s -skipping training candidate: asmbl_725.p1, not unique enough 587s -skipping training candidate: asmbl_507.p1, not unique enough 587s -skipping training candidate: asmbl_814.p1, not unique enough 587s -skipping training candidate: asmbl_632.p1, not unique enough 587s -skipping training candidate: asmbl_654.p1, not unique enough 587s -skipping training candidate: asmbl_777.p1, not unique enough 587s -skipping training candidate: asmbl_290.p1, not unique enough 587s -skipping training candidate: asmbl_745.p2, not unique enough 587s -skipping training candidate: asmbl_746.p1, not unique enough 587s -skipping training candidate: asmbl_290.p2, not unique enough 587s -skipping training candidate: asmbl_746.p2, not unique enough 587s -skipping training candidate: asmbl_115.p1, not unique enough 587s -skipping training candidate: asmbl_560.p1, not unique enough 587s -skipping training candidate: asmbl_561.p1, not unique enough 587s -skipping training candidate: asmbl_784.p1, not unique enough 587s -skipping training candidate: asmbl_778.p1, not unique enough 587s -skipping training candidate: asmbl_508.p1, not unique enough 587s -skipping training candidate: asmbl_21.p1, not unique enough 587s -skipping training candidate: asmbl_22.p1, not unique enough 587s -skipping training candidate: asmbl_450.p1, not unique enough 587s -skipping training candidate: asmbl_448.p1, not unique enough 587s -skipping training candidate: asmbl_449.p1, not unique enough 587s -skipping training candidate: asmbl_772.p1, not unique enough 587s -skipping training candidate: asmbl_556.p1, not unique enough 587s -skipping training candidate: asmbl_68.p1, not unique enough 587s -skipping training candidate: asmbl_363.p1, not unique enough 587s -skipping training candidate: asmbl_470.p1, not unique enough 587s -skipping training candidate: asmbl_471.p1, not unique enough 587s -skipping training candidate: asmbl_773.p1, not unique enough 587s -skipping training candidate: asmbl_667.p1, not unique enough 587s -skipping training candidate: asmbl_576.p1, not unique enough 587s -skipping training candidate: asmbl_774.p1, not unique enough 587s -skipping training candidate: asmbl_234.p1, not unique enough 587s -skipping training candidate: asmbl_639.p1, not unique enough 587s -skipping training candidate: asmbl_640.p1, not unique enough 588s -skipping training candidate: asmbl_727.p1, not unique enough 588s -skipping training candidate: asmbl_672.p1, not unique enough 588s -skipping training candidate: asmbl_852.p1, not unique enough 588s -skipping training candidate: asmbl_565.p1, not unique enough 588s -skipping training candidate: asmbl_813.p1, not unique enough 588s -skipping training candidate: asmbl_786.p1, not unique enough 588s -skipping training candidate: asmbl_726.p1, not unique enough 588s -skipping training candidate: asmbl_635.p1, not unique enough 588s -skipping training candidate: asmbl_501.p1, not unique enough 588s -skipping training candidate: asmbl_559.p1, not unique enough 588s -skipping training candidate: asmbl_624.p1, not unique enough 588s -skipping training candidate: asmbl_599.p1, not unique enough 588s -skipping training candidate: asmbl_768.p1, not unique enough 588s -skipping training candidate: asmbl_537.p1, not unique enough 588s -skipping training candidate: asmbl_787.p1, not unique enough 588s -skipping training candidate: asmbl_585.p1, not unique enough 588s -skipping training candidate: asmbl_519.p1, not unique enough 588s -skipping training candidate: asmbl_734.p1, not unique enough 588s -skipping training candidate: asmbl_844.p1, not unique enough 588s -skipping training candidate: asmbl_789.p1, not unique enough 588s -skipping training candidate: asmbl_847.p1, not unique enough 588s -skipping training candidate: asmbl_554.p1, not unique enough 588s -skipping training candidate: asmbl_462.p1, not unique enough 588s -skipping training candidate: asmbl_514.p1, not unique enough 588s -skipping training candidate: asmbl_711.p1, not unique enough 588s -skipping training candidate: asmbl_790.p1, not unique enough 588s -skipping training candidate: asmbl_744.p1, not unique enough 588s -skipping training candidate: asmbl_50.p1, not unique enough 588s -skipping training candidate: asmbl_491.p1, not unique enough 588s -skipping training candidate: asmbl_489.p1, not unique enough 588s -skipping training candidate: asmbl_49.p1, not unique enough 588s -skipping training candidate: asmbl_51.p1, not unique enough 588s -skipping training candidate: asmbl_492.p1, not unique enough 588s -skipping training candidate: asmbl_490.p1, not unique enough 588s -skipping training candidate: asmbl_621.p1, not unique enough 588s -skipping training candidate: asmbl_728.p1, not unique enough 588s -skipping training candidate: asmbl_167.p1, not unique enough 588s -skipping training candidate: asmbl_625.p1, not unique enough 588s -skipping training candidate: asmbl_8.p1, not unique enough 588s -skipping training candidate: asmbl_460.p1, not unique enough 588s -skipping training candidate: asmbl_815.p1, not unique enough 588s -skipping training candidate: asmbl_9.p1, not unique enough 588s -skipping training candidate: asmbl_459.p1, not unique enough 588s -skipping training candidate: asmbl_662.p1, not unique enough 588s -skipping training candidate: asmbl_854.p1, not unique enough 588s -skipping training candidate: asmbl_636.p1, not unique enough 588s -skipping training candidate: asmbl_851.p1, not unique enough 588s -skipping training candidate: asmbl_291.p1, not unique enough 588s -skipping training candidate: asmbl_743.p1, not unique enough 588s -skipping training candidate: asmbl_467.p1, not unique enough 588s -skipping training candidate: asmbl_569.p1, not unique enough 588s -skipping training candidate: asmbl_592.p1, not unique enough 588s -skipping training candidate: asmbl_710.p1, not unique enough 588s -skipping training candidate: asmbl_686.p1, not unique enough 588s -skipping training candidate: asmbl_649.p1, not unique enough 588s -skipping training candidate: asmbl_431.p1, not unique enough 588s -skipping training candidate: asmbl_32.p1, not unique enough 588s -skipping training candidate: asmbl_441.p1, not unique enough 588s -skipping training candidate: asmbl_438.p1, not unique enough 588s -skipping training candidate: asmbl_740.p1, not unique enough 588s -skipping training candidate: asmbl_30.p1, not unique enough 588s -skipping training candidate: asmbl_439.p1, not unique enough 588s -skipping training candidate: asmbl_779.p1, not unique enough 588s -skipping training candidate: asmbl_447.p1, not unique enough 588s -skipping training candidate: asmbl_780.p1, not unique enough 588s -skipping training candidate: asmbl_803.p1, not unique enough 588s -skipping training candidate: asmbl_442.p1, not unique enough 588s -skipping training candidate: asmbl_503.p1, not unique enough 588s -skipping training candidate: asmbl_443.p1, not unique enough 588s -skipping training candidate: asmbl_531.p1, not unique enough 588s -skipping training candidate: asmbl_687.p1, not unique enough 588s -skipping training candidate: asmbl_719.p1, not unique enough 588s -skipping training candidate: asmbl_822.p1, not unique enough 588s -skipping training candidate: asmbl_287.p1, not unique enough 588s -skipping training candidate: asmbl_685.p1, not unique enough 588s -skipping training candidate: asmbl_260.p1, not unique enough 588s -skipping training candidate: asmbl_715.p1, not unique enough 588s -skipping training candidate: asmbl_775.p1, not unique enough 588s -skipping training candidate: asmbl_31.p1, not unique enough 588s -skipping training candidate: asmbl_440.p1, not unique enough 588s -skipping training candidate: asmbl_377.p1, not unique enough 588s -skipping training candidate: asmbl_378.p1, not unique enough 588s -skipping training candidate: asmbl_821.p1, not unique enough 588s -skipping training candidate: asmbl_818.p1, not unique enough 588s -skipping training candidate: asmbl_493.p1, not unique enough 588s -skipping training candidate: asmbl_553.p1, not unique enough 588s -skipping training candidate: asmbl_659.p1, not unique enough 588s -skipping training candidate: asmbl_258.p1, not unique enough 588s -skipping training candidate: asmbl_713.p1, not unique enough 588s -skipping training candidate: asmbl_653.p1, not unique enough 588s -skipping training candidate: asmbl_628.p1, not unique enough 588s -skipping training candidate: asmbl_824.p1, not unique enough 588s -skipping training candidate: asmbl_597.p1, not unique enough 588s -skipping training candidate: asmbl_753.p1, not unique enough 588s -skipping training candidate: asmbl_614.p1, not unique enough 588s -skipping training candidate: asmbl_310.p1, not unique enough 588s -skipping training candidate: asmbl_724.p1, not unique enough 588s -skipping training candidate: asmbl_382.p1, not unique enough 588s -skipping training candidate: asmbl_819.p1, not unique enough 588s -skipping training candidate: asmbl_699.p1, not unique enough 588s -skipping training candidate: asmbl_700.p1, not unique enough 588s -skipping training candidate: asmbl_643.p1, not unique enough 588s -skipping training candidate: asmbl_571.p1, not unique enough 588s -skipping training candidate: asmbl_259.p1, not unique enough 588s -skipping training candidate: asmbl_521.p1, not unique enough 588s -skipping training candidate: asmbl_761.p1, not unique enough 588s -skipping training candidate: asmbl_735.p1, not unique enough 588s -skipping training candidate: asmbl_856.p1, not unique enough 588s -skipping training candidate: asmbl_648.p1, not unique enough 588s -skipping training candidate: asmbl_607.p1, not unique enough 588s -skipping training candidate: asmbl_163.p1, not unique enough 588s -skipping training candidate: asmbl_629.p1, not unique enough 588s -skipping training candidate: asmbl_517.p1, not unique enough 588s -skipping training candidate: asmbl_178.p1, not unique enough 588s -skipping training candidate: asmbl_482.p1, not unique enough 588s -skipping training candidate: asmbl_770.p1, not unique enough 588s -skipping training candidate: asmbl_858.p1, not unique enough 588s -skipping training candidate: asmbl_481.p1, not unique enough 588s -skipping training candidate: asmbl_776.p1, not unique enough 588s -skipping training candidate: asmbl_609.p1, not unique enough 588s -skipping training candidate: asmbl_457.p1, not unique enough 588s -skipping training candidate: asmbl_796.p1, not unique enough 588s -skipping training candidate: asmbl_329.p1, not unique enough 588s -skipping training candidate: asmbl_509.p1, not unique enough 588s -skipping training candidate: asmbl_755.p1, not unique enough 588s -skipping training candidate: asmbl_812.p1, not unique enough 588s -skipping training candidate: asmbl_483.p1, not unique enough 588s -skipping training candidate: asmbl_730.p1, not unique enough 588s -skipping training candidate: asmbl_795.p1, not unique enough 588s -skipping training candidate: asmbl_227.p1, not unique enough 588s -skipping training candidate: asmbl_647.p1, not unique enough 588s -skipping training candidate: asmbl_479.p1, not unique enough 588s -skipping training candidate: asmbl_13.p1, not unique enough 588s -skipping training candidate: asmbl_224.p1, not unique enough 588s -skipping training candidate: asmbl_458.p1, not unique enough 588s -skipping training candidate: asmbl_651.p1, not unique enough 588s -skipping training candidate: asmbl_650.p1, not unique enough 588s -skipping training candidate: asmbl_682.p1, not unique enough 588s -skipping training candidate: asmbl_633.p1, not unique enough 588s -skipping training candidate: asmbl_522.p1, not unique enough 588s -skipping training candidate: asmbl_630.p1, not unique enough 588s -skipping training candidate: asmbl_512.p1, not unique enough 588s -skipping training candidate: asmbl_737.p1, not unique enough 588s -skipping training candidate: asmbl_739.p1, not unique enough 588s -skipping training candidate: asmbl_829.p1, not unique enough 588s -skipping training candidate: asmbl_702.p1, not unique enough 588s -skipping training candidate: asmbl_568.p1, not unique enough 588s -skipping training candidate: asmbl_158.p1, not unique enough 588s -skipping training candidate: asmbl_634.p1, not unique enough 588s -skipping training candidate: asmbl_542.p1, not unique enough 588s -skipping training candidate: asmbl_854.p2, not unique enough 588s -skipping training candidate: asmbl_598.p1, not unique enough 588s -skipping training candidate: asmbl_788.p1, not unique enough 588s -skipping training candidate: asmbl_69.p1, not unique enough 588s -skipping training candidate: asmbl_472.p1, not unique enough 588s -skipping training candidate: asmbl_717.p1, not unique enough 588s -skipping training candidate: asmbl_365.p1, not unique enough 588s -skipping training candidate: asmbl_771.p1, not unique enough 588s -skipping training candidate: asmbl_619.p1, not unique enough 588s -skipping training candidate: asmbl_616.p1, not unique enough 588s -skipping training candidate: asmbl_85.p1, not unique enough 588s -skipping training candidate: asmbl_518.p1, not unique enough 588s -skipping training candidate: asmbl_668.p1, not unique enough 588s -skipping training candidate: asmbl_828.p1, not unique enough 588s -skipping training candidate: asmbl_608.p1, not 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not unique enough 588s -skipping training candidate: asmbl_513.p1, not unique enough 588s -skipping training candidate: asmbl_615.p1, not unique enough 588s -skipping training candidate: asmbl_551.p1, not unique enough 588s -skipping training candidate: asmbl_816.p1, not unique enough 588s -skipping training candidate: asmbl_837.p1, not unique enough 588s -skipping training candidate: asmbl_853.p1, not unique enough 588s -skipping training candidate: asmbl_693.p1, not unique enough 588s -skipping training candidate: asmbl_546.p1, not unique enough 588s -skipping training candidate: asmbl_538.p1, not unique enough 588s -skipping training candidate: asmbl_539.p1, not unique enough 588s -skipping training candidate: asmbl_631.p1, not unique enough 588s -skipping training candidate: asmbl_463.p1, not unique enough 588s -skipping training candidate: asmbl_452.p1, not unique enough 588s -skipping training candidate: asmbl_146.p1, not unique enough 588s -skipping training candidate: asmbl_173.p1, not unique enough 588s -skipping training candidate: asmbl_549.p1, not unique enough 588s -skipping training candidate: asmbl_586.p1, not unique enough 588s -skipping training candidate: asmbl_618.p1, not unique enough 588s -skipping training candidate: asmbl_52.p1, not unique enough 588s -skipping training candidate: asmbl_53.p1, not unique enough 588s -skipping training candidate: asmbl_461.p1, not unique enough 588s -skipping training candidate: asmbl_486.p1, not unique enough 588s -skipping training candidate: asmbl_487.p1, not unique enough 588s -skipping training candidate: asmbl_765.p1, not unique enough 588s -skipping training candidate: asmbl_785.p1, not unique enough 588s -skipping training candidate: asmbl_432.p1, not unique enough 588s -skipping training candidate: asmbl_246.p1, not unique enough 588s -skipping training candidate: asmbl_328.p1, not unique enough 588s -skipping training candidate: asmbl_678.p1, not unique enough 588s -skipping training candidate: asmbl_754.p1, not unique enough 588s -skipping training candidate: asmbl_515.p1, not unique enough 588s -skipping training candidate: asmbl_105.p1, not unique enough 588s -skipping training candidate: asmbl_572.p1, not unique enough 588s -skipping training candidate: asmbl_611.p1, not unique enough 588s -skipping training candidate: asmbl_172.p1, not unique enough 588s -skipping training candidate: asmbl_617.p1, not unique enough 588s -skipping training candidate: asmbl_823.p1, not unique enough 588s -skipping training candidate: asmbl_1.p1, not unique enough 588s -skipping training candidate: asmbl_146.p2, not unique enough 588s -skipping training candidate: asmbl_528.p1, not unique enough 588s -skipping training candidate: asmbl_586.p2, not unique enough 588s -skipping training candidate: asmbl_606.p1, not unique enough 588s -skipping training candidate: asmbl_454.p1, not unique enough 588s -skipping training candidate: asmbl_110.p1, not unique enough 588s -skipping training candidate: asmbl_525.p1, not unique enough 588s -skipping training candidate: asmbl_566.p1, not unique enough 588s -skipping training candidate: asmbl_626.p1, not unique enough 588s -skipping training candidate: asmbl_681.p1, not unique enough 588s -skipping training candidate: asmbl_792.p1, not unique enough 588s -skipping training candidate: asmbl_310.p2, not unique enough 588s -skipping training candidate: asmbl_724.p2, not unique enough 588s -skipping training candidate: asmbl_304.p1, not unique enough 588s -skipping training candidate: asmbl_732.p1, not unique enough 588s -skipping training candidate: asmbl_451.p1, not unique enough 588s -skipping training candidate: asmbl_57.p1, not unique enough 588s -skipping training candidate: asmbl_246.p2, not unique enough 588s -skipping training candidate: asmbl_484.p1, not unique enough 588s -skipping training candidate: asmbl_678.p2, not unique enough 588s -skipping training candidate: asmbl_682.p2, not unique enough 588s -skipping training candidate: asmbl_35.p1, not unique enough 588s -skipping training candidate: asmbl_436.p1, not unique enough 588s -skipping training candidate: asmbl_437.p1, not unique enough 588s -skipping training candidate: asmbl_848.p1, not unique enough 588s -skipping training candidate: asmbl_478.p1, not unique enough 588s -skipping training candidate: asmbl_720.p1, not unique enough 588s -skipping training candidate: asmbl_857.p1, not unique enough 588s -skipping training candidate: asmbl_846.p1, not unique enough 588s -skipping training candidate: asmbl_125.p1, not unique enough 588s -skipping training candidate: asmbl_444.p1, not unique enough 588s -skipping training candidate: asmbl_552.p1, not unique enough 588s -skipping training candidate: asmbl_845.p1, not unique enough 588s -skipping training candidate: asmbl_246.p3, not unique enough 588s -skipping training candidate: asmbl_659.p2, not unique enough 588s -skipping training candidate: asmbl_678.p3, not unique enough 588s -skipping training candidate: asmbl_420.p2, not unique enough 588s -skipping training candidate: asmbl_855.p2, not unique enough 588s -skipping training candidate: asmbl_809.p1, not unique enough 588s -skipping training candidate: asmbl_303.p1, not unique enough 588s -skipping training candidate: asmbl_390.p1, not unique enough 588s -skipping training candidate: asmbl_731.p1, not unique enough 588s -skipping training candidate: asmbl_810.p1, not unique enough 588s -skipping training candidate: asmbl_494.p1, not unique enough 588s -skipping training candidate: asmbl_693.p2, not unique enough 588s -skipping training candidate: asmbl_199.p1, not unique enough 588s -skipping training candidate: asmbl_605.p1, not unique enough 588s -skipping training candidate: asmbl_593.p1, not unique enough 588s -skipping training candidate: asmbl_504.p1, not unique enough 588s -skipping training candidate: asmbl_575.p1, not unique enough 588s -skipping training candidate: asmbl_745.p3, not unique enough 588s -skipping training candidate: asmbl_574.p1, not unique enough 588s -skipping training candidate: asmbl_817.p1, not unique enough 588s -skipping training candidate: asmbl_455.p1, not unique enough 588s -skipping training candidate: asmbl_480.p1, not unique enough 588s -skipping training candidate: asmbl_77.p1, not unique enough 588s -skipping training candidate: asmbl_453.p1, not unique enough 588s -skipping training candidate: asmbl_526.p1, not unique enough 588s -skipping training candidate: asmbl_584.p1, not unique enough 588s -skipping training candidate: asmbl_778.p2, not unique enough 588s -skipping training candidate: asmbl_101.p1, not unique enough 588s -skipping training candidate: asmbl_165.p1, not unique enough 588s -skipping training candidate: asmbl_366.p1, not unique enough 588s -skipping training candidate: asmbl_502.p1, not unique enough 588s -skipping training candidate: asmbl_627.p1, not unique enough 588s -skipping training candidate: asmbl_769.p1, not unique enough 588s -skipping training candidate: asmbl_765.p2, not unique enough 588s -skipping training candidate: asmbl_207.p1, not unique enough 588s -skipping training candidate: asmbl_242.p1, not unique enough 588s -skipping training candidate: asmbl_331.p1, not unique enough 588s -skipping training candidate: asmbl_669.p1, not unique enough 588s -skipping training candidate: asmbl_684.p1, not unique enough 588s -skipping training candidate: asmbl_757.p1, not unique enough 588s -skipping training candidate: asmbl_199.p2, not unique enough 588s -skipping training candidate: asmbl_200.p1, not unique enough 588s -skipping training candidate: asmbl_593.p2, not unique enough 588s -skipping training candidate: asmbl_594.p1, not unique enough 588s -skipping training candidate: asmbl_536.p1, not unique enough 588s -skipping training candidate: asmbl_660.p1, not unique enough 588s -skipping training candidate: asmbl_794.p1, not unique enough 588s -skipping training candidate: asmbl_435.p1, not unique enough 588s -skipping training candidate: asmbl_554.p2, not unique enough 588s -skipping training candidate: asmbl_614.p2, not unique enough 588s -skipping training candidate: asmbl_588.p1, not unique enough 588s -skipping training candidate: asmbl_676.p1, not unique enough 588s -skipping training candidate: asmbl_706.p1, not unique enough 588s -skipping training candidate: asmbl_590.p1, not unique enough 588s -skipping training candidate: asmbl_68.p2, not unique enough 588s -skipping training candidate: asmbl_197.p1, not unique enough 588s -skipping training candidate: asmbl_246.p4, not unique enough 588s -skipping training candidate: asmbl_470.p2, not unique enough 588s -skipping training candidate: asmbl_471.p2, not unique enough 588s -skipping training candidate: asmbl_591.p1, not unique enough 588s -skipping training candidate: asmbl_678.p4, not unique enough 588s -skipping training candidate: asmbl_564.p1, not unique enough 588s -skipping training candidate: asmbl_200.p2, not unique enough 588s -skipping training candidate: asmbl_612.p1, not unique enough 588s -skipping training candidate: asmbl_594.p2, not unique enough 588s -skipping training candidate: asmbl_436.p2, not unique enough 588s -skipping training candidate: asmbl_532.p1, not unique enough 588s -skipping training candidate: asmbl_688.p2, not unique enough 588s -skipping training candidate: asmbl_122.p1, not unique enough 588s -skipping training candidate: asmbl_555.p1, not unique enough 588s -skipping training candidate: asmbl_646.p1, not unique enough 588s -skipping training candidate: asmbl_807.p1, not unique enough 588s -skipping training candidate: asmbl_498.p1, not unique enough 588s -skipping training candidate: asmbl_724.p3, not unique enough 588s -skipping training candidate: asmbl_122.p2, not unique enough 588s -skipping training candidate: asmbl_555.p2, not unique enough 588s -skipping training candidate: asmbl_718.p1, not unique enough 588s -skipping training candidate: asmbl_35.p2, not unique enough 588s -skipping training candidate: asmbl_437.p2, not unique enough 588s -skipping training candidate: asmbl_588.p2, not unique enough 588s -skipping training candidate: asmbl_791.p1, not unique enough 588s -skipping training candidate: asmbl_856.p2, not unique enough 588s -skipping training candidate: asmbl_548.p1, not unique enough 588s -skipping training candidate: asmbl_602.p1, not unique enough 588s -skipping training candidate: asmbl_497.p1, not unique enough 588s -skipping training candidate: asmbl_311.p2, not unique enough 588s -skipping training candidate: asmbl_601.p1, not unique enough 588s -skipping training candidate: asmbl_725.p2, not unique enough 588s -skipping training candidate: asmbl_73.p1, not unique enough 588s -skipping training candidate: asmbl_529.p1, not unique enough 588s -skipping training candidate: asmbl_2.p1, not unique enough 588s -skipping training candidate: asmbl_241.p1, not unique enough 588s -skipping training candidate: asmbl_683.p1, not unique enough 588s -skipping training candidate: asmbl_816.p2, not unique enough 588s -skipping training candidate: asmbl_231.p1, not unique enough 588s -skipping training candidate: asmbl_644.p1, not unique enough 588s -skipping training candidate: asmbl_133.p1, not unique enough 588s -skipping training candidate: asmbl_544.p1, not unique enough 588s -skipping training candidate: asmbl_577.p1, not unique enough 588s -skipping training candidate: asmbl_623.p1, not unique enough 588s -skipping training candidate: asmbl_134.p1, not unique enough 588s -skipping training candidate: asmbl_545.p1, not unique enough 588s -skipping training candidate: asmbl_649.p2, not unique enough 588s -skipping training candidate: asmbl_69.p2, not unique enough 588s -skipping training candidate: asmbl_132.p1, not unique enough 588s -skipping training candidate: asmbl_472.p2, not unique enough 588s -skipping training candidate: asmbl_533.p1, not unique enough 588s -skipping training candidate: asmbl_543.p1, not unique enough 588s -skipping training candidate: asmbl_664.p1, not unique enough 588s -skipping training candidate: asmbl_677.p1, not unique enough 588s -skipping training candidate: asmbl_748.p1, not unique enough 588s -skipping training candidate: asmbl_802.p1, not unique enough 588s -skipping training candidate: asmbl_117.p2, not unique enough 588s -skipping training candidate: asmbl_559.p2, not unique enough 588s -skipping training candidate: asmbl_825.p1, not unique enough 588s -skipping training candidate: asmbl_596.p1, not unique enough 588s -skipping training candidate: asmbl_703.p1, not unique enough 588s -skipping training candidate: asmbl_838.p1, not unique enough 588s -skipping training candidate: asmbl_469.p1, not unique enough 588s -skipping training candidate: asmbl_698.p1, not unique enough 588s -skipping training candidate: asmbl_798.p1, not unique enough 588s -skipping training candidate: asmbl_290.p3, not unique enough 588s -skipping training candidate: asmbl_409.p2, not unique enough 588s -skipping training candidate: asmbl_746.p3, not unique enough 588s -skipping training candidate: asmbl_780.p2, not unique enough 588s -skipping training candidate: asmbl_838.p2, not unique enough 588s -skipping training candidate: asmbl_295.p1, not unique enough 588s -skipping training candidate: asmbl_741.p1, not unique enough 588s -skipping training candidate: asmbl_232.p1, not unique enough 588s -skipping training candidate: asmbl_645.p1, not unique enough 588s -skipping training candidate: asmbl_589.p1, not unique enough 588s -skipping training candidate: asmbl_657.p1, not unique enough 588s -skipping training candidate: asmbl_218.p1, not unique enough 588s -skipping training candidate: asmbl_658.p1, not unique enough 588s -skipping training candidate: asmbl_656.p1, not unique enough 588s -skipping training candidate: asmbl_675.p1, not unique enough 588s -skipping training candidate: asmbl_697.p1, not unique enough 588s -skipping training candidate: asmbl_808.p1, not unique enough 588s -skipping training candidate: asmbl_674.p1, not unique enough 588s -skipping training candidate: asmbl_465.p1, not unique enough 588s -skipping training candidate: asmbl_443.p2, not unique enough 588s -skipping training candidate: asmbl_673.p1, not unique enough 588s -skipping training candidate: asmbl_788.p2, not unique enough 588s -skipping training candidate: asmbl_4.p1, not unique enough 588s -skipping training candidate: asmbl_278.p3, not unique enough 588s -skipping training candidate: asmbl_408.p2, not unique enough 588s -skipping training candidate: asmbl_464.p1, not unique enough 588s -skipping training candidate: asmbl_693.p3, not unique enough 588s -skipping training candidate: asmbl_837.p2, not unique enough 588s -skipping training candidate: asmbl_463.p2, not unique enough 588s -skipping training candidate: asmbl_13.p2, not unique enough 588s -skipping training candidate: asmbl_457.p2, not unique enough 588s -skipping training candidate: asmbl_458.p2, not unique enough 588s -skipping training candidate: asmbl_637.p1, not unique enough 588s -skipping training candidate: asmbl_750.p1, not unique enough 588s -skipping training candidate: asmbl_485.p1, not unique enough 588s -skipping training candidate: asmbl_562.p1, not unique enough 588s -skipping training candidate: asmbl_636.p2, not unique enough 588s -skipping training candidate: asmbl_748.p2, not unique enough 588s -skipping training candidate: asmbl_310.p4, not unique enough 588s -skipping training candidate: asmbl_724.p4, not unique enough 588s -skipping training candidate: asmbl_723.p1, not unique enough 588s -skipping training candidate: asmbl_305.p1, not unique enough 588s -skipping training candidate: asmbl_733.p1, not unique enough 588s -skipping training candidate: asmbl_644.p2, not unique enough 588s -skipping training candidate: asmbl_498.p2, not unique enough 588s -skipping training candidate: asmbl_704.p1, not unique enough 588s -skipping training candidate: asmbl_725.p3, not unique enough 588s -skipping training candidate: asmbl_230.p2, not unique enough 588s -skipping training candidate: asmbl_221.p1, not unique enough 588s -skipping training candidate: asmbl_622.p1, not unique enough 588s -skipping training candidate: asmbl_655.p1, not unique enough 588s -skipping training candidate: asmbl_643.p2, not unique enough 588s -skipping training candidate: asmbl_716.p1, not unique enough 588s -skipping training candidate: asmbl_726.p2, not unique enough 588s -skipping training candidate: asmbl_516.p1, not unique enough 588s -skipping training candidate: asmbl_587.p1, not unique enough 588s -skipping training candidate: asmbl_813.p2, not unique enough 588s -skipping training candidate: asmbl_310.p5, not unique enough 588s -skipping training candidate: asmbl_537.p2, not unique enough 588s -skipping training candidate: asmbl_578.p1, not unique enough 588s -skipping training candidate: asmbl_724.p5, not unique enough 588s -skipping training candidate: asmbl_751.p1, not unique enough 588s -skipping training candidate: asmbl_815.p2, not unique enough 588s -skipping training candidate: asmbl_151.p1, not unique enough 588s -skipping training candidate: asmbl_410.p1, not unique enough 588s -skipping training candidate: asmbl_582.p1, not unique enough 588s -skipping training candidate: asmbl_580.p1, not unique enough 588s -skipping training candidate: asmbl_839.p1, not unique enough 588s -skipping training candidate: asmbl_290.p4, not unique enough 588s -skipping training candidate: asmbl_557.p1, not unique enough 588s -skipping training candidate: asmbl_660.p2, not unique enough 588s -skipping training candidate: asmbl_700.p2, not unique enough 588s -skipping training candidate: asmbl_745.p4, not unique enough 588s -skipping training candidate: asmbl_746.p4, not unique enough 588s -skipping training candidate: asmbl_779.p2, not unique enough 588s -skipping training candidate: asmbl_696.p1, not unique enough 588s -skipping training candidate: asmbl_452.p2, not unique enough 588s -skipping training candidate: asmbl_763.p1, not unique enough 588s -skipping training candidate: asmbl_814.p2, not unique enough 588s -skipping training candidate: asmbl_523.p1, not unique enough 588s -skipping training candidate: asmbl_752.p1, not unique enough 588s -skipping training candidate: asmbl_797.p1, not unique enough 588s -skipping training candidate: asmbl_607.p2, not unique enough 588s -skipping training candidate: asmbl_780.p3, not unique enough 588s -skipping training candidate: asmbl_127.p1, not unique enough 588s -skipping training candidate: asmbl_550.p1, not unique enough 588s -skipping training candidate: asmbl_646.p2, not unique enough 588s -skipping training candidate: asmbl_782.p1, not unique enough 588s -skipping training candidate: asmbl_362.p2, not unique enough 588s -skipping training candidate: asmbl_507.p2, not unique enough 588s -skipping training candidate: asmbl_530.p1, not unique enough 588s -skipping training candidate: asmbl_784.p2, not unique enough 588s -skipping training candidate: asmbl_772.p2, not unique enough 588s -skipping training candidate: asmbl_786.p2, not unique enough 588s -skipping training candidate: asmbl_773.p2, not unique enough 588s -skipping training candidate: asmbl_826.p1, not unique enough 588s -skipping training candidate: asmbl_15.p1, not unique enough 588s -skipping training candidate: asmbl_456.p1, not unique enough 588s -skipping training candidate: asmbl_530.p2, not unique enough 588s -skipping training candidate: asmbl_601.p2, not unique enough 588s -skipping training candidate: asmbl_641.p1, not unique enough 588s -skipping training candidate: asmbl_290.p5, not unique enough 588s -skipping training candidate: asmbl_519.p2, not unique enough 588s -skipping training candidate: asmbl_691.p1, not unique enough 588s -skipping training candidate: asmbl_745.p5, not unique enough 588s -skipping training candidate: asmbl_746.p5, not unique enough 588s -skipping training candidate: asmbl_288.p2, not unique enough 588s -skipping training candidate: asmbl_431.p2, not unique enough 588s -skipping training candidate: asmbl_687.p2, not unique enough 588s -skipping training candidate: asmbl_689.p1, not unique enough 588s -skipping training candidate: asmbl_685.p2, not unique enough 588s -skipping training candidate: asmbl_742.p1, not unique enough 588s -skipping training candidate: asmbl_765.p3, not unique enough 588s -skipping training candidate: asmbl_21.p2, not unique enough 588s -skipping training candidate: asmbl_22.p2, not unique enough 588s -skipping training candidate: asmbl_228.p2, not unique enough 588s -skipping training candidate: asmbl_378.p2, not unique enough 588s -skipping training candidate: asmbl_379.p2, not unique enough 588s -skipping training candidate: asmbl_450.p2, not unique enough 588s -skipping training candidate: asmbl_448.p2, not unique enough 588s -skipping training candidate: asmbl_449.p2, not unique enough 588s -skipping training candidate: asmbl_642.p1, not unique enough 588s -skipping training candidate: asmbl_647.p2, not unique enough 588s -skipping training candidate: asmbl_648.p2, not unique enough 588s -skipping training candidate: asmbl_821.p2, not unique enough 588s -skipping training candidate: asmbl_822.p2, not unique enough 588s -skipping training candidate: asmbl_335.p2, not unique enough 588s -skipping training candidate: asmbl_331.p2, not unique enough 588s -skipping training candidate: asmbl_328.p2, not unique enough 588s -skipping training candidate: asmbl_330.p1, not unique enough 588s -skipping training candidate: asmbl_528.p2, not unique enough 588s -skipping training candidate: asmbl_628.p2, not unique enough 588s -skipping training candidate: asmbl_736.p1, not unique enough 588s -skipping training candidate: asmbl_751.p2, not unique enough 588s -skipping training candidate: asmbl_756.p1, not unique enough 588s -skipping training candidate: asmbl_757.p2, not unique enough 588s -skipping training candidate: asmbl_754.p2, not unique enough 589s -skipping training candidate: asmbl_592.p2, not unique enough 589s -skipping training candidate: asmbl_670.p1, not unique enough 589s -skipping training candidate: asmbl_834.p1, not unique enough 589s -skipping training candidate: asmbl_90.p2, not unique enough 589s -skipping training candidate: asmbl_512.p2, not unique enough 589s -skipping training candidate: asmbl_513.p2, not unique enough 589s -skipping training candidate: asmbl_635.p2, not unique enough 589s -skipping training candidate: asmbl_764.p1, not unique enough 589s -skipping training candidate: asmbl_835.p1, not unique enough 589s -skipping training candidate: asmbl_303.p2, not unique enough 589s -skipping training candidate: asmbl_414.p1, not unique enough 589s -skipping training candidate: asmbl_479.p2, not unique enough 589s -skipping training candidate: asmbl_693.p4, not unique enough 589s -skipping training candidate: asmbl_716.p2, not unique enough 589s -skipping training candidate: asmbl_742.p2, not unique enough 589s -skipping training candidate: asmbl_731.p2, not unique enough 589s -skipping training candidate: asmbl_794.p2, not unique enough 589s -skipping training candidate: asmbl_799.p1, not unique enough 589s -skipping training candidate: asmbl_833.p1, not unique enough 589s -skipping training candidate: asmbl_433.p1, not unique enough 589s -skipping training candidate: asmbl_677.p2, not unique enough 589s -skipping training candidate: asmbl_847.p2, not unique enough 589s -skipping training candidate: asmbl_570.p2, not unique enough 589s -skipping training candidate: asmbl_535.p1, not unique enough 589s -skipping training candidate: asmbl_627.p2, not unique enough 589s -skipping training candidate: asmbl_719.p2, not unique enough 589s -skipping training candidate: asmbl_722.p1, not unique enough 589s -skipping training candidate: asmbl_150.p1, not unique enough 589s -skipping training candidate: asmbl_579.p1, not unique enough 589s -skipping training candidate: asmbl_584.p2, not unique enough 589s -skipping training candidate: asmbl_682.p3, not unique enough 589s -skipping training candidate: asmbl_712.p2, not unique enough 589s -skipping training candidate: asmbl_815.p3, not unique enough 589s -skipping training candidate: asmbl_49.p2, not unique enough 589s -skipping training candidate: asmbl_50.p2, not unique enough 589s -skipping training candidate: asmbl_51.p2, not unique enough 589s -skipping training candidate: asmbl_343.p1, not unique enough 589s -skipping training candidate: asmbl_491.p2, not unique enough 589s -skipping training candidate: asmbl_492.p2, not unique enough 589s -skipping training candidate: asmbl_489.p2, not unique enough 589s -skipping training candidate: asmbl_490.p2, not unique enough 589s -skipping training candidate: asmbl_793.p1, not unique enough 589s -skipping training candidate: asmbl_198.p3, not unique enough 589s -skipping training candidate: asmbl_199.p3, not unique enough 589s -skipping training candidate: asmbl_200.p3, not unique enough 589s -skipping training candidate: asmbl_507.p3, not unique enough 589s -skipping training candidate: asmbl_592.p3, not unique enough 589s -skipping training candidate: asmbl_606.p2, not unique enough 589s -skipping training candidate: asmbl_593.p3, not unique enough 589s -skipping training candidate: asmbl_594.p3, not unique enough 589s -skipping training candidate: asmbl_839.p2, not unique enough 589s -skipping training candidate: asmbl_6.p1, not unique enough 589s -skipping training candidate: asmbl_146.p3, not unique enough 589s -skipping training candidate: asmbl_446.p2, not unique enough 589s -skipping training candidate: asmbl_466.p1, not unique enough 589s -skipping training candidate: asmbl_531.p2, not unique enough 589s -skipping training candidate: asmbl_585.p2, not unique enough 589s -skipping training candidate: asmbl_586.p3, not unique enough 589s -skipping training candidate: asmbl_606.p3, not unique enough 589s -skipping training candidate: asmbl_635.p3, not unique enough 589s -skipping training candidate: asmbl_726.p3, not unique enough 589s -skipping training candidate: asmbl_8.p2, not unique enough 589s -skipping training candidate: asmbl_9.p2, not unique enough 589s -skipping training candidate: asmbl_57.p2, not unique enough 589s -skipping training candidate: asmbl_365.p2, not unique enough 589s -skipping training candidate: asmbl_459.p2, not unique enough 589s -skipping training candidate: asmbl_460.p2, not unique enough 589s -skipping training candidate: asmbl_461.p2, not unique enough 589s -skipping training candidate: asmbl_462.p2, not unique enough 589s -skipping training candidate: asmbl_484.p2, not unique enough 589s -skipping training candidate: asmbl_770.p2, not unique enough 589s -skipping training candidate: asmbl_771.p2, not unique enough 589s -skipping training candidate: asmbl_820.p1, not unique enough 589s -skipping training candidate: asmbl_259.p2, not unique enough 589s -skipping training candidate: asmbl_349.p2, not unique enough 589s -skipping training candidate: asmbl_692.p2, not unique enough 589s -skipping training candidate: asmbl_713.p2, not unique enough 589s -skipping training candidate: asmbl_765.p4, not unique enough 589s -skipping training candidate: asmbl_787.p2, not unique enough 589s -skipping training candidate: asmbl_85.p2, not unique enough 589s -skipping training candidate: asmbl_518.p2, not unique enough 589s -skipping training candidate: asmbl_517.p2, not unique enough 589s -skipping training candidate: asmbl_709.p2, not unique enough 589s -skipping training candidate: asmbl_778.p3, not unique enough 589s -skipping training candidate: asmbl_830.p1, not unique enough 589s -skipping training candidate: asmbl_847.p3, not unique enough 589s -skipping training candidate: asmbl_530.p3, not unique enough 589s -skipping training candidate: asmbl_722.p2, not unique enough 589s -skipping training candidate: asmbl_817.p2, not unique enough 589s -skipping training candidate: asmbl_799.p2, not unique enough 589s -skipping training candidate: asmbl_813.p3, not unique enough 589s -skipping training candidate: asmbl_290.p6, not unique enough 589s -skipping training candidate: asmbl_746.p6, not unique enough 589s -skipping training candidate: asmbl_536.p2, not unique enough 589s -skipping training candidate: asmbl_534.p1, not unique enough 589s -skipping training candidate: asmbl_692.p3, not unique enough 589s -skipping training candidate: asmbl_115.p2, not unique enough 589s -skipping training candidate: asmbl_278.p5, not unique enough 589s -skipping training candidate: asmbl_320.p1, not unique enough 589s -skipping training candidate: asmbl_452.p3, not unique enough 589s -skipping training candidate: asmbl_569.p2, not unique enough 589s -skipping training candidate: asmbl_560.p2, not unique enough 589s -skipping training candidate: asmbl_561.p2, not unique enough 589s -skipping training candidate: asmbl_693.p5, not unique enough 589s -skipping training candidate: asmbl_695.p1, not unique enough 589s -skipping training candidate: asmbl_734.p2, not unique enough 589s -skipping training candidate: asmbl_721.p1, not unique enough 589s -skipping training candidate: asmbl_765.p5, not unique enough 589s -skipping training candidate: asmbl_766.p1, not unique enough 589s -skipping training candidate: asmbl_807.p2, not unique enough 589s -skipping training candidate: asmbl_800.p1, not unique enough 589s -skipping training candidate: asmbl_164.p2, not unique enough 589s -skipping training candidate: asmbl_531.p3, not unique enough 589s -skipping training candidate: asmbl_558.p2, not unique enough 589s -skipping training candidate: asmbl_626.p2, not unique enough 589s -skipping training candidate: asmbl_831.p1, not unique enough 589s 589s -redundancy-minimized set includes 396 / 1067 = 37.11% 589s 589s * [Sat Mar 16 21:13:57 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 589s PCT_GC: 42 589s * [Sat Mar 16 21:13:57 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores 592s * [Sat Mar 16 21:14:00 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores 614s * [Sat Mar 16 21:14:22 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 615s Selecting best orfs 615s * [Sat Mar 16 21:14:23 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement 615s Training start codon pattern recognition* [Sat Mar 16 21:14:23 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 616s * [Sat Mar 16 21:14:24 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores 616s -round: 1 634s -round: 2 652s -round: 3 670s -round: 4 689s -round: 5 707s * [Sat Mar 16 21:15:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 707s -parsing scores 729s * [Sat Mar 16 21:16:17 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 730s Error in library(ggplot2) : there is no package called ‘ggplot2’ 730s Execution halted 730s * [Sat Mar 16 21:16:18 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc 730s Error in library(ggplot2) : there is no package called ‘ggplot2’ 730s Execution halted 730s * [Sat Mar 16 21:16:18 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : 731s Error in library(seqLogo) : there is no package called ‘seqLogo’ 731s Execution halted 731s * [Sat Mar 16 21:16:19 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : 732s Error in library(seqLogo) : there is no package called ‘seqLogo’ 732s Execution halted 732s * [Sat Mar 16 21:16:20 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced 732s num features: 238 num_incorporate: 71 732s -feature swap of score: 0.52233068358735 instead of -2.4838353992418 732s -feature swap of score: 3.4925122435335 instead of -2.69571560364119 732s -feature swap of score: -0.479799656028566 instead of -2.28706103601398 732s -feature swap of score: -0.0881342990948846 instead of -2.01923571762916 732s -feature swap of score: 3.70320425069563 instead of -2.540266312821 732s -feature swap of score: -1.18001089627022 instead of -2.19874275195072 732s -feature swap of score: 0.890711131288117 instead of -1.48110814799594 732s -feature swap of score: -1.05010135127967 instead of -1.29405271062499 732s -feature swap of score: -0.0660971314530546 instead of -1.10945144224631 732s -feature swap of score: 4.44453897240347 instead of -0.978468124148539 732s -feature swap of score: -0.464399759591707 instead of -0.841794961146521 732s -feature swap of score: 0.255068847557726 instead of -0.83142113951215 732s -feature swap of score: 1.95582633064074 instead of -0.76896518568472 732s -feature swap of score: -0.0332453222172366 instead of -0.682979129272786 732s -feature swap of score: 1.8228745697833 instead of -0.653744437026382 732s -feature swap of score: 1.00115669145456 instead of -0.336891026477184 732s -feature swap of score: 0.672803798904712 instead of -0.578246064931 732s -feature swap of score: 1.8162642359003 instead of -0.452564095078051 732s -feature swap of score: 0.280846761877589 instead of -0.647264557316993 732s -feature swap of score: 0.366355095526699 instead of -0.615212412314209 732s -feature swap of score: 2.52986097726451 instead of -0.758989032460075 732s -feature swap of score: -0.0952627696553691 instead of -0.817191160815284 732s -feature swap of score: 0.996754631653053 instead of -0.80551837636419 732s -feature swap of score: 0.354999699462731 instead of -0.274911636492182 732s -feature swap of score: 1.28605443964402 instead of 0.0980797372313064 732s -feature swap of score: 0.32578718956916 instead of -0.042861330285221 732s -feature swap of score: 2.48770150611293 instead of -0.0868957590364158 732s -feature swap of score: 2.64754362015744 instead of 0.2916904256282 732s -feature swap of score: 1.01988302433125 instead of 0.036666467034015 732s -feature swap of score: 0.702376236311601 instead of -0.128287580103504 732s -feature swap of score: 2.99676647453095 instead of 0.320673377955444 732s -feature swap of score: 4.3305495710187 instead of 0.295875888654129 732s -feature swap of score: 1.17421891679809 instead of 0.254710288367653 732s -feature swap of score: 0.401521517315352 instead of 0.370606147577384 732s -feature swap of score: 3.89634731515857 instead of 0.389772413567672 732s -feature swap of score: 2.74749373854816 instead of 0.451140083480975 732s -feature swap of score: 4.14790539102617 instead of 0.173512045799991 732s -feature swap of score: 2.68928352460324 instead of 0.0987413441847772 732s -feature swap of score: 0.570947526770153 instead of -0.152678189275884 732s -feature swap of score: 2.87693452246047 instead of 0.175971771120871 732s -feature swap of score: 0.345761582949679 instead of 0.189210540579853 732s -feature swap of score: 1.75381703871986 instead of -0.176138170873724 732s -feature swap of score: 6.3225755214291 instead of 0.182318752228176 732s -feature swap of score: -0.00356336589610784 instead of -0.074332288426649 732s -feature swap of score: 1.25652300984573 instead of 0.440440454930295 732s -feature swap of score: 4.35627103288236 instead of 0.601792868596411 732s -feature swap of score: 3.34305077634812 instead of 0.646355594435306 732s -feature swap of score: 0.89148415481126 instead of 0.847522010634187 732s -feature swap of score: 3.6953445371134 instead of 0.751030612474935 732s -feature swap of score: 5.78699079524925 instead of 0.699840066363169 732s -feature swap of score: 2.15409587173251 instead of 0.715035855107118 732s -feature swap of score: 1.47994164306661 instead of 0.417255934795064 732s -feature swap of score: 4.91570803685393 instead of 0.612782191206777 732s -feature swap of score: 0.527551455366298 instead of 0.495108302468003 732s -feature swap of score: 3.40423853426828 instead of 0.883665117310717 732s -feature swap of score: 0.802539851871931 instead of 0.787642557429234 732s -num feature swaps: 56 732s * [Sat Mar 16 21:16:20 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 732s -round: 1 750s -round: 2 767s -round: 3 785s -round: 4 802s -round: 5 820s * [Sat Mar 16 21:17:48 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 820s -parsing scores 841s * [Sat Mar 16 21:18:09 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 842s Error in library(ggplot2) : there is no package called ‘ggplot2’ 842s Execution halted 842s * [Sat Mar 16 21:18:10 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 842s Error in library(ggplot2) : there is no package called ‘ggplot2’ 842s Execution halted 842s * [Sat Mar 16 21:18:10 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 843s Error in library(seqLogo) : there is no package called ‘seqLogo’ 843s Execution halted 843s * [Sat Mar 16 21:18:11 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 844s Refining start codon selections. 844s -number of revised start positions: 83 844s * [Sat Mar 16 21:18:12 2024] Running CMD: cp /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 844s copying output to final output file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Sat Mar 16 21:18:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 844s Making bed file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed 844s * [Sat Mar 16 21:18:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 845s Making pep file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 846s * [Sat Mar 16 21:18:14 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 846s Making cds file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds 847s transdecoder is finished. See output files /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* 847s 847s 847s 847s ../../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 847s 847s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 847s CDS coords: 205, 828 848s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_117.p2. 848s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_127.p1. 848s -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 142, 1281 848s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_177.p1. 848s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_198.p3. 848s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_199.p3. 848s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_200.p3. 848s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. 848s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. 848s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. 848s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. 848s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. 848s -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 107, 466 848s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_289.p2. 848s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_290.p1. 848s -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [21], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [22], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [23], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_420.p1. 848s -Warning [25], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 140, 700 848s -Warning [26], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 340, 816 848s -Warning [27], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 93, 1106 848s -Warning [28], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [29], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [30], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 312, 1253 848s -Warning [31], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_550.p1. 848s -Warning [32], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_559.p2. 848s -Warning [33], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [34], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_592.p3. 848s -Warning [35], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_593.p3. 848s -Warning [36], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_594.p3. 848s -Warning [37], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [38], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_615.p1. 848s -Warning [39], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 80, 427 848s -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. 848s -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. 848s -Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. 848s -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. 848s -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 112, 447 848s -Warning [46], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_745.p2. 848s -Warning [47], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_746.p1. 848s -Warning [48], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 108, 452 848s -Warning [49], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 2, 562 848s -Warning [50], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 848s -Warning [51], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 141, 545 848s -Warning [52], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 848s CDS coords: 178, 1623 848s -Warning [53], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_855.p1. 848s 848s 848s Done. 765 / 792 transcript orfs could be propagated to the genome 848s 848s 848s 848s ../../util/fasta_prot_checker.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep 849s 849s 849s echo "Done. See pasa_assemblies.fasta.transdecoder.\*" 849s 849s 849s exit 0 849s Done. See pasa_assemblies.fasta.transdecoder.\* 849s make[1]: Leaving directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/pasa_example' 849s Running example in $... 849s make[1]: Entering directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 849s ./runMe.sh 849s CMD: mkdir -p /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir 849s * [Sat Mar 16 21:18:17 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl Trinity.fasta 0 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat 849s 849s 849s -first extracting base frequencies, we'll need them later. 850s 850s 850s - extracting ORFs from transcripts. 850s -total transcripts to examine: 921 855s [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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 855s 855s 855s ################################# 855s ### Done preparing long ORFs. ### 855s ################################## 855s 855s Use file: /tmp/autopkgtest.x2gTgS/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. 855s 855s Then, run TransDecoder.Predict for your final coding region predictions. 855s 855s 856s * [Sat Mar 16 21:18:24 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 856s * [Sat Mar 16 21:18:24 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 857s -skipping training candidate: comp847_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp992_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp718_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp1177_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp999_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp989_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp836_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp621_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp844_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp594_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp956_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp1044_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp835_c0_seq2.p2, not unique enough 857s -skipping training candidate: comp1029_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp1016_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp1207_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp862_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp703_c0_seq1.p2, not unique enough 857s -skipping training candidate: comp1191_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp867_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp1207_c0_seq2.p2, not unique enough 857s -skipping training candidate: comp905_c0_seq1.p1, not unique enough 857s -skipping training candidate: comp784_c0_seq2.p1, not unique enough 857s -skipping training candidate: comp674_c0_seq1.p1, not unique enough 858s -skipping training candidate: comp924_c0_seq1.p2, not unique enough 858s -skipping training candidate: comp1174_c0_seq2.p1, not unique enough 858s -skipping training candidate: comp1046_c0_seq2.p1, not unique enough 858s -skipping training candidate: comp1191_c0_seq2.p2, not unique enough 858s -skipping training candidate: comp1044_c0_seq2.p2, not unique enough 858s -skipping training candidate: comp873_c0_seq1.p1, not unique enough 858s -skipping training candidate: comp1177_c0_seq2.p2, not unique enough 858s -skipping training candidate: comp1196_c0_seq2.p1, not unique enough 858s -skipping training candidate: comp999_c0_seq2.p2, not unique enough 858s -skipping training candidate: comp985_c0_seq2.p1, not unique enough 858s 858s -redundancy-minimized set includes 810 / 844 = 95.97% 858s 858s * [Sat Mar 16 21:18:26 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 858s PCT_GC: 38 858s * [Sat Mar 16 21:18:26 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores 864s * [Sat Mar 16 21:18:32 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores 885s * [Sat Mar 16 21:18:53 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 886s Selecting best orfs 886s * [Sat Mar 16 21:18:54 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement 886s Training start codon pattern recognition* [Sat Mar 16 21:18:54 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 887s * [Sat Mar 16 21:18:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores 887s -round: 1 908s -round: 2 927s -round: 3 945s -round: 4 964s -round: 5 983s * [Sat Mar 16 21:20:31 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 983s -parsing scores 1005s * [Sat Mar 16 21:20:53 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 1006s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1006s Execution halted 1006s * [Sat Mar 16 21:20:54 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc 1007s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1007s Execution halted 1007s * [Sat Mar 16 21:20:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : 1007s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1007s Execution halted 1007s * [Sat Mar 16 21:20:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : 1008s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1008s Execution halted 1008s * [Sat Mar 16 21:20:56 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced 1008s num features: 358 num_incorporate: 107 1008s -feature swap of score: 2.01860755745774 instead of -2.43253294753209 1008s -feature swap of score: 2.34732451463516 instead of -2.03515280104856 1008s -feature swap of score: 2.42600756963178 instead of -1.88586714183678 1008s -feature swap of score: 4.04692570560011 instead of -2.07838396233827 1008s -feature swap of score: -2.10349049055208 instead of -2.14357898216183 1008s -feature swap of score: 3.34270681682176 instead of -1.68919591401722 1008s -feature swap of score: 0.785638027271692 instead of -1.75537844488172 1008s -feature swap of score: 0.124937617546208 instead of -1.42423447927029 1008s -feature swap of score: 3.80360939610757 instead of -1.25581956645478 1008s -feature swap of score: 2.22972790847055 instead of -1.43724022198391 1008s -feature swap of score: 1.87223224767761 instead of -1.39134963935408 1008s -feature swap of score: -0.869196741065359 instead of -1.45437592553593 1008s -feature swap of score: 2.61126122082178 instead of -1.4644389491732 1008s -feature swap of score: 0.041614898233897 instead of -1.38236698907653 1008s -feature swap of score: 5.23702512832804 instead of -1.06647647854364 1008s -feature swap of score: 0.489018424262898 instead of -0.95713076184448 1008s -feature swap of score: 1.06810458576389 instead of -0.894284983683669 1008s -feature swap of score: -0.226298629660561 instead of -0.948994050642804 1008s -feature swap of score: 0.450699974271914 instead of -0.959497695240219 1008s -feature swap of score: 4.28695919068754 instead of -0.978907600609435 1008s -feature swap of score: 2.14133448495559 instead of -0.753180766675387 1008s -feature swap of score: 4.12202729113471 instead of -0.76828282708309 1008s -feature swap of score: -0.104946382094106 instead of -0.628776084467911 1008s -feature swap of score: 0.000572807808514326 instead of -0.53263942949094 1008s -feature swap of score: 0.198006134044188 instead of -0.34106805075173 1008s -feature swap of score: 3.6047163749624 instead of -0.51212082035361 1008s -feature swap of score: 0.814286538900709 instead of -0.339061555243772 1008s -feature swap of score: 4.97523538835402 instead of -0.219644205392414 1008s -feature swap of score: 1.97045125499639 instead of -0.113036838336636 1008s -feature swap of score: 4.13053733045551 instead of -0.170052581383971 1008s -feature swap of score: 0.00206436128981199 instead of -0.181062974960661 1009s -feature swap of score: 1.604245252388 instead of 0.0517161275151237 1009s -feature swap of score: 4.3932806981529 instead of 0.0860431565952234 1009s -feature swap of score: 1.72957229182765 instead of 0.221968210457067 1009s -feature swap of score: 1.57263236697426 instead of 0.288968311790631 1009s -feature swap of score: 0.203166281459456 instead of 0.10534662338876 1009s -feature swap of score: 4.38190400149154 instead of 0.196370432457334 1009s -feature swap of score: 5.04613038233112 instead of 0.150614918926321 1009s -feature swap of score: 2.26071953474249 instead of 0.230526386115092 1009s -feature swap of score: 5.13639850152629 instead of 0.252892697647447 1009s -feature swap of score: 1.17098382473728 instead of 0.282995900530861 1009s -feature swap of score: 4.34776268138483 instead of 0.41430990147474 1009s -feature swap of score: 2.15329616437699 instead of 0.429451771590664 1009s -feature swap of score: 5.09229418476461 instead of 0.297828956020416 1009s -feature swap of score: 1.13675328930652 instead of 0.171694593520241 1009s -feature swap of score: 2.02231900226323 instead of 0.206703978994726 1009s -feature swap of score: 2.66734827613583 instead of 0.443525927859022 1009s -feature swap of score: 3.77684820014943 instead of 0.599510264128007 1009s -feature swap of score: 1.29789971226826 instead of 0.51658385615187 1009s -feature swap of score: 3.74256664801257 instead of 0.445260647950643 1009s -feature swap of score: 4.32680419305246 instead of 0.596611075477652 1009s -feature swap of score: 1.77920876164079 instead of 0.52605377488021 1009s -feature swap of score: 1.61583261588263 instead of 0.65317830698915 1009s -feature swap of score: 4.10400531839299 instead of 0.789843632233928 1009s -feature swap of score: 1.83659343125585 instead of 0.716731928502843 1009s -feature swap of score: 1.6438027810344 instead of 0.767790779444299 1009s -feature swap of score: 2.51637019194037 instead of 0.699527206449989 1009s -feature swap of score: 1.60560873858958 instead of 1.07464412670026 1009s -feature swap of score: 2.89883210321421 instead of 1.07157389032513 1009s -feature swap of score: 2.93101514977772 instead of 0.988616846801185 1009s -feature swap of score: 3.72069918320373 instead of 0.868454192870146 1009s -feature swap of score: 1.03519107357972 instead of 0.753010048444791 1009s -feature swap of score: 4.01020820806659 instead of 0.886358064075704 1009s -feature swap of score: 0.879618323769624 instead of 0.61109819149034 1009s -feature swap of score: 7.15234940921215 instead of 1.03360771341683 1009s -feature swap of score: 1.83921458905268 instead of 1.02334035960285 1009s -feature swap of score: 2.23998772164463 instead of 0.834483027752134 1009s -feature swap of score: 2.16522830829353 instead of 1.1968190751818 1009s -feature swap of score: 3.565902255058 instead of 1.04816444694555 1009s -feature swap of score: 1.1156878707122 instead of 0.972785593550388 1009s -feature swap of score: 1.63015648897591 instead of 1.12916093095551 1009s -feature swap of score: 3.15623525707792 instead of 1.19443129843577 1009s -feature swap of score: 1.75064193312005 instead of 1.22439213990375 1009s -feature swap of score: 2.22558017270471 instead of 1.41095670579146 1009s -feature swap of score: 1.69472767650654 instead of 1.47090708539632 1009s -feature swap of score: 5.71675848798316 instead of 1.54417528485585 1009s -feature swap of score: 2.36834513989863 instead of 1.56065511814006 1009s -feature swap of score: 4.72132107671951 instead of 1.39108914413569 1009s -feature swap of score: 2.98996061269645 instead of 1.4726797291019 1009s -feature swap of score: 2.30202014931778 instead of 1.35942459345001 1009s -feature swap of score: 6.94448025054924 instead of 1.53071141968655 1009s -feature swap of score: 2.02147832129674 instead of 1.39293685217156 1009s -feature swap of score: 3.0540382236436 instead of 1.47682791921283 1009s -feature swap of score: 8.35170655675059 instead of 1.54271367706925 1009s -feature swap of score: 2.3591087448739 instead of 1.62983627612991 1009s -feature swap of score: 3.33896220987853 instead of 1.74551832680512 1009s -feature swap of score: 4.47931807129169 instead of 1.65656837994906 1009s -feature swap of score: 6.43889512650897 instead of 1.63523856658065 1009s -feature swap of score: 4.44139726355316 instead of 1.62413947257281 1009s -feature swap of score: 4.3934217091148 instead of 1.5563895897064 1009s -feature swap of score: 2.4178749161712 instead of 1.53540854291086 1009s -feature swap of score: 4.50084537762944 instead of 1.99813615680005 1009s -feature swap of score: 4.36085158331683 instead of 1.81509165074822 1009s -feature swap of score: 3.50540200807125 instead of 1.84763588301182 1009s -feature swap of score: 2.14307301177581 instead of 1.58943578807425 1009s -feature swap of score: 2.80249705432441 instead of 2.03323063135445 1009s -feature swap of score: 2.51995823874979 instead of 1.80649830131556 1009s -feature swap of score: 2.18546699630314 instead of 2.01678734343503 1009s -feature swap of score: 6.02870360838808 instead of 2.11230538713769 1009s -feature swap of score: 4.79559537621424 instead of 1.93041915648434 1009s -feature swap of score: 8.43445355562363 instead of 2.187388349484 1009s -feature swap of score: 3.43057432858564 instead of 2.04524276099259 1009s -feature swap of score: 2.64567534439595 instead of 1.91708045098195 1010s -num feature swaps: 103 1010s * [Sat Mar 16 21:20:57 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 1010s -round: 1 1027s -round: 2 1044s -round: 3 1062s -round: 4 1080s -round: 5 1098s * [Sat Mar 16 21:22:26 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1098s -parsing scores 1119s * [Sat Mar 16 21:22:47 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 1119s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1119s Execution halted 1119s * [Sat Mar 16 21:22:47 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1120s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1120s Execution halted 1120s * [Sat Mar 16 21:22:48 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 1121s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1121s Execution halted 1121s * [Sat Mar 16 21:22:49 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 1121s Refining start codon selections. 1122s -number of revised start positions: 43 1122s * [Sat Mar 16 21:22:49 2024] Running CMD: cp /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 1122s copying output to final output file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Sat Mar 16 21:22:50 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 1122s Making bed file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed 1122s * [Sat Mar 16 21:22:50 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 1123s Making pep file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep 1123s * [Sat Mar 16 21:22:51 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 1124s Making cds file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds 1124s transdecoder is finished. See output files /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* 1124s 1124s 1125s 1125s -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 266, 796 1125s -WARNING, comp1008_c0_seq1 has no genome representation... skipping 1125s -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 1125s -WARNING, comp1021_c0_seq1 has no genome representation... skipping 1125s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1026_c0_seq1.p1. 1125s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1037_c0_seq1.p2. 1125s -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 561, 1325 1125s Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'gene_id' => '', 1125s 'coords' => [ 1125s [ 1125s '1642973', 1125s '1644586' 1125s ] 1125s ], 1125s 'orient' => '-', 1125s 'trans_id' => '', 1125s 'contig' => 'III', 1125s 'asmbl' => 'comp1051_c1_seq1' 1125s }; 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s is_3prime_partial: 0 1125s mid_pt: 808 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s com_name: ORF type:5prime_partial (+),score=83.26 1125s classification: annotated_genes 1125s asmbl_id: comp1051_c1_seq1 1125s source: transdecoder 1125s gene_length: 1616 1125s Model_feat_name: comp1051_c1_seq1.p1 1125s TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 1125s strand: + 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1616 CDS-exon: 2, 820 1125s gene_span: 1-1616 1125s model_span: 2-820 1125s 1125s Error, couldn't localize pt [1615] within coordsets: $VAR1 = [ 1125s [ 1125s '1642973', 1125s '1644586' 1125s ] 1125s ]; 1125s -WARNING, comp1053_c0_seq1 has no genome representation... skipping 1125s Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'asmbl' => 'comp1058_c0_seq1', 1125s 'contig' => 'I', 1125s 'trans_id' => '', 1125s 'coords' => [ 1125s [ 1125s 5095548, 1125s '5095878' 1125s ], 1125s [ 1125s 5095142, 1125s '5095301' 1125s ] 1125s ], 1125s 'orient' => '-', 1125s 'gene_id' => '' 1125s }; 1125s com_name: ORF type:5prime_partial (+),score=32.57 1125s mid_pt: 248 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s is_3prime_partial: 0 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s strand: + 1125s gene_length: 496 1125s source: transdecoder 1125s Model_feat_name: comp1058_c0_seq1.p1 1125s TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 1125s classification: annotated_genes 1125s asmbl_id: comp1058_c0_seq1 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 496 CDS-exon: 3, 422 1125s gene_span: 1-496 1125s model_span: 3-422 1125s 1125s Error, couldn't localize pt [494] within coordsets: $VAR1 = [ 1125s [ 1125s 5095142, 1125s '5095301' 1125s ], 1125s [ 1125s 5095548, 1125s '5095878' 1125s ] 1125s ]; 1125s -Warning [6], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 3441, 3773 1125s -WARNING, comp1075_c0_seq1 has no genome representation... skipping 1125s Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'asmbl' => 'comp1112_c0_seq1', 1125s 'contig' => 'III', 1125s 'orient' => '-', 1125s 'coords' => [ 1125s [ 1125s 2380416, 1125s '2380466' 1125s ], 1125s [ 1125s 2379717, 1125s '2380336' 1125s ] 1125s ], 1125s 'gene_id' => '', 1125s 'trans_id' => '' 1125s }; 1125s strand: + 1125s TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 1125s Model_feat_name: comp1112_c0_seq1.p1 1125s source: transdecoder 1125s gene_length: 2081 1125s classification: annotated_genes 1125s asmbl_id: comp1112_c0_seq1 1125s com_name: ORF type:complete (+),score=155.28 1125s mid_pt: 1041 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s is_3prime_partial: 0 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 2081 CDS-exon: 365, 1903 1125s gene_span: 1-2081 1125s model_span: 365-1903 1125s 1125s Error, couldn't localize pt [1717] within coordsets: $VAR1 = [ 1125s [ 1125s 2379717, 1125s '2380336' 1125s ], 1125s [ 1125s 2380416, 1125s '2380466' 1125s ] 1125s ]; 1125s -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 1125s -WARNING, comp1124_c0_seq1 has no genome representation... skipping 1125s Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'asmbl' => 'comp1198_c0_seq1', 1125s 'contig' => 'II', 1125s 'trans_id' => '', 1125s 'orient' => '-', 1125s 'coords' => [ 1125s [ 1125s 402195, 1125s '402246' 1125s ], 1125s [ 1125s 402017, 1125s '402141' 1125s ], 1125s [ 1125s 401844, 1125s '401910' 1125s ], 1125s [ 1125s 401352, 1125s '401683' 1125s ] 1125s ], 1125s 'gene_id' => '' 1125s }; 1125s strand: + 1125s source: transdecoder 1125s gene_length: 597 1125s Model_feat_name: comp1198_c0_seq1.p1 1125s TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 1125s classification: annotated_genes 1125s asmbl_id: comp1198_c0_seq1 1125s com_name: ORF type:internal (+),score=37.56 1125s mid_pt: 299 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s is_3prime_partial: 0 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 597 CDS-exon: 2, 595 1125s gene_span: 1-597 1125s model_span: 2-595 1125s 1125s Error, couldn't localize pt [596] within coordsets: $VAR1 = [ 1125s [ 1125s 401352, 1125s '401683' 1125s ], 1125s [ 1125s 401844, 1125s '401910' 1125s ], 1125s [ 1125s 402017, 1125s '402141' 1125s ], 1125s [ 1125s 402195, 1125s '402246' 1125s ] 1125s ]; 1125s Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'asmbl' => 'comp1210_c0_seq1', 1125s 'contig' => 'III', 1125s 'trans_id' => '', 1125s 'coords' => [ 1125s [ 1125s 368840, 1125s '369008' 1125s ], 1125s [ 1125s 367430, 1125s '368790' 1125s ] 1125s ], 1125s 'orient' => '-', 1125s 'gene_id' => '' 1125s }; 1125s source: transdecoder 1125s gene_length: 1554 1125s TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 1125s Model_feat_name: comp1210_c0_seq1.p1 1125s asmbl_id: comp1210_c0_seq1 1125s classification: annotated_genes 1125s strand: + 1125s is_3prime_partial: 0 1125s gene_type: protein-coding 1125s is_pseudogene: 0 1125s com_name: ORF type:5prime_partial (+),score=12.16 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s mid_pt: 777 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1554 CDS-exon: 2, 781 1125s gene_span: 1-1554 1125s model_span: 2-781 1125s 1125s Error, couldn't localize pt [1553] within coordsets: $VAR1 = [ 1125s [ 1125s 367430, 1125s '368790' 1125s ], 1125s [ 1125s 368840, 1125s '369008' 1125s ] 1125s ]; 1125s -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 1125s -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 1125s -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 3, 392 1125s -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). 1125s Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'orient' => '-', 1125s 'coords' => [ 1125s [ 1125s '3840968', 1125s '3841303' 1125s ] 1125s ], 1125s 'gene_id' => '', 1125s 'trans_id' => '', 1125s 'asmbl' => 'comp366_c0_seq1', 1125s 'contig' => 'II' 1125s }; 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s is_3prime_partial: 0 1125s mid_pt: 170 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s com_name: ORF type:internal (-),score=12.83 1125s classification: annotated_genes 1125s asmbl_id: comp366_c0_seq1 1125s TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 1125s Model_feat_name: comp366_c0_seq1.p1 1125s source: transdecoder 1125s gene_length: 340 1125s strand: - 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 340, 1 CDS-exon: 339, 1 1125s gene_span: 340-1 1125s model_span: 339-1 1125s 1125s Error, couldn't localize pt [340] within coordsets: $VAR1 = [ 1125s [ 1125s '3840968', 1125s '3841303' 1125s ] 1125s ]; 1125s -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 1, 384 1125s -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 3, 347 1125s -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 1, 492 1125s -WARNING, comp504_c0_seq1 has no genome representation... skipping 1125s -WARNING, comp576_c0_seq1 has no genome representation... skipping 1125s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp583_c0_seq1.p1. 1125s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. 1125s Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'asmbl' => 'comp610_c0_seq1', 1125s 'contig' => 'I', 1125s 'trans_id' => '', 1125s 'coords' => [ 1125s [ 1125s '5471264', 1125s '5472770' 1125s ] 1125s ], 1125s 'orient' => '-', 1125s 'gene_id' => '' 1125s }; 1125s classification: annotated_genes 1125s asmbl_id: comp610_c0_seq1 1125s Model_feat_name: comp610_c0_seq1.p1 1125s TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 1125s gene_length: 1509 1125s source: transdecoder 1125s strand: + 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s is_3prime_partial: 0 1125s mid_pt: 755 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s com_name: ORF type:5prime_partial (+),score=50.55 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1509 CDS-exon: 2, 1210 1125s gene_span: 1-1509 1125s model_span: 2-1210 1125s 1125s Error, couldn't localize pt [1508] within coordsets: $VAR1 = [ 1125s [ 1125s '5471264', 1125s '5472770' 1125s ] 1125s ]; 1125s -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). 1125s CDS coords: 1441, 1941 1125s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. 1125s Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'trans_id' => '', 1125s 'gene_id' => '', 1125s 'orient' => '-', 1125s 'coords' => [ 1125s [ 1125s '4333088', 1125s '4336727' 1125s ] 1125s ], 1125s 'contig' => 'I', 1125s 'asmbl' => 'comp645_c0_seq1' 1125s }; 1125s gene_length: 3653 1125s source: transdecoder 1125s TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 1125s Model_feat_name: comp645_c0_seq1.p1 1125s asmbl_id: comp645_c0_seq1 1125s classification: annotated_genes 1125s strand: + 1125s is_3prime_partial: 0 1125s gene_type: protein-coding 1125s is_pseudogene: 0 1125s com_name: ORF type:5prime_partial (+),score=273.35 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s mid_pt: 1827 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 3653 CDS-exon: 2, 3571 1125s gene_span: 1-3653 1125s model_span: 2-3571 1125s 1125s Error, couldn't localize pt [3652] within coordsets: $VAR1 = [ 1125s [ 1125s '4333088', 1125s '4336727' 1125s ] 1125s ]; 1125s Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'contig' => 'II', 1125s 'asmbl' => 'comp688_c0_seq1', 1125s 'gene_id' => '', 1125s 'coords' => [ 1125s [ 1125s 380308, 1125s '380560' 1125s ], 1125s [ 1125s 380624, 1125s '381243' 1125s ] 1125s ], 1125s 'orient' => '+', 1125s 'trans_id' => '' 1125s }; 1125s strand: + 1125s classification: annotated_genes 1125s asmbl_id: comp688_c0_seq1 1125s TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 1125s Model_feat_name: comp688_c0_seq1.p1 1125s gene_length: 2784 1125s source: transdecoder 1125s mid_pt: 1392 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s com_name: ORF type:complete (+),score=172.54 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s is_3prime_partial: 0 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 2784 CDS-exon: 83, 2578 1125s gene_span: 1-2784 1125s model_span: 83-2578 1125s 1125s Error, couldn't localize pt [2578] within coordsets: $VAR1 = [ 1125s [ 1125s 380308, 1125s '380560' 1125s ], 1125s [ 1125s 380624, 1125s '381243' 1125s ] 1125s ]; 1125s -WARNING, comp701_c0_seq1 has no genome representation... skipping 1125s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp703_c0_seq1.p2. 1125s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp707_c0_seq1.p2. 1125s -WARNING, comp831_c0_seq1 has no genome representation... skipping 1125s Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'gene_id' => '', 1125s 'orient' => '+', 1125s 'coords' => [ 1125s [ 1125s 3753910, 1125s '3754392' 1125s ], 1125s [ 1125s 3754438, 1125s '3755057' 1125s ] 1125s ], 1125s 'trans_id' => '', 1125s 'contig' => 'II', 1125s 'asmbl' => 'comp856_c0_seq1' 1125s }; 1125s com_name: ORF type:complete (+),score=71.94 1125s mid_pt: 785 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s is_3prime_partial: 0 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s strand: + 1125s source: transdecoder 1125s gene_length: 1569 1125s TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 1125s Model_feat_name: comp856_c0_seq1.p1 1125s classification: annotated_genes 1125s asmbl_id: comp856_c0_seq1 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1569 CDS-exon: 161, 1504 1125s gene_span: 1-1569 1125s model_span: 161-1504 1125s 1125s Error, couldn't localize pt [1504] within coordsets: $VAR1 = [ 1125s [ 1125s 3753910, 1125s '3754392' 1125s ], 1125s [ 1125s 3754438, 1125s '3755057' 1125s ] 1125s ]; 1125s Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'contig' => 'II', 1125s 'asmbl' => 'comp873_c0_seq2', 1125s 'trans_id' => '', 1125s 'gene_id' => '', 1125s 'coords' => [ 1125s [ 1125s 3727877, 1125s '3728121' 1125s ], 1125s [ 1125s 3727705, 1125s '3727810' 1125s ], 1125s [ 1125s 3726988, 1125s '3727657' 1125s ] 1125s ], 1125s 'orient' => '-' 1125s }; 1125s strand: + 1125s classification: annotated_genes 1125s asmbl_id: comp873_c0_seq2 1125s Model_feat_name: comp873_c0_seq2.p1 1125s TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 1125s source: transdecoder 1125s gene_length: 1025 1125s mid_pt: 513 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s com_name: ORF type:5prime_partial (+),score=8.59 1125s is_pseudogene: 0 1125s gene_type: protein-coding 1125s is_3prime_partial: 0 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1025 CDS-exon: 3, 677 1125s gene_span: 1-1025 1125s model_span: 3-677 1125s 1125s Error, couldn't localize pt [1023] within coordsets: $VAR1 = [ 1125s [ 1125s 3726988, 1125s '3727657' 1125s ], 1125s [ 1125s 3727705, 1125s '3727810' 1125s ], 1125s [ 1125s 3727877, 1125s '3728121' 1125s ] 1125s ]; 1125s Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'contig' => 'III', 1125s 'asmbl' => 'comp888_c0_seq1', 1125s 'trans_id' => '', 1125s 'gene_id' => '', 1125s 'coords' => [ 1125s [ 1125s 1268244, 1125s '1268583' 1125s ], 1125s [ 1125s 1267938, 1125s '1268172' 1125s ] 1125s ], 1125s 'orient' => '-' 1125s }; 1125s asmbl_id: comp888_c0_seq1 1125s classification: annotated_genes 1125s Model_feat_name: comp888_c0_seq1.p1 1125s TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 1125s gene_length: 589 1125s source: transdecoder 1125s strand: + 1125s gene_type: protein-coding 1125s is_pseudogene: 0 1125s is_3prime_partial: 0 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s mid_pt: 295 1125s com_name: ORF type:5prime_partial (+),score=23.94 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 589 CDS-exon: 2, 355 1125s gene_span: 1-589 1125s model_span: 2-355 1125s 1125s Error, couldn't localize pt [588] within coordsets: $VAR1 = [ 1125s [ 1125s 1267938, 1125s '1268172' 1125s ], 1125s [ 1125s 1268244, 1125s '1268583' 1125s ] 1125s ]; 1125s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp924_c0_seq1.p2. 1125s -WARNING, comp932_c0_seq1 has no genome representation... skipping 1125s Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'gene_id' => '', 1125s 'coords' => [ 1125s [ 1125s 105641, 1125s '105736' 1125s ], 1125s [ 1125s 105785, 1125s '106404' 1125s ] 1125s ], 1125s 'orient' => '+', 1125s 'trans_id' => '', 1125s 'contig' => 'III', 1125s 'asmbl' => 'comp940_c0_seq1' 1125s }; 1125s strand: + 1125s source: transdecoder 1125s gene_length: 2129 1125s TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 1125s Model_feat_name: comp940_c0_seq1.p1 1125s asmbl_id: comp940_c0_seq1 1125s classification: annotated_genes 1125s com_name: ORF type:complete (+),score=94.37 1125s num_exons: 1 1125s is_5prime_partial: 0 1125s mid_pt: 1065 1125s is_3prime_partial: 0 1125s gene_type: protein-coding 1125s is_pseudogene: 0 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 2129 CDS-exon: 40, 1731 1125s gene_span: 1-2129 1125s model_span: 40-1731 1125s 1125s Error, couldn't localize pt [1731] within coordsets: $VAR1 = [ 1125s [ 1125s 105641, 1125s '105736' 1125s ], 1125s [ 1125s 105785, 1125s '106404' 1125s ] 1125s ]; 1125s Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: 1125s $VAR1 = { 1125s 'contig' => 'I', 1125s 'asmbl' => 'comp983_c0_seq1', 1125s 'gene_id' => '', 1125s 'orient' => '-', 1125s 'coords' => [ 1125s [ 1125s 4100066, 1125s '4100163' 1125s ], 1125s [ 1125s 4098246, 1125s '4100014' 1125s ] 1125s ], 1125s 'trans_id' => '' 1125s }; 1125s is_5prime_partial: 0 1125s num_exons: 1 1125s mid_pt: 935 1125s com_name: ORF type:5prime_partial (+),score=143.65 1125s gene_type: protein-coding 1125s is_pseudogene: 0 1125s is_3prime_partial: 0 1125s strand: + 1125s asmbl_id: comp983_c0_seq1 1125s classification: annotated_genes 1125s gene_length: 1870 1125s source: transdecoder 1125s Model_feat_name: comp983_c0_seq1.p1 1125s TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 1125s gene_synonyms: 1125s mRNA_coords 1125s CDS_coords 1125s RNA-exon: 1, 1870 CDS-exon: 2, 1810 1125s gene_span: 1-1870 1125s model_span: 2-1810 1125s 1125s Error, couldn't localize pt [1869] within coordsets: $VAR1 = [ 1125s [ 1125s 4098246, 1125s '4100014' 1125s ], 1125s [ 1125s 4100066, 1125s '4100163' 1125s ] 1125s ]; 1125s -WARNING, comp995_c0_seq1 has no genome representation... skipping 1125s 1125s 1125s Done. 646 / 679 transcript orfs could be propagated to the genome 1125s 1126s make[1]: Leaving directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/simple_transcriptome_target' 1126s Running example in $... 1126s make[1]: Entering directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 1126s ./runMe.sh 1126s #!/bin/bash -ve 1126s 1126s export PERL_HASH_SEED=0 1126s 1126s 1126s 1126s ## generate alignment gff3 formatted output 1126s ../../util/gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3 1130s 1130s 1130s ## generate transcripts fasta file 1130s # not including the genome here... too big, but here's how you'd do it. 1130s #../../util/gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta 1130s 1130s ## Extract the long ORFs 1130s ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S 1130s CMD: mkdir -p /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir 1130s * [Sat Mar 16 21:22:58 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat 1130s 1130s 1130s -first extracting base frequencies, we'll need them later. 1136s 1136s 1136s - extracting ORFs from transcripts. 1136s -total transcripts to examine: 3501 1169s [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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 1169s 1169s 1169s ################################# 1169s ### Done preparing long ORFs. ### 1169s ################################## 1169s 1169s Use file: /tmp/autopkgtest.x2gTgS/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. 1169s 1169s Then, run TransDecoder.Predict for your final coding region predictions. 1169s 1169s 1169s 1169s 1169s ## Predict likely ORFs 1169s 1169s ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS 1169s * [Sat Mar 16 21:23:37 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 1171s * [Sat Mar 16 21:23:39 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 1172s -skipping training candidate: NM_198270.p1, not unique enough 1172s -skipping training candidate: NR_104391.p1, not unique enough 1172s -skipping training candidate: NR_104395.p1, not unique enough 1172s -skipping training candidate: NM_001282622.p1, not unique enough 1172s -skipping training candidate: MSTRG.376.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.839.3.p1, not unique enough 1172s -skipping training candidate: NR_104394.p1, not unique enough 1172s -skipping training candidate: MSTRG.397.18.p1, not unique enough 1172s -skipping training candidate: NM_020717.p1, not unique enough 1172s -skipping training candidate: MSTRG.505.14.p1, not unique enough 1172s -skipping training candidate: NM_001136024.p1, not unique enough 1172s -skipping training candidate: MSTRG.538.2.p1, not unique enough 1172s -skipping training candidate: NM_001291868.p1, not unique enough 1172s -skipping training candidate: MSTRG.236.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.404.8.p1, not unique enough 1172s -skipping training candidate: NM_001555.p1, not unique enough 1172s -skipping training candidate: NM_001282224.p1, not unique enough 1172s -skipping training candidate: NM_001170962.p1, not unique enough 1172s -skipping training candidate: NM_001291416.p1, not unique enough 1172s -skipping training candidate: NM_021140.p1, not unique enough 1172s -skipping training candidate: MSTRG.376.9.p1, not unique enough 1172s -skipping training candidate: NM_014710.p1, not unique enough 1172s -skipping training candidate: NM_001099411.p1, not unique enough 1172s -skipping training candidate: NM_001184727.p1, not unique enough 1172s -skipping training candidate: NM_001146702.p1, not unique enough 1172s -skipping training candidate: MSTRG.258.8.p1, not unique enough 1172s -skipping training candidate: NM_005096.p1, not unique enough 1172s -skipping training candidate: MSTRG.258.9.p1, not unique enough 1172s -skipping training candidate: MSTRG.502.3.p1, not unique enough 1172s -skipping training candidate: NM_001171162.p1, not unique enough 1172s -skipping training candidate: MSTRG.502.2.p1, not unique enough 1172s -skipping training candidate: MSTRG.502.1.p1, not unique enough 1172s -skipping training candidate: NM_001291417.p1, not unique enough 1172s -skipping training candidate: NM_001168360.p1, not unique enough 1172s -skipping training candidate: NM_032969.p1, not unique enough 1172s -skipping training candidate: NM_001168363.p1, not unique enough 1172s -skipping training candidate: MSTRG.236.3.p1, not unique enough 1172s -skipping training candidate: NM_001168362.p1, not unique enough 1172s -skipping training candidate: NM_001291418.p1, not unique enough 1172s -skipping training candidate: NM_001169123.p1, not unique enough 1172s -skipping training candidate: MSTRG.570.10.p1, not unique enough 1172s -skipping training candidate: NR_111960.p1, not unique enough 1172s -skipping training candidate: NM_001169122.p1, not unique enough 1172s -skipping training candidate: NM_001169124.p1, not unique enough 1172s -skipping training candidate: NM_001169125.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.14.p1, not unique enough 1172s -skipping training candidate: NM_001042749.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.13.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.7.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.12.p1, not unique enough 1172s -skipping training candidate: NM_000425.p1, not unique enough 1172s -skipping training candidate: NM_024003.p1, not unique enough 1172s -skipping training candidate: NM_001143963.p1, not unique enough 1172s -skipping training candidate: MSTRG.477.3.p1, not unique enough 1172s -skipping training candidate: NM_012310.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.11.p1, not unique enough 1172s -skipping training candidate: NM_001042751.p1, not unique enough 1172s -skipping training candidate: NM_006603.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.4.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.2.p1, not unique enough 1172s -skipping training candidate: NM_001282418.p1, not unique enough 1172s -skipping training candidate: MSTRG.848.6.p1, not unique enough 1172s -skipping training candidate: NM_004022.p1, not unique enough 1172s -skipping training candidate: NM_004013.p1, not unique enough 1172s -skipping training candidate: MSTRG.570.9.p1, not unique enough 1172s -skipping training candidate: MSTRG.147.2.p1, not unique enough 1172s -skipping training candidate: NM_006044.p1, not unique enough 1172s -skipping training candidate: MSTRG.331.3.p1, not unique enough 1172s -skipping training candidate: MSTRG.331.2.p1, not unique enough 1172s -skipping training candidate: MSTRG.331.4.p1, not unique enough 1172s -skipping training candidate: NM_001281463.p1, not unique enough 1172s -skipping training candidate: NM_001122670.p1, not unique enough 1172s -skipping training candidate: MSTRG.147.3.p1, not unique enough 1172s -skipping training candidate: NM_021949.p1, not unique enough 1172s -skipping training candidate: MSTRG.456.2.p1, not unique enough 1172s -skipping training candidate: NM_001130860.p1, not unique enough 1172s -skipping training candidate: NM_001172436.p1, not unique enough 1172s -skipping training candidate: MSTRG.442.1.p1, not unique enough 1172s -skipping training candidate: NM_004023.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.2.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.3.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.8.p1, not unique enough 1172s -skipping training candidate: MSTRG.518.1.p1, not unique enough 1172s -skipping training candidate: NM_001010986.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.1.p1, not unique enough 1172s -skipping training candidate: NM_004020.p1, not unique enough 1172s -skipping training candidate: NM_153280.p1, not unique enough 1172s -skipping training candidate: NM_001291421.p1, not unique enough 1172s -skipping training candidate: NM_001105243.p1, not unique enough 1172s -skipping training candidate: NM_020766.p1, not unique enough 1172s -skipping training candidate: NM_007309.p1, not unique enough 1172s -skipping training candidate: NM_005756.p1, not unique enough 1172s -skipping training candidate: NM_001113490.p1, not unique enough 1172s -skipping training candidate: NM_001079859.p1, not unique enough 1172s -skipping training candidate: NM_001184833.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.6.p1, not unique enough 1172s -skipping training candidate: NM_001168361.p1, not unique enough 1172s -skipping training candidate: NM_001079860.p1, not unique enough 1172s -skipping training candidate: NM_001184836.p1, not unique enough 1172s -skipping training candidate: NM_001184837.p1, not unique enough 1172s -skipping training candidate: NM_001257231.p1, not unique enough 1172s -skipping training candidate: NM_001184835.p1, not unique enough 1172s -skipping training candidate: NM_001282875.p1, not unique enough 1172s -skipping training candidate: NM_003069.p1, not unique enough 1172s -skipping training candidate: MSTRG.88.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.387.2.p1, not unique enough 1172s -skipping training candidate: MSTRG.387.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.860.6.p1, not unique enough 1172s -skipping training candidate: NM_001184834.p1, not unique enough 1172s -skipping training candidate: NM_138636.p1, not unique enough 1172s -skipping training candidate: NM_181673.p1, not unique enough 1172s -skipping training candidate: NM_001271184.p1, not unique enough 1172s -skipping training candidate: MSTRG.759.13.p1, not unique enough 1172s -skipping training candidate: MSTRG.759.12.p1, not unique enough 1172s -skipping training candidate: NM_001037343.p1, not unique enough 1172s -skipping training candidate: NM_015107.p1, not unique enough 1172s -skipping training candidate: NM_014725.p1, not unique enough 1172s -skipping training candidate: NM_001142504.p1, not unique enough 1172s -skipping training candidate: MSTRG.945.7.p1, not unique enough 1172s -skipping training candidate: NM_001168647.p1, not unique enough 1172s -skipping training candidate: NM_001099855.p1, not unique enough 1172s -skipping training candidate: NM_004014.p1, not unique enough 1172s -skipping training candidate: MSTRG.110.1.p1, not unique enough 1172s -skipping training candidate: NM_001282141.p1, not unique enough 1172s -skipping training candidate: NM_001666.p1, not unique enough 1172s -skipping training candidate: NM_001271183.p1, not unique enough 1172s -skipping training candidate: NM_001257237.p1, not unique enough 1172s -skipping training candidate: NM_001257230.p1, not unique enough 1172s -skipping training candidate: NM_001257234.p1, not unique enough 1172s -skipping training candidate: NM_001170628.p1, not unique enough 1172s -skipping training candidate: NM_015075.p1, not unique enough 1172s -skipping training candidate: NM_001587.p1, not unique enough 1172s -skipping training candidate: NM_001184897.p1, not unique enough 1172s -skipping training candidate: NM_001171879.p1, not unique enough 1172s -skipping training candidate: MSTRG.759.11.p1, not unique enough 1172s -skipping training candidate: MSTRG.110.4.p1, not unique enough 1172s -skipping training candidate: NM_005676.p1, not unique enough 1172s -skipping training candidate: MSTRG.110.5.p1, not unique enough 1172s -skipping training candidate: NM_001204467.p1, not unique enough 1172s -skipping training candidate: NM_031276.p1, not unique enough 1172s -skipping training candidate: NM_005369.p1, not unique enough 1172s -skipping training candidate: MSTRG.250.1.p1, not unique enough 1172s -skipping training candidate: MSTRG.387.3.p1, not unique enough 1172s -skipping training candidate: MSTRG.1005.1.p1, not unique enough 1172s -skipping training candidate: NM_001300788.p1, not unique enough 1172s -skipping training candidate: MSTRG.508.1.p1, not unique enough 1172s -skipping training candidate: NM_001126054.p1, not unique enough 1172s -skipping training candidate: NM_003588.p1, not unique enough 1172s -skipping training candidate: NM_001126055.p1, not unique enough 1173s -skipping training candidate: MSTRG.110.7.p1, not unique enough 1173s -skipping training candidate: NM_001184965.p1, not unique enough 1173s -skipping training candidate: NM_001085354.p1, not unique enough 1173s -skipping training candidate: NM_001168648.p1, not unique enough 1173s -skipping training candidate: NM_001079872.p1, not unique enough 1173s -skipping training candidate: NM_007325.p1, not unique enough 1173s -skipping training candidate: NM_014799.p1, not unique enough 1173s -skipping training candidate: MSTRG.110.8.p1, not unique enough 1173s -skipping training candidate: MSTRG.855.3.p1, not unique enough 1173s -skipping training candidate: NM_001171184.p1, not unique enough 1173s -skipping training candidate: MSTRG.110.6.p1, not unique enough 1173s -skipping training candidate: NM_001184898.p1, not unique enough 1173s -skipping training candidate: MSTRG.276.2.p1, not unique enough 1173s -skipping training candidate: NM_024597.p1, not unique enough 1173s -skipping training candidate: MSTRG.839.4.p1, not unique enough 1173s -skipping training candidate: NM_007156.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.21.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.22.p1, not unique enough 1173s -skipping training candidate: NM_182540.p1, not unique enough 1173s -skipping training candidate: NM_001171878.p1, not unique enough 1173s -skipping training candidate: NM_152633.p1, not unique enough 1173s -skipping training candidate: MSTRG.442.2.p1, not unique enough 1173s -skipping training candidate: NM_001173516.p1, not unique enough 1173s -skipping training candidate: MSTRG.921.2.p1, not unique enough 1173s -skipping training candidate: NM_001204466.p1, not unique enough 1173s -skipping training candidate: NM_152856.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.20.p1, not unique enough 1173s -skipping training candidate: MSTRG.855.4.p1, not unique enough 1173s -skipping training candidate: NM_001168649.p1, not unique enough 1173s -skipping training candidate: NM_001077445.p1, not unique enough 1173s -skipping training candidate: MSTRG.839.6.p1, not unique enough 1173s -skipping training candidate: NM_001144004.p1, not unique enough 1173s -skipping training candidate: NM_001144010.p1, not unique enough 1173s -skipping training candidate: NM_001144003.p1, not unique enough 1173s -skipping training candidate: NM_001144009.p1, not unique enough 1173s -skipping training candidate: NM_001144005.p1, not unique enough 1173s -skipping training candidate: NM_001144006.p1, not unique enough 1173s -skipping training candidate: NM_032539.p1, not unique enough 1173s -skipping training candidate: NM_139289.p1, not unique enough 1173s -skipping training candidate: MSTRG.839.5.p1, not unique enough 1173s -skipping training candidate: NM_001173517.p1, not unique enough 1173s -skipping training candidate: NM_001184875.p1, not unique enough 1173s -skipping training candidate: NM_138437.p1, not unique enough 1173s -skipping training candidate: NM_001199818.p1, not unique enough 1173s -skipping training candidate: NM_001004051.p1, not unique enough 1173s -skipping training candidate: NM_001184874.p1, not unique enough 1173s -skipping training candidate: MSTRG.110.11.p1, not unique enough 1173s -skipping training candidate: NM_001184749.p1, not unique enough 1173s -skipping training candidate: NM_173078.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.24.p1, not unique enough 1173s -skipping training candidate: NM_018977.p1, not unique enough 1173s -skipping training candidate: NM_001184966.p1, not unique enough 1173s -skipping training candidate: NM_014735.p1, not unique enough 1173s -skipping training candidate: NM_001171877.p1, not unique enough 1173s -skipping training candidate: NM_001282146.p1, not unique enough 1173s -skipping training candidate: NM_001282145.p1, not unique enough 1173s -skipping training candidate: NM_020742.p1, not unique enough 1173s -skipping training candidate: NM_001127898.p1, not unique enough 1173s -skipping training candidate: NM_001005332.p1, not unique enough 1173s -skipping training candidate: NM_001166660.p1, not unique enough 1173s -skipping training candidate: MSTRG.189.10.p1, not unique enough 1173s -skipping training candidate: NM_001178085.p1, not unique enough 1173s -skipping training candidate: MSTRG.189.1.p1, not unique enough 1173s -skipping training candidate: NM_001178084.p1, not unique enough 1173s -skipping training candidate: NM_003410.p1, not unique enough 1173s -skipping training candidate: MSTRG.189.7.p1, not unique enough 1173s -skipping training candidate: MSTRG.921.3.p1, not unique enough 1173s -skipping training candidate: MSTRG.110.10.p1, not unique enough 1173s -skipping training candidate: NM_001287242.p1, not unique enough 1173s -skipping training candidate: MSTRG.76.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.6.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.189.11.p1, not unique enough 1173s -skipping training candidate: MSTRG.189.9.p1, not unique enough 1173s -skipping training candidate: NM_153380.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.11.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.3.p1, not unique enough 1173s -skipping training candidate: NM_007130.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.10.p1, not unique enough 1173s -skipping training candidate: NM_006986.p1, not unique enough 1173s -skipping training candidate: MSTRG.1005.3.p1, not unique enough 1173s -skipping training candidate: NM_001271696.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.8.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.7.p1, not unique enough 1173s -skipping training candidate: NM_024778.p1, not unique enough 1173s -skipping training candidate: NM_032591.p1, not unique enough 1173s -skipping training candidate: NM_152780.p1, not unique enough 1173s -skipping training candidate: NM_013423.p1, not unique enough 1173s -skipping training candidate: NM_032512.p1, not unique enough 1173s -skipping training candidate: MSTRG.166.5.p1, not unique enough 1173s -skipping training candidate: NM_001282163.p1, not unique enough 1173s -skipping training candidate: NM_006125.p1, not unique enough 1173s -skipping training candidate: MSTRG.604.2.p1, not unique enough 1173s -skipping training candidate: NM_001243963.p1, not unique enough 1173s -skipping training candidate: NM_001184782.p1, not unique enough 1173s -skipping training candidate: NM_001272061_dup1.p1, not unique enough 1173s -skipping training candidate: MSTRG.654.4.p1, not unique enough 1173s -skipping training candidate: NM_006733.p1, not unique enough 1173s -skipping training candidate: MSTRG.654.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.925.2.p1, not unique enough 1173s -skipping training candidate: NM_001163280.p1, not unique enough 1173s -skipping training candidate: NR_033717.p1, not unique enough 1173s -skipping training candidate: NM_001177466.p1, not unique enough 1173s -skipping training candidate: NM_001271698.p1, not unique enough 1173s -skipping training candidate: NM_000084.p1, not unique enough 1173s -skipping training candidate: MSTRG.654.3.p1, not unique enough 1173s -skipping training candidate: NM_001272062.p1, not unique enough 1173s -skipping training candidate: NM_001272063.p1, not unique enough 1173s -skipping training candidate: MSTRG.308.3.p1, not unique enough 1173s -skipping training candidate: NM_030801_dup1.p1, not unique enough 1173s -skipping training candidate: NM_177535_dup1.p1, not unique enough 1173s -skipping training candidate: NM_177537.p1, not unique enough 1173s -skipping training candidate: NM_177537_dup1.p1, not unique enough 1173s -skipping training candidate: MSTRG.572.4.p1, not unique enough 1173s -skipping training candidate: NM_001271699.p1, not unique enough 1173s -skipping training candidate: NM_001271697.p1, not unique enough 1173s -skipping training candidate: MSTRG.308.4.p1, not unique enough 1173s -skipping training candidate: NM_001163335.p1, not unique enough 1173s -skipping training candidate: NM_138780.p1, not unique enough 1173s -skipping training candidate: NM_001271835.p1, not unique enough 1173s -skipping training candidate: NM_001163323.p1, not unique enough 1173s -skipping training candidate: NM_001168466.p1, not unique enough 1173s -skipping training candidate: MSTRG.147.4.p1, not unique enough 1173s -skipping training candidate: MSTRG.572.5.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.10.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.759.9.p1, not unique enough 1173s -skipping training candidate: NM_001166221.p1, not unique enough 1173s -skipping training candidate: NM_019117.p1, not unique enough 1173s -skipping training candidate: NM_001170649.p1, not unique enough 1173s -skipping training candidate: MSTRG.451.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.929.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.376.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.161.3.p1, not unique enough 1173s -skipping training candidate: NM_152787.p1, not unique enough 1173s -skipping training candidate: MSTRG.208.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.161.2.p1, not unique enough 1173s -skipping training candidate: MSTRG.376.4.p1, not unique enough 1173s -skipping training candidate: NM_177556.p1, not unique enough 1173s -skipping training candidate: NM_016157.p1, not unique enough 1173s -skipping training candidate: NM_001173487.p1, not unique enough 1173s -skipping training candidate: NM_052817.p1, not unique enough 1173s -skipping training candidate: MSTRG.215.2.p1, not unique enough 1173s -skipping training candidate: NM_001306193.p1, not unique enough 1173s -skipping training candidate: NM_152423.p1, not unique enough 1173s -skipping training candidate: NM_001163321.p1, not unique enough 1173s -skipping training candidate: MSTRG.572.6.p1, not unique enough 1173s -skipping training candidate: NM_001282754.p1, not unique enough 1173s -skipping training candidate: NM_001171135.p1, not unique enough 1173s -skipping training candidate: NM_001171136.p1, not unique enough 1173s -skipping training candidate: NM_001303515.p1, not unique enough 1173s -skipping training candidate: MSTRG.922.1.p1, not unique enough 1173s -skipping training candidate: MSTRG.279.5.p1, not unique enough 1173s -skipping training candidate: NM_022117.p1, not unique enough 1173s -skipping training candidate: NM_001178107.p1, not unique enough 1173s -skipping training candidate: NM_001173488.p1, not unique enough 1173s -skipping training candidate: NM_144657.p1, not unique enough 1173s -skipping training candidate: NM_001178108.p1, not unique enough 1173s -skipping training candidate: NR_109776.p1, not unique enough 1173s -skipping training candidate: NM_007150.p1, not unique enough 1173s -skipping training candidate: NM_001303516.p1, not unique enough 1173s -skipping training candidate: NM_198881.p1, not unique enough 1173s -skipping training candidate: MSTRG.376.3.p1, not unique enough 1173s -skipping training candidate: MSTRG.376.8.p1, not unique enough 1173s -skipping training candidate: MSTRG.208.3.p1, not unique enough 1173s -skipping training candidate: NM_001025242.p1, not unique enough 1173s -skipping training candidate: MSTRG.345.1.p1, not unique enough 1173s -skipping training candidate: NR_073148.p1, not unique enough 1173s -skipping training candidate: NM_001168467.p1, not unique enough 1173s -skipping training candidate: MSTRG.308.1.p1, not unique enough 1173s -skipping training candidate: NM_001170650.p1, not unique enough 1173s -skipping training candidate: NM_001721.p1, not unique enough 1173s -skipping training candidate: NM_133265.p1, not unique enough 1173s -skipping training candidate: NM_001303513.p1, not unique enough 1173s -skipping training candidate: NM_006777.p1, not unique enough 1173s -skipping training candidate: NM_001129896.p1, not unique enough 1173s -skipping training candidate: NM_001174068.p1, not unique enough 1173s -skipping training candidate: MSTRG.732.1.p1, not unique enough 1173s -skipping training candidate: NM_004458.p1, not unique enough 1173s -skipping training candidate: MSTRG.732.2.p1, not unique enough 1173s -skipping training candidate: NM_133499.p1, not unique enough 1173s -skipping training candidate: NM_006359.p1, not unique enough 1173s -skipping training candidate: NM_033290.p1, not unique enough 1173s -skipping training candidate: NM_001098624.p1, not unique enough 1173s -skipping training candidate: NM_001193277.p1, not unique enough 1173s -skipping training candidate: NM_001256944.p1, not unique enough 1173s -skipping training candidate: NM_004192.p1, not unique enough 1173s -skipping training candidate: NM_031892.p1, not unique enough 1173s -skipping training candidate: NM_003828.p1, not unique enough 1173s -skipping training candidate: MSTRG.508.2.p1, not unique enough 1173s -skipping training candidate: NR_110311.p1, not unique enough 1173s -skipping training candidate: NM_001127197.p1, not unique enough 1173s -skipping training candidate: MSTRG.862.3.p1, not unique enough 1173s -skipping training candidate: NM_001421.p1, not unique enough 1173s -skipping training candidate: MSTRG.862.4.p1, not unique enough 1173s -skipping training candidate: MSTRG.641.6.p1, not unique enough 1173s -skipping training candidate: NM_001356.p1, not unique enough 1173s -skipping training candidate: NM_007137.p1, not unique enough 1173s -skipping training candidate: MSTRG.292.4.p1, not unique enough 1173s -skipping training candidate: NM_004016.p1, not unique enough 1173s -skipping training candidate: NM_001193416.p1, not unique enough 1173s -skipping training candidate: NM_001303514.p1, not unique enough 1173s -skipping training candidate: NM_001178109.p1, not unique enough 1173s -skipping training candidate: NM_000061.p1, not unique enough 1173s -skipping training candidate: NM_001080975.p1, not unique enough 1173s -skipping training candidate: NM_001168299.p1, not unique enough 1173s -skipping training candidate: MSTRG.468.4.p1, not unique enough 1173s 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MSTRG.669.10.p1, not unique enough 1173s -skipping training candidate: MSTRG.669.3.p1, not unique enough 1173s -skipping training candidate: NM_014782.p1, not unique enough 1173s -skipping training candidate: MSTRG.669.9.p1, not unique enough 1173s -skipping training candidate: MSTRG.669.4.p1, not unique enough 1173s -skipping training candidate: NM_001282231.p1, not unique enough 1173s -skipping training candidate: MSTRG.456.6.p1, not unique enough 1173s -skipping training candidate: MSTRG.306.3.p1, not unique enough 1173s -skipping training candidate: NM_001178110.p1, not unique enough 1173s -skipping training candidate: NM_004017.p1, not unique enough 1173s -skipping training candidate: NM_033626.p1, not unique enough 1173s -skipping training candidate: NM_001271836.p1, not unique enough 1174s -skipping training candidate: NM_005032.p1, not unique enough 1174s -skipping training candidate: NM_033289.p1, not unique enough 1174s -skipping training candidate: NM_001024666.p1, not 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not unique enough 1175s -skipping training candidate: MSTRG.9.5.p1, not unique enough 1175s -skipping training candidate: NM_001143983.p1, not unique enough 1175s -skipping training candidate: MSTRG.2.1.p1, not unique enough 1175s -skipping training candidate: MSTRG.9.4.p1, not unique enough 1175s -skipping training candidate: MSTRG.9.3.p1, not unique enough 1175s -skipping training candidate: NM_012151.p1, not unique enough 1175s -skipping training candidate: NM_012151_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001184797.p1, not unique enough 1175s -skipping training candidate: MSTRG.976.2.p1, not unique enough 1175s -skipping training candidate: NM_001129765.p1, not unique enough 1175s -skipping training candidate: NM_001171038.p1, not unique enough 1175s -skipping training candidate: NM_001282174.p1, not unique enough 1175s -skipping training candidate: NM_001007524_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001007523.p1, not unique 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NM_001080141.p1, not unique enough 1175s -skipping training candidate: NM_001080141_dup9.p1, not unique enough 1175s -skipping training candidate: NM_001080141_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup5.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup9.p1, not unique enough 1175s -skipping training candidate: NM_001080138.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup6.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup8.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup4.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup7.p1, not unique enough 1175s -skipping training candidate: NM_001080138_dup3.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup5.p1, not unique enough 1175s -skipping training candidate: NM_001080145.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup8.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup3.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup7.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup9.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup6.p1, not unique enough 1175s -skipping training candidate: NM_001080145_dup4.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup4.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup8.p1, not unique enough 1175s -skipping training candidate: NM_001080143.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup7.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup5.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup6.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup3.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup9.p1, not unique enough 1175s -skipping training candidate: NM_001080143_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001099685.p1, not unique enough 1175s -skipping training candidate: NM_001099685_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001142421.p1, not unique enough 1175s -skipping training candidate: NM_001142430.p1, not unique enough 1175s -skipping training candidate: NM_012286.p1, not unique enough 1175s -skipping training candidate: NM_001142426.p1, not unique enough 1175s -skipping training candidate: NM_001142418.p1, not unique enough 1175s -skipping training candidate: NM_001142427.p1, not unique enough 1175s -skipping training candidate: NM_001142419.p1, not unique enough 1175s -skipping training candidate: NM_001142420.p1, not unique enough 1175s -skipping training candidate: NM_001142432.p1, not unique enough 1175s -skipping training candidate: NM_001142429.p1, not unique enough 1175s -skipping training candidate: NM_001142428.p1, not unique enough 1175s -skipping training candidate: NM_001142431.p1, not unique enough 1175s -skipping training candidate: NM_001142425.p1, not unique enough 1175s -skipping training candidate: NM_001142423.p1, not unique enough 1175s -skipping training candidate: MSTRG.695.1.p1, not unique enough 1175s -skipping training candidate: NM_001142422.p1, not unique enough 1175s -skipping training candidate: NM_001080140.p1, not unique enough 1175s -skipping training candidate: NM_001242922.p1, not unique enough 1175s -skipping training candidate: NM_001242922_dup2.p1, not unique enough 1175s -skipping training candidate: 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not unique enough 1175s -skipping training candidate: NM_001080144_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080144_dup7.p1, not unique enough 1175s -skipping training candidate: NM_001080144_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001080144_dup8.p1, not unique enough 1175s -skipping training candidate: NM_001080144_dup5.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup9.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup8.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup6.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup1.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup2.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup5.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup7.p1, not unique enough 1175s -skipping training candidate: NM_001080142_dup4.p1, not unique 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not unique enough 1176s -skipping training candidate: NM_001256119.p1, not unique enough 1176s -skipping training candidate: NM_001171581.p1, not unique enough 1176s -skipping training candidate: NM_001144885.p1, not unique enough 1176s -skipping training candidate: NM_001291529.p1, not unique enough 1176s -skipping training candidate: NM_000950.p1, not unique enough 1176s -skipping training candidate: NM_001277710.p1, not unique enough 1176s -skipping training candidate: NM_001282648.p1, not unique enough 1176s -skipping training candidate: NM_001173489.p1, not unique enough 1176s -skipping training candidate: NM_001142395.p1, not unique enough 1176s -skipping training candidate: MSTRG.759.24.p2, not unique enough 1176s -skipping training candidate: NM_003372.p1, not unique enough 1176s -skipping training candidate: NM_002025.p2, not unique enough 1176s -skipping training candidate: NM_001169124.p2, not unique enough 1176s -skipping training candidate: MSTRG.913.2.p1, not unique 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NM_001171689.p1, not unique enough 1176s -skipping training candidate: NM_013346.p1, not unique enough 1176s -skipping training candidate: NM_001291543_dup2.p1, not unique enough 1176s -skipping training candidate: NM_001291543.p1, not unique enough 1176s -skipping training candidate: NM_001291543_dup1.p1, not unique enough 1176s -skipping training candidate: MSTRG.1025.2.p1, not unique enough 1176s -skipping training candidate: NM_004840.p2, not unique enough 1176s -skipping training candidate: MSTRG.929.1.p2, not unique enough 1176s -skipping training candidate: MSTRG.142.5.p1, not unique enough 1176s -skipping training candidate: NM_001037536.p1, not unique enough 1176s -skipping training candidate: NM_001037535.p1, not unique enough 1176s -skipping training candidate: MSTRG.1025.3.p1, not unique enough 1176s -skipping training candidate: MSTRG.1025.6.p1, not unique enough 1176s -skipping training candidate: MSTRG.912.5.p2, not unique enough 1176s -skipping training candidate: 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MSTRG.973.3.p1, not unique enough 1176s -skipping training candidate: NM_001013845.p1, not unique enough 1176s -skipping training candidate: MSTRG.109.10.p1, not unique enough 1176s -skipping training candidate: NM_005089.p2, not unique enough 1176s -skipping training candidate: MSTRG.128.1.p3, not unique enough 1176s -skipping training candidate: NM_001171908.p1, not unique enough 1176s -skipping training candidate: NM_178124.p1, not unique enough 1176s -skipping training candidate: NM_001171907.p2, not unique enough 1176s -skipping training candidate: NM_001039891.p2, not unique enough 1176s -skipping training candidate: NM_001190417.p2, not unique enough 1176s -skipping training candidate: NM_001146291.p2, not unique enough 1176s -skipping training candidate: MSTRG.266.4.p2, not unique enough 1176s -skipping training candidate: NM_001278740.p1, not unique enough 1176s -skipping training candidate: NM_001278741.p1, not unique enough 1176s -skipping training candidate: MSTRG.324.2.p1, not unique enough 1176s -skipping training candidate: NR_104107.p2, not unique enough 1176s -skipping training candidate: NM_001184897.p2, not unique enough 1176s -skipping training candidate: NM_015107.p3, not unique enough 1176s -skipping training candidate: MSTRG.387.3.p3, not unique enough 1176s -skipping training candidate: NM_001184896.p3, not unique enough 1176s -skipping training candidate: MSTRG.387.1.p2, not unique enough 1176s -skipping training candidate: NM_001282462.p1, not unique enough 1176s -skipping training candidate: NM_001282461.p1, not unique enough 1176s -skipping training candidate: NM_001012755.p2, not unique enough 1176s -skipping training candidate: MSTRG.705.2.p2, not unique enough 1176s -skipping training candidate: MSTRG.705.4.p2, not unique enough 1176s -skipping training candidate: MSTRG.718.6.p1, not unique enough 1176s -skipping training candidate: NM_001007088.p3, not unique enough 1176s -skipping training candidate: NM_006962.p3, not unique enough 1176s -skipping training candidate: MSTRG.294.4.p3, not unique enough 1176s -skipping training candidate: NM_000054.p3, not unique enough 1176s -skipping training candidate: MSTRG.53.1.p1, not unique enough 1176s -skipping training candidate: NM_177537.p2, not unique enough 1176s -skipping training candidate: MSTRG.1029.1.p2, not unique enough 1176s -skipping training candidate: NM_019045.p2, not unique enough 1176s -skipping training candidate: NM_001184966.p2, not unique enough 1176s -skipping training candidate: NM_177535_dup1.p2, not unique enough 1176s -skipping training candidate: NM_177537_dup1.p2, not unique enough 1176s -skipping training candidate: NR_033380.p1, not unique enough 1176s -skipping training candidate: MSTRG.38.1.p1, not unique enough 1176s -skipping training candidate: NM_001163265.p2, not unique enough 1176s -skipping training candidate: NM_001163264.p2, not unique enough 1176s -skipping training candidate: NM_001135998.p1, not unique enough 1176s -skipping training candidate: MSTRG.961.2.p2, not unique enough 1176s -skipping training candidate: MSTRG.961.7.p2, not unique enough 1176s -skipping training candidate: MSTRG.961.4.p2, not unique enough 1176s -skipping training candidate: MSTRG.68.20.p1, not unique enough 1176s -skipping training candidate: NM_001040612.p1, not unique enough 1176s -skipping training candidate: MSTRG.925.2.p3, not unique enough 1176s -skipping training candidate: NM_001163280.p3, not unique enough 1176s -skipping training candidate: NM_175729.p1, not unique enough 1176s -skipping training candidate: NM_175729_dup1.p1, not unique enough 1176s -skipping training candidate: NR_126093.p2, not unique enough 1176s -skipping training candidate: NM_001193417.p2, not unique enough 1176s -skipping training candidate: NM_001356.p2, not unique enough 1176s -skipping training candidate: NM_005393.p3, not unique enough 1176s -skipping training candidate: MSTRG.799.2.p1, not unique enough 1176s -skipping training candidate: MSTRG.275.3.p2, not unique enough 1176s -skipping training candidate: MSTRG.275.4.p2, not unique enough 1176s -skipping training candidate: NM_000425.p4, not unique enough 1176s -skipping training candidate: NM_024003.p4, not unique enough 1176s -skipping training candidate: NM_001143963.p4, not unique enough 1176s -skipping training candidate: NM_170750.p1, not unique enough 1176s -skipping training candidate: NM_001291421.p2, not unique enough 1176s -skipping training candidate: NM_022117.p2, not unique enough 1176s -skipping training candidate: MSTRG.459.1.p2, not unique enough 1176s -skipping training candidate: MSTRG.459.2.p2, not unique enough 1176s -skipping training candidate: NM_001146151.p3, not unique enough 1176s -skipping training candidate: MSTRG.345.2.p2, not unique enough 1176s -skipping training candidate: MSTRG.345.4.p2, not unique enough 1176s -skipping training candidate: MSTRG.1012.4.p2, not unique enough 1176s -skipping training candidate: NM_005334.p2, not unique enough 1176s -skipping training candidate: MSTRG.1012.3.p2, not unique enough 1176s -skipping training candidate: MSTRG.68.10.p2, not unique enough 1176s -skipping training candidate: NM_015075.p3, not unique enough 1176s -skipping training candidate: NR_030774.p2, not unique enough 1176s -skipping training candidate: MSTRG.34.8.p1, not unique enough 1176s -skipping training candidate: MSTRG.34.3.p1, not unique enough 1176s -skipping training candidate: NM_001164619.p2, not unique enough 1176s -skipping training candidate: NM_001164618.p2, not unique enough 1176s -skipping training candidate: NM_001164617.p2, not unique enough 1176s -skipping training candidate: MSTRG.663.1.p1, not unique enough 1176s -skipping training candidate: MSTRG.734.6.p1, not unique enough 1176s -skipping training candidate: NM_017698.p1, not unique enough 1176s -skipping training candidate: NM_001005613.p1, not unique enough 1176s -skipping training candidate: MSTRG.1029.12.p2, not unique enough 1176s -skipping training candidate: MSTRG.216.5.p3, not unique enough 1176s -skipping training candidate: NM_021242.p3, not unique enough 1176s -skipping training candidate: MSTRG.994.4.p2, not unique enough 1176s -skipping training candidate: NM_001130997.p2, not unique enough 1176s -skipping training candidate: NM_016120.p2, not unique enough 1176s -skipping training candidate: MSTRG.537.1.p2, not unique enough 1176s -skipping training candidate: NM_183353.p2, not unique enough 1176s -skipping training candidate: MSTRG.867.6.p1, not unique enough 1176s -skipping training candidate: NM_001272062.p3, not unique enough 1176s -skipping training candidate: NM_001272063.p2, not unique enough 1176s -skipping training candidate: NM_177537.p3, not unique enough 1176s -skipping training candidate: MSTRG.973.2.p1, not unique enough 1176s -skipping training candidate: MSTRG.973.1.p1, not unique enough 1176s -skipping training candidate: NM_001171909.p1, not unique enough 1176s -skipping training candidate: MSTRG.963.2.p1, not unique enough 1176s -skipping training candidate: MSTRG.963.3.p2, not unique enough 1176s -skipping training candidate: MSTRG.963.1.p2, not unique enough 1176s -skipping training candidate: NM_001097604_dup1.p1, not unique enough 1176s -skipping training candidate: MSTRG.268.3.p2, not unique enough 1176s -skipping training candidate: NM_001272061_dup1.p2, not unique enough 1176s -skipping training candidate: NM_030801_dup1.p2, not unique enough 1176s -skipping training candidate: NM_177535_dup1.p3, not unique enough 1176s -skipping training candidate: NM_177537_dup1.p3, not unique enough 1176s -skipping training candidate: NM_001097594_dup1.p1, not unique enough 1176s -skipping training candidate: NM_001097594.p1, not unique enough 1176s -skipping training candidate: NM_020717.p3, not unique enough 1176s -skipping training candidate: MSTRG.302.6.p1, not unique enough 1176s -skipping training candidate: MSTRG.1025.5.p1, not unique enough 1176s -skipping training candidate: NM_001287760.p2, not unique enough 1176s -skipping training candidate: NM_033641.p2, not unique enough 1176s -skipping training candidate: NM_001847.p2, not unique enough 1176s -skipping training candidate: MSTRG.131.6.p1, not unique enough 1176s -skipping training candidate: MSTRG.131.5.p1, not unique enough 1176s -skipping training candidate: NM_001303465.p2, not unique enough 1176s -skipping training candidate: MSTRG.1029.3.p2, not unique enough 1176s -skipping training candidate: NM_206917.p1, not unique enough 1176s -skipping training candidate: NM_031407.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.21.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.6.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.7.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.5.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.18.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.26.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.17.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.24.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.2.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.27.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.8.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.23.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.12.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.19.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.22.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.9.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.14.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.25.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.10.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.11.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.15.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.4.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.28.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.3.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.20.p2, not unique enough 1176s -skipping training candidate: MSTRG.397.16.p2, not unique enough 1176s -skipping training candidate: NR_045560.p1, not unique enough 1176s -skipping training candidate: MSTRG.268.7.p2, not unique enough 1176s -skipping training candidate: NM_001291421.p3, not unique enough 1176s -skipping training candidate: NM_001291417.p2, not unique enough 1176s -skipping training candidate: NM_021140.p2, not unique enough 1176s -skipping training candidate: NM_001291418.p2, not unique enough 1176s -skipping training candidate: NM_001291416.p2, not unique enough 1176s -skipping training candidate: NM_001291415.p2, not unique enough 1176s -skipping training candidate: NM_001256187.p1, not unique enough 1176s -skipping training candidate: MSTRG.305.1.p3, not unique enough 1176s -skipping training candidate: MSTRG.459.3.p2, not unique enough 1176s -skipping training candidate: NM_021783.p2, not unique enough 1176s -skipping training candidate: MSTRG.459.1.p3, not unique enough 1176s -skipping training candidate: NM_020994.p2, not unique enough 1176s -skipping training candidate: NM_001282621.p1, not unique enough 1176s -skipping training candidate: NM_001146257.p1, not unique enough 1176s -skipping training candidate: MSTRG.109.1.p1, not unique enough 1176s -skipping training candidate: NM_001168649.p2, not unique enough 1176s -skipping training candidate: NM_014927.p2, not unique enough 1176s -skipping training candidate: NM_001168647.p2, not unique enough 1176s -skipping training candidate: NM_001242617.p1, not unique enough 1176s -skipping training candidate: NM_021029.p1, not unique enough 1176s -skipping training candidate: MSTRG.68.10.p3, not unique enough 1176s -skipping training candidate: MSTRG.68.8.p2, not unique enough 1176s -skipping training candidate: MSTRG.68.2.p1, not unique enough 1176s -skipping training candidate: MSTRG.68.16.p2, not unique enough 1176s -skipping training candidate: MSTRG.258.8.p2, not unique enough 1176s -skipping training candidate: MSTRG.250.5.p1, not unique enough 1176s -skipping training candidate: NM_001011658.p1, not unique enough 1176s -skipping training candidate: MSTRG.258.9.p2, not unique enough 1176s -skipping training candidate: NM_001184898.p2, not unique enough 1176s -skipping training candidate: MSTRG.992.7.p2, not unique enough 1176s -skipping training candidate: MSTRG.476.2.p1, not unique enough 1176s -skipping training candidate: NM_020717.p4, not unique enough 1176s -skipping training candidate: NM_001256186.p1, not unique enough 1176s -skipping training candidate: NM_017711.p3, not unique enough 1176s -skipping training candidate: NM_017883.p2, not unique enough 1176s -skipping training candidate: NM_001171192.p3, not unique enough 1176s -skipping training candidate: NM_001282621.p2, not unique enough 1176s -skipping training candidate: MSTRG.921.1.p2, not unique enough 1176s -skipping training candidate: MSTRG.921.3.p2, not unique enough 1176s -skipping training candidate: MSTRG.921.2.p2, not unique enough 1176s -skipping training candidate: MSTRG.718.1.p1, not unique enough 1177s -skipping training candidate: NM_001184819.p2, not unique enough 1177s -skipping training candidate: MSTRG.641.8.p1, not unique enough 1177s -skipping training candidate: NM_001099857.p2, not unique enough 1177s -skipping training candidate: NM_001008534.p1, not unique enough 1177s -skipping training candidate: NM_001278742.p1, not unique enough 1177s -skipping training candidate: MSTRG.305.6.p2, not unique enough 1177s -skipping training candidate: MSTRG.306.1.p2, not unique enough 1177s -skipping training candidate: NM_014725.p2, not unique enough 1177s -skipping training candidate: NM_001142504.p2, not unique enough 1177s -skipping training candidate: NM_001271183.p2, not unique enough 1177s -skipping training candidate: MSTRG.404.8.p2, not unique enough 1177s -skipping training candidate: NM_001271184.p2, not unique enough 1177s -skipping training candidate: NM_001172739.p2, not unique enough 1177s -skipping training candidate: MSTRG.734.6.p2, not unique enough 1177s -skipping training candidate: NM_017698.p2, not unique enough 1177s -skipping training candidate: MSTRG.734.5.p2, not unique enough 1177s -skipping training candidate: MSTRG.734.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.734.2.p2, not unique enough 1177s -skipping training candidate: NM_001005609.p2, not unique enough 1177s -skipping training candidate: MSTRG.438.2.p1, not unique enough 1177s -skipping training candidate: NR_001564.p1, not unique enough 1177s -skipping training candidate: MSTRG.531.1.p1, not unique enough 1177s -skipping training candidate: MSTRG.531.3.p1, not unique enough 1177s -skipping training candidate: MSTRG.275.3.p3, not unique enough 1177s -skipping training candidate: NM_001170460.p2, not unique enough 1177s -skipping training candidate: MSTRG.275.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.275.4.p3, not unique enough 1177s -skipping training candidate: MSTRG.275.7.p2, not unique enough 1177s -skipping training candidate: MSTRG.275.6.p2, not unique enough 1177s -skipping training candidate: NM_006201.p2, not unique enough 1177s -skipping training candidate: MSTRG.615.2.p1, not unique enough 1177s -skipping training candidate: MSTRG.615.1.p1, not unique enough 1177s -skipping training candidate: MSTRG.16.1.p6, not unique enough 1177s -skipping training candidate: NM_000495.p2, not unique enough 1177s -skipping training candidate: MSTRG.992.3.p1, not unique enough 1177s -skipping training candidate: NR_073156.p2, not unique enough 1177s -skipping training candidate: MSTRG.62.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.62.1.p2, not unique enough 1177s -skipping training candidate: NM_006521.p2, not unique enough 1177s -skipping training candidate: MSTRG.488.1.p1, not unique enough 1177s -skipping training candidate: NR_033212.p1, not unique enough 1177s -skipping training candidate: NM_145305.p2, not unique enough 1177s -skipping training candidate: NM_001005610.p1, not unique enough 1177s -skipping training candidate: NR_001564.p2, not unique enough 1177s -skipping training candidate: MSTRG.531.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.531.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.275.4.p4, not unique enough 1177s -skipping training candidate: NM_006201.p3, not unique enough 1177s -skipping training candidate: NM_001300788.p3, not unique enough 1177s -skipping training candidate: NM_001144003.p2, not unique enough 1177s -skipping training candidate: MSTRG.284.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.963.2.p2, not unique enough 1177s -skipping training candidate: NM_001039582.p2, not unique enough 1177s -skipping training candidate: NM_001144005.p2, not unique enough 1177s -skipping training candidate: MSTRG.933.1.p2, not unique enough 1177s -skipping training candidate: NM_001005609.p3, not unique enough 1177s -skipping training candidate: NM_001005612.p2, not unique enough 1177s -skipping training candidate: NM_001005612.p3, not unique enough 1177s -skipping training candidate: MSTRG.759.10.p2, not unique enough 1177s -skipping training candidate: MSTRG.759.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.759.21.p2, not unique enough 1177s -skipping training candidate: MSTRG.759.11.p2, not unique enough 1177s -skipping training candidate: NM_001168385.p1, not unique enough 1177s -skipping training candidate: NM_001143982.p2, not unique enough 1177s -skipping training candidate: MSTRG.305.8.p2, not unique enough 1177s -skipping training candidate: NM_145234.p2, not unique enough 1177s -skipping training candidate: MSTRG.641.7.p1, not unique enough 1177s -skipping training candidate: NM_001145252.p2, not unique enough 1177s -skipping training candidate: NM_001143981.p2, not unique enough 1177s -skipping training candidate: NM_174951.p2, not unique enough 1177s -skipping training candidate: NR_027383.p4, not unique enough 1177s -skipping training candidate: MSTRG.32.4.p4, not unique enough 1177s -skipping training candidate: MSTRG.327.3.p3, not unique enough 1177s -skipping training candidate: NM_003173.p3, not unique enough 1177s -skipping training candidate: NR_024048.p2, not unique enough 1177s -skipping training candidate: NM_001123385.p2, not unique enough 1177s -skipping training candidate: NM_130467.p1, not unique enough 1177s -skipping training candidate: NM_005676.p2, not unique enough 1177s -skipping training candidate: NM_001204468.p2, not unique enough 1177s -skipping training candidate: NR_029427.p3, not unique enough 1177s -skipping training candidate: MSTRG.325.4.p2, not unique enough 1177s -skipping training candidate: NM_001166426.p2, not unique enough 1177s -skipping training candidate: NM_017883.p3, not unique enough 1177s -skipping training candidate: NM_001080851.p2, not unique enough 1177s -skipping training candidate: NM_001278743.p1, not unique enough 1177s -skipping training candidate: MSTRG.822.4.p1, not unique enough 1177s -skipping training candidate: NM_033053.p2, not unique enough 1177s -skipping training candidate: NM_033053_dup1.p2, not unique enough 1177s -skipping training candidate: NM_005647.p3, not unique enough 1177s -skipping training candidate: MSTRG.1023.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.1023.2.p2, not unique enough 1177s -skipping training candidate: NM_001166700.p1, not unique enough 1177s -skipping training candidate: MSTRG.1074.8.p2, not unique enough 1177s -skipping training candidate: NR_026594.p1, not unique enough 1177s -skipping training candidate: NR_110830.p3, not unique enough 1177s -skipping training candidate: NM_001080485.p2, not unique enough 1177s -skipping training candidate: MSTRG.1025.5.p2, not unique enough 1177s -skipping training candidate: NM_001166701.p1, not unique enough 1177s -skipping training candidate: NM_138362.p1, not unique enough 1177s -skipping training candidate: NM_001256119.p2, not unique enough 1177s -skipping training candidate: NM_001256120.p2, not unique enough 1177s -skipping training candidate: NM_005676.p3, not unique enough 1177s -skipping training candidate: NM_001204466.p2, not unique enough 1177s -skipping training candidate: NM_001204468.p3, not unique enough 1177s -skipping training candidate: NM_152856.p2, not unique enough 1177s -skipping training candidate: NM_021949.p2, not unique enough 1177s -skipping training candidate: MSTRG.109.7.p1, not unique enough 1177s -skipping training candidate: NM_001168401.p1, not unique enough 1177s -skipping training candidate: NM_032621.p1, not unique enough 1177s -skipping training candidate: NM_003918.p2, not unique enough 1177s -skipping training candidate: MSTRG.913.3.p1, not unique enough 1177s -skipping training candidate: NM_001129826_dup1.p1, not unique enough 1177s -skipping training candidate: MSTRG.502.3.p2, not unique enough 1177s -skipping training candidate: NM_001171162.p2, not unique enough 1177s -skipping training candidate: NM_005096.p2, not unique enough 1177s -skipping training candidate: MSTRG.502.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.502.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.9.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.654.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.654.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.654.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.794.2.p2, not unique enough 1177s -skipping training candidate: NM_001109879.p2, not unique enough 1177s -skipping training candidate: MSTRG.230.7.p2, not unique enough 1177s -skipping training candidate: NM_001145140_dup1.p2, not unique enough 1177s -skipping training candidate: NM_001145139_dup1.p2, not unique enough 1177s -skipping training candidate: NM_001145139.p2, not unique enough 1177s -skipping training candidate: NM_001303624.p2, not unique enough 1177s -skipping training candidate: NM_001114937.p1, not unique enough 1177s -skipping training candidate: NM_001291868.p2, not unique enough 1177s -skipping training candidate: MSTRG.405.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.405.4.p2, not unique enough 1177s -skipping training candidate: NM_001291867.p2, not unique enough 1177s -skipping training candidate: NM_001136024.p2, not unique enough 1177s -skipping training candidate: NM_000166.p2, not unique enough 1177s -skipping training candidate: MSTRG.324.2.p2, not unique enough 1177s -skipping training candidate: NM_001168302.p2, not unique enough 1177s -skipping training candidate: MSTRG.311.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.921.5.p3, not unique enough 1177s -skipping training candidate: MSTRG.921.6.p3, not unique enough 1177s -skipping training candidate: NM_000425.p5, not unique enough 1177s -skipping training candidate: NM_024003.p5, not unique enough 1177s -skipping training candidate: NM_001143963.p5, not unique enough 1177s -skipping training candidate: NM_019863.p2, not unique enough 1177s -skipping training candidate: NM_001242310.p2, not unique enough 1177s -skipping training candidate: MSTRG.363.1.p1, not unique enough 1177s -skipping training candidate: NM_001037343.p2, not unique enough 1177s -skipping training candidate: MSTRG.76.2.p3, not unique enough 1177s -skipping training candidate: NM_001204811.p1, not unique enough 1177s -skipping training candidate: MSTRG.992.5.p2, not unique enough 1177s -skipping training candidate: MSTRG.992.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.602.3.p1, not unique enough 1177s -skipping training candidate: NM_001146256.p2, not unique enough 1177s -skipping training candidate: NM_001146257.p2, not unique enough 1177s -skipping training candidate: MSTRG.208.3.p2, not unique enough 1177s -skipping training candidate: NM_152787.p2, not unique enough 1177s -skipping training candidate: MSTRG.208.2.p2, not unique enough 1177s -skipping training candidate: NM_021048.p2, not unique enough 1177s -skipping training candidate: NM_001011543.p2, not unique enough 1177s -skipping training candidate: MSTRG.147.4.p2, not unique enough 1177s -skipping training candidate: NM_001170931.p2, not unique enough 1177s -skipping training candidate: MSTRG.1041.5.p1, not unique enough 1177s -skipping training candidate: MSTRG.794.3.p2, not unique enough 1177s -skipping training candidate: NM_001356.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.18.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.10.p4, not unique enough 1177s -skipping training candidate: MSTRG.68.8.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.5.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.6.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.16.p3, not unique enough 1177s -skipping training candidate: NR_034031.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.14.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.17.p2, not unique enough 1177s -skipping training candidate: NR_027401.p1, not unique enough 1177s -skipping training candidate: NM_001303513.p2, not unique enough 1177s -skipping training candidate: MSTRG.258.9.p3, not unique enough 1177s -skipping training candidate: NM_001037536.p2, not unique enough 1177s -skipping training candidate: NM_001037540.p2, not unique enough 1177s -skipping training candidate: NM_001037535.p2, not unique enough 1177s -skipping training candidate: NM_006746.p2, not unique enough 1177s -skipping training candidate: MSTRG.541.3.p2, not unique enough 1177s -skipping training candidate: NM_005088.p3, not unique enough 1177s -skipping training candidate: NM_001080485.p3, not unique enough 1177s -skipping training candidate: NM_020922.p2, not unique enough 1177s -skipping training candidate: MSTRG.604.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.311.3.p1, not unique enough 1177s -skipping training candidate: NM_001080425.p1, not unique enough 1177s -skipping training candidate: MSTRG.68.17.p3, not unique enough 1177s -skipping training candidate: NR_130733.p1, not unique enough 1177s -skipping training candidate: NM_001282535.p3, not unique enough 1177s -skipping training candidate: NM_001282607.p2, not unique enough 1177s -skipping training candidate: NR_026551.p2, not unique enough 1177s -skipping training candidate: NM_013423.p2, not unique enough 1177s -skipping training candidate: NM_001287242.p2, not unique enough 1177s -skipping training candidate: NM_013427.p3, not unique enough 1177s -skipping training candidate: NR_015353.p2, not unique enough 1177s -skipping training candidate: MSTRG.438.2.p2, not unique enough 1177s -skipping training candidate: NM_001282161.p2, not unique enough 1177s -skipping training candidate: MSTRG.397.11.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.4.p2, not unique enough 1177s -skipping training candidate: MSTRG.921.5.p4, not unique enough 1177s -skipping training candidate: NM_001139466.p2, not unique enough 1177s -skipping training candidate: NR_033714.p1, not unique enough 1177s -skipping training candidate: MSTRG.4.3.p5, not unique enough 1177s -skipping training candidate: NM_018390.p5, not unique enough 1177s -skipping training candidate: NR_028057.p2, not unique enough 1177s -skipping training candidate: MSTRG.109.9.p1, not unique enough 1177s -skipping training candidate: NM_001257291.p2, not unique enough 1177s -skipping training candidate: NM_001170703.p2, not unique enough 1177s -skipping training candidate: MSTRG.889.4.p3, not unique enough 1177s -skipping training candidate: MSTRG.889.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.889.2.p2, not unique enough 1177s -skipping training candidate: NM_133486.p2, not unique enough 1177s -skipping training candidate: NM_018388.p2, not unique enough 1177s -skipping training candidate: NM_001170701.p2, not unique enough 1177s -skipping training candidate: NM_001170702.p2, not unique enough 1177s -skipping training candidate: MSTRG.889.1.p2, not unique enough 1177s -skipping training candidate: NR_033835.p2, not unique enough 1177s -skipping training candidate: NM_178151.p2, not unique enough 1177s -skipping training candidate: MSTRG.4.3.p6, not unique enough 1177s -skipping training candidate: NM_018390.p6, not unique enough 1177s -skipping training candidate: NM_001171706.p1, not unique enough 1177s -skipping training candidate: NR_104390.p2, not unique enough 1177s -skipping training candidate: NR_104395.p3, not unique enough 1177s -skipping training candidate: NR_104393.p2, not unique enough 1177s -skipping training candidate: NR_104389.p2, not unique enough 1177s -skipping training candidate: NR_104392.p3, not unique enough 1177s -skipping training candidate: NR_104387.p2, not unique enough 1177s -skipping training candidate: NR_104391.p3, not unique enough 1177s -skipping training candidate: NR_104394.p3, not unique enough 1177s -skipping training candidate: NR_104388.p2, not unique enough 1177s -skipping training candidate: NM_178153.p2, not unique enough 1177s -skipping training candidate: MSTRG.76.2.p4, not unique enough 1177s -skipping training candidate: NM_000555.p2, not unique enough 1177s -skipping training candidate: NM_001195553.p2, not unique enough 1177s -skipping training candidate: MSTRG.992.2.p2, not unique enough 1177s -skipping training candidate: NM_001168399.p2, not unique enough 1177s -skipping training candidate: MSTRG.216.5.p4, not unique enough 1177s -skipping training candidate: NM_001098791.p3, not unique enough 1177s -skipping training candidate: NM_021242.p4, not unique enough 1177s -skipping training candidate: NM_001098790.p3, not unique enough 1177s -skipping training candidate: NM_001127199_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001127199_dup6.p1, not unique enough 1177s -skipping training candidate: NM_001127199.p1, not unique enough 1177s -skipping training candidate: NM_001127199_dup5.p1, not unique enough 1177s -skipping training candidate: NM_001127199_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001127199_dup4.p1, not unique enough 1177s -skipping training candidate: NM_001127199_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098407.p1, not unique enough 1177s -skipping training candidate: NM_001476.p1, not unique enough 1177s -skipping training candidate: NM_001476_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001476_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098418_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098418_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001098418_dup5.p1, not unique enough 1177s -skipping training candidate: NM_001098418.p1, not unique enough 1177s -skipping training candidate: NM_001098418_dup4.p1, not unique enough 1177s -skipping training candidate: NM_001098418_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098409_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001098409_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098409.p1, not unique enough 1177s -skipping training candidate: NM_001098409_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098409_dup4.p1, not unique enough 1177s -skipping training candidate: NM_001098409_dup5.p1, not unique enough 1177s -skipping training candidate: MSTRG.68.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.7.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.19.p1, not unique enough 1177s -skipping training candidate: NM_001306144.p3, not unique enough 1177s -skipping training candidate: NM_003828.p2, not unique enough 1177s -skipping training candidate: MSTRG.921.6.p4, not unique enough 1177s -skipping training candidate: NM_012196.p1, not unique enough 1177s -skipping training candidate: NM_001474_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001474_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001474.p1, not unique enough 1177s -skipping training candidate: NM_001271187.p1, not unique enough 1177s -skipping training candidate: MSTRG.887.3.p1, not unique enough 1177s -skipping training candidate: MSTRG.887.8.p2, not unique enough 1177s -skipping training candidate: NM_001098406.p1, not unique enough 1177s -skipping training candidate: NM_013453.p1, not unique enough 1177s -skipping training candidate: NM_001006684.p1, not unique enough 1177s -skipping training candidate: NM_021949.p3, not unique enough 1177s -skipping training candidate: NM_001127345.p1, not unique enough 1177s -skipping training candidate: NM_001127345_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001127345_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001477.p1, not unique enough 1177s -skipping training candidate: NM_001477_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001477_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098408.p1, not unique enough 1177s -skipping training candidate: NM_001098408_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098408_dup5.p1, not unique enough 1177s -skipping training candidate: NM_001098408_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098408_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001098408_dup4.p1, not unique enough 1177s -skipping training candidate: NM_001475_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001475_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001475.p1, not unique enough 1177s -skipping training candidate: NM_021123_dup2.p1, not unique enough 1177s -skipping training candidate: NM_021123_dup1.p1, not unique enough 1177s -skipping training candidate: NM_021123.p1, not unique enough 1177s -skipping training candidate: NM_001456.p2, not unique enough 1177s -skipping training candidate: NM_001098410_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098410_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098410_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001098410.p1, not unique enough 1177s -skipping training candidate: NM_001040663.p1, not unique enough 1177s -skipping training candidate: NM_001127200.p1, not unique enough 1177s -skipping training candidate: NM_145662_dup1.p1, not unique enough 1177s -skipping training candidate: NM_145662.p1, not unique enough 1177s -skipping training candidate: NM_080720_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001098412.p1, not unique enough 1177s -skipping training candidate: NM_001017990.p1, not unique enough 1177s -skipping training candidate: NM_001098405_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001098405.p1, not unique enough 1177s -skipping training candidate: NM_001098405_dup5.p1, not unique enough 1177s -skipping training candidate: NM_001098405_dup3.p1, not unique enough 1177s -skipping training candidate: NM_001098405_dup4.p1, not unique enough 1177s -skipping training candidate: NM_001098405_dup1.p1, not unique enough 1177s -skipping training candidate: MSTRG.1055.2.p1, not unique enough 1177s -skipping training candidate: MSTRG.275.3.p5, not unique enough 1177s -skipping training candidate: NM_001170460.p3, not unique enough 1177s -skipping training candidate: MSTRG.275.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.275.4.p5, not unique enough 1177s -skipping training candidate: MSTRG.275.7.p3, not unique enough 1177s -skipping training candidate: MSTRG.275.6.p3, not unique enough 1177s -skipping training candidate: NM_006201.p4, not unique enough 1177s -skipping training candidate: MSTRG.443.1.p2, not unique enough 1177s -skipping training candidate: NM_001173480.p2, not unique enough 1177s -skipping training candidate: MSTRG.443.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.443.2.p2, not unique enough 1177s -skipping training candidate: NM_001173479.p2, not unique enough 1177s -skipping training candidate: MSTRG.443.9.p2, not unique enough 1177s -skipping training candidate: NM_015185.p2, not unique enough 1177s -skipping training candidate: MSTRG.443.5.p3, not unique enough 1177s -skipping training candidate: NM_001472.p1, not unique enough 1177s -skipping training candidate: NM_001199687.p2, not unique enough 1177s -skipping training candidate: MSTRG.459.4.p2, not unique enough 1177s -skipping training candidate: MSTRG.459.2.p3, not unique enough 1177s -skipping training candidate: NM_015075.p4, not unique enough 1177s -skipping training candidate: NM_016542.p2, not unique enough 1177s -skipping training candidate: NM_001127212.p1, not unique enough 1177s -skipping training candidate: NR_037859.p3, not unique enough 1177s -skipping training candidate: NM_145799.p2, not unique enough 1177s -skipping training candidate: MSTRG.1005.2.p4, not unique enough 1177s -skipping training candidate: NM_001128166.p2, not unique enough 1177s -skipping training candidate: NM_001129896.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.5.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.7.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.17.p4, not unique enough 1177s -skipping training candidate: MSTRG.718.3.p1, not unique enough 1177s -skipping training candidate: NM_001170780.p1, not unique enough 1177s -skipping training candidate: NM_001178106.p2, not unique enough 1177s -skipping training candidate: NM_016542.p3, not unique enough 1177s -skipping training candidate: NM_001174068.p2, not unique enough 1177s -skipping training candidate: NM_001017991_dup2.p1, not unique enough 1177s -skipping training candidate: NM_001017991_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001017991.p1, not unique enough 1177s -skipping training candidate: NM_001097605.p1, not unique enough 1177s -skipping training candidate: NM_001304990.p3, not unique enough 1177s -skipping training candidate: NM_181762.p2, not unique enough 1177s -skipping training candidate: NM_003336.p2, not unique enough 1177s -skipping training candidate: NM_001080485.p4, not unique enough 1177s -skipping training candidate: NM_001184875.p3, not unique enough 1177s -skipping training candidate: NM_138437.p3, not unique enough 1177s -skipping training candidate: NM_001199818.p3, not unique enough 1177s -skipping training candidate: NM_001004051.p3, not unique enough 1177s -skipping training candidate: NM_001184874.p3, not unique enough 1177s -skipping training candidate: NM_004135.p2, not unique enough 1177s -skipping training candidate: NM_001830.p2, not unique enough 1177s -skipping training candidate: NM_001103151.p2, not unique enough 1177s -skipping training candidate: NM_001282875.p2, not unique enough 1177s -skipping training candidate: NM_001282874.p2, not unique enough 1177s -skipping training candidate: NM_001166703.p1, not unique enough 1177s -skipping training candidate: NM_001204402.p1, not unique enough 1177s -skipping training candidate: NM_001081550.p2, not unique enough 1177s -skipping training candidate: MSTRG.839.4.p2, not unique enough 1177s -skipping training candidate: MSTRG.839.5.p2, not unique enough 1177s -skipping training candidate: MSTRG.839.3.p2, not unique enough 1177s -skipping training candidate: NM_001142386.p2, not unique enough 1177s -skipping training candidate: MSTRG.456.6.p2, not unique enough 1177s -skipping training candidate: NM_014799.p2, not unique enough 1177s -skipping training candidate: NM_001282141.p2, not unique enough 1177s -skipping training candidate: NM_138737.p2, not unique enough 1177s -skipping training candidate: MSTRG.456.2.p2, not unique enough 1177s -skipping training candidate: NM_001449.p2, not unique enough 1177s -skipping training candidate: NM_001159703.p2, not unique enough 1177s -skipping training candidate: NM_001103150.p2, not unique enough 1177s -skipping training candidate: NM_001097596_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001097596.p1, not unique enough 1177s -skipping training candidate: MSTRG.1041.8.p2, not unique enough 1177s -skipping training candidate: MSTRG.906.2.p1, not unique enough 1177s -skipping training candidate: MSTRG.933.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.992.1.p3, not unique enough 1177s -skipping training candidate: NM_052926.p2, not unique enough 1177s -skipping training candidate: NM_013364.p3, not unique enough 1177s -skipping training candidate: NM_031892.p2, not unique enough 1177s -skipping training candidate: MSTRG.151.5.p2, not unique enough 1177s -skipping training candidate: NM_006521.p3, not unique enough 1177s -skipping training candidate: NM_182680.p2, not unique enough 1177s -skipping training candidate: NM_001142.p2, not unique enough 1177s -skipping training candidate: NM_001017931.p1, not unique enough 1177s -skipping training candidate: NM_001199974.p2, not unique enough 1177s -skipping training candidate: NR_033349.p2, not unique enough 1177s -skipping training candidate: NM_001171252.p1, not unique enough 1177s -skipping training candidate: NM_001078173.p1, not unique enough 1177s -skipping training candidate: MSTRG.438.4.p1, not unique enough 1177s -skipping training candidate: NM_001304990.p4, not unique enough 1177s -skipping training candidate: NR_034116_dup1.p1, not unique enough 1177s -skipping training candidate: NM_002414.p2, not unique enough 1177s -skipping training candidate: NM_001277710.p2, not unique enough 1177s -skipping training candidate: NM_001654.p3, not unique enough 1177s -skipping training candidate: NM_001256196.p3, not unique enough 1177s -skipping training candidate: MSTRG.1074.9.p1, not unique enough 1177s -skipping training candidate: NM_001141920.p2, not unique enough 1177s -skipping training candidate: NM_198511.p3, not unique enough 1177s -skipping training candidate: NM_021806.p2, not unique enough 1177s -skipping training candidate: NM_001282311.p2, not unique enough 1177s -skipping training candidate: MSTRG.1037.1.p2, not unique enough 1177s -skipping training candidate: NM_001171134.p2, not unique enough 1177s -skipping training candidate: NR_120493.p1, not unique enough 1177s -skipping training candidate: NR_120493_dup1.p1, not unique enough 1177s -skipping training candidate: NM_002893.p3, not unique enough 1177s -skipping training candidate: MSTRG.376.9.p2, not unique enough 1177s -skipping training candidate: MSTRG.376.4.p3, not unique enough 1177s -skipping training candidate: NM_004187.p2, not unique enough 1177s -skipping training candidate: NM_001282622.p2, not unique enough 1177s -skipping training candidate: MSTRG.376.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.376.8.p3, not unique enough 1177s -skipping training candidate: MSTRG.376.1.p2, not unique enough 1177s -skipping training candidate: NM_001146702.p2, not unique enough 1177s -skipping training candidate: NM_014380.p1, not unique enough 1177s -skipping training candidate: MSTRG.799.2.p2, not unique enough 1177s -skipping training candidate: NM_001282161.p3, not unique enough 1177s -skipping training candidate: NM_022117.p3, not unique enough 1177s -skipping training candidate: NM_134445.p2, not unique enough 1177s -skipping training candidate: NM_134446.p2, not unique enough 1177s -skipping training candidate: NM_001242614.p2, not unique enough 1177s -skipping training candidate: NM_001184808.p2, not unique enough 1177s -skipping training candidate: NM_001291868.p3, not unique enough 1177s -skipping training candidate: NM_001025242.p3, not unique enough 1177s -skipping training candidate: NM_001025243.p3, not unique enough 1177s -skipping training candidate: NR_033348.p3, not unique enough 1177s -skipping training candidate: NM_024087.p2, not unique enough 1177s -skipping training candidate: NM_001168530.p2, not unique enough 1177s -skipping training candidate: NM_001159560.p1, not unique enough 1177s -skipping training candidate: MSTRG.702.2.p3, not unique enough 1177s -skipping training candidate: NM_001195578.p1, not unique enough 1177s -skipping training candidate: NM_001195576.p1, not unique enough 1177s -skipping training candidate: NM_175569.p2, not unique enough 1177s -skipping training candidate: NM_000044.p2, not unique enough 1177s -skipping training candidate: NM_001291867.p3, not unique enough 1177s -skipping training candidate: NM_001136024.p3, not unique enough 1177s -skipping training candidate: NM_130776.p1, not unique enough 1177s -skipping training candidate: NM_207339.p1, not unique enough 1177s -skipping training candidate: MSTRG.719.3.p1, not unique enough 1177s -skipping training candidate: MSTRG.17.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.17.2.p3, not unique enough 1177s -skipping training candidate: NM_004192.p2, not unique enough 1177s -skipping training candidate: NM_001173473.p2, not unique enough 1177s -skipping training candidate: NM_001173474.p2, not unique enough 1177s -skipping training candidate: MSTRG.17.6.p3, not unique enough 1177s -skipping training candidate: NR_001564.p3, not unique enough 1177s -skipping training candidate: MSTRG.531.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.531.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.26.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.763.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.397.6.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.7.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.5.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.8.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.4.p3, not unique enough 1177s -skipping training candidate: MSTRG.397.3.p3, not unique enough 1177s -skipping training candidate: NM_001129828.p1, not unique enough 1177s -skipping training candidate: NM_001129828_dup1.p1, not unique enough 1177s -skipping training candidate: MSTRG.68.19.p2, not unique enough 1177s -skipping training candidate: NM_000425.p6, not unique enough 1177s -skipping training candidate: NM_024003.p6, not unique enough 1177s -skipping training candidate: NM_001143963.p6, not unique enough 1177s -skipping training candidate: NM_001244892_dup1.p1, not unique enough 1177s -skipping training candidate: NR_037927.p1, not unique enough 1177s -skipping training candidate: NM_001144064_dup1.p1, not unique enough 1177s -skipping training candidate: NM_001144064.p1, not unique enough 1177s -skipping training candidate: NM_001145414.p1, not unique enough 1177s -skipping training candidate: MSTRG.36.2.p1, not unique enough 1177s -skipping training candidate: MSTRG.36.1.p1, not unique enough 1177s -skipping training candidate: MSTRG.1041.5.p2, not unique enough 1177s -skipping training candidate: NM_001134321.p1, not unique enough 1177s -skipping training candidate: NM_033380.p4, not unique enough 1177s -skipping training candidate: MSTRG.992.4.p2, not unique enough 1177s -skipping training candidate: NM_001184875.p4, not unique enough 1177s -skipping training candidate: NM_138437.p4, not unique enough 1177s -skipping training candidate: NM_001004051.p4, not unique enough 1177s -skipping training candidate: NM_001184874.p4, not unique enough 1177s -skipping training candidate: NM_001145409.p2, not unique enough 1177s -skipping training candidate: NM_001145410.p2, not unique enough 1177s -skipping training candidate: NM_007363.p2, not unique enough 1177s -skipping training candidate: MSTRG.693.4.p2, not unique enough 1177s -skipping training candidate: NM_001006933.p2, not unique enough 1177s -skipping training candidate: MSTRG.693.3.p2, not unique enough 1177s -skipping training candidate: NM_001145140_dup1.p3, not unique enough 1177s -skipping training candidate: NM_014725.p3, not unique enough 1177s -skipping training candidate: NM_001142504.p3, not unique enough 1177s -skipping training candidate: MSTRG.992.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.992.6.p2, not unique enough 1177s -skipping training candidate: MSTRG.992.7.p3, not unique enough 1177s -skipping training candidate: NM_001184704.p2, not unique enough 1177s -skipping training candidate: MSTRG.108.3.p2, not unique enough 1177s -skipping training candidate: NM_001042480.p3, not unique enough 1177s -skipping training candidate: NM_001042479.p2, not unique enough 1177s -skipping training candidate: MSTRG.108.1.p2, not unique enough 1177s -skipping training candidate: NM_017856.p2, not unique enough 1177s -skipping training candidate: NM_001448.p4, not unique enough 1177s -skipping training candidate: NM_001145139_dup1.p3, not unique enough 1177s -skipping training candidate: NM_001145139.p3, not unique enough 1177s -skipping training candidate: NM_001018024.p1, not unique enough 1177s -skipping training candidate: NR_033772_dup1.p3, not unique enough 1177s -skipping training candidate: NR_120499.p1, not unique enough 1177s -skipping training candidate: NR_120499_dup1.p1, not unique enough 1177s -skipping training candidate: MSTRG.364.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.364.3.p2, not unique enough 1177s -skipping training candidate: NM_001171095.p2, not unique enough 1177s -skipping training candidate: MSTRG.369.2.p2, not unique enough 1177s -skipping training candidate: NR_120494_dup1.p1, not unique enough 1177s -skipping training candidate: NR_120494.p1, not unique enough 1177s -skipping training candidate: MSTRG.702.3.p1, not unique enough 1177s -skipping training candidate: NM_001171092.p2, not unique enough 1177s -skipping training candidate: NM_001114123.p2, not unique enough 1177s -skipping training candidate: NR_033773_dup1.p3, not unique enough 1177s -skipping training candidate: NR_033773.p3, not unique enough 1177s -skipping training candidate: NM_133499.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.12.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.4.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.1029.11.p2, not unique enough 1177s -skipping training candidate: MSTRG.992.5.p3, not unique enough 1177s -skipping training candidate: MSTRG.331.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.331.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.331.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.331.4.p2, not unique enough 1177s -skipping training candidate: NM_001104544.p2, not unique enough 1177s -skipping training candidate: MSTRG.822.4.p2, not unique enough 1177s -skipping training candidate: NM_001104545.p2, not unique enough 1177s -skipping training candidate: NR_033181.p2, not unique enough 1177s -skipping training candidate: NM_001128167.p3, not unique enough 1177s -skipping training candidate: MSTRG.16.1.p9, not unique enough 1177s -skipping training candidate: NM_001184830.p2, not unique enough 1177s -skipping training candidate: MSTRG.945.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.887.7.p1, not unique enough 1177s -skipping training candidate: NM_005676.p4, not unique enough 1177s -skipping training candidate: NM_001204466.p3, not unique enough 1177s -skipping training candidate: NM_001204468.p4, not unique enough 1177s -skipping training candidate: NM_152856.p3, not unique enough 1177s -skipping training candidate: MSTRG.973.1.p3, not unique enough 1177s -skipping training candidate: NM_001171909.p2, not unique enough 1177s -skipping training candidate: MSTRG.963.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.963.2.p4, not unique enough 1177s -skipping training candidate: MSTRG.963.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.963.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.1074.10.p2, not unique enough 1177s -skipping training candidate: MSTRG.1074.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.1074.2.p3, not unique enough 1177s -skipping training candidate: MSTRG.1074.5.p2, not unique enough 1177s -skipping training candidate: MSTRG.1074.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.1074.8.p3, not unique enough 1177s -skipping training candidate: NM_198511.p4, not unique enough 1177s -skipping training candidate: NM_004595.p2, not unique enough 1177s -skipping training candidate: NM_001199972.p1, not unique enough 1177s -skipping training candidate: NR_024499.p1, not unique enough 1177s -skipping training candidate: MSTRG.74.2.p1, not unique enough 1177s -skipping training candidate: MSTRG.108.1.p3, not unique enough 1177s -skipping training candidate: MSTRG.862.1.p3, not unique enough 1177s -skipping training candidate: NM_001127197.p2, not unique enough 1177s -skipping training candidate: MSTRG.862.3.p2, not unique enough 1177s -skipping training candidate: NM_001421.p2, not unique enough 1177s -skipping training candidate: MSTRG.862.4.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.12.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.9.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.13.p2, not unique enough 1177s -skipping training candidate: MSTRG.68.8.p4, not unique enough 1177s -skipping training candidate: MSTRG.68.3.p4, not unique enough 1177s -skipping training candidate: MSTRG.68.6.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.16.p5, not unique enough 1177s -skipping training candidate: NR_034031.p4, not unique enough 1177s -skipping training candidate: MSTRG.68.14.p4, not unique enough 1177s -skipping training candidate: MSTRG.68.17.p5, not unique enough 1177s -skipping training candidate: NM_001256789.p3, not unique enough 1177s -skipping training candidate: MSTRG.860.1.p2, not unique enough 1177s -skipping training candidate: NM_001184772.p2, not unique enough 1177s -skipping training candidate: MSTRG.860.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.860.6.p2, not unique enough 1177s -skipping training candidate: MSTRG.860.2.p2, not unique enough 1177s -skipping training candidate: NM_021949.p4, not unique enough 1177s -skipping training candidate: NM_001143983.p3, not unique enough 1177s -skipping training candidate: NM_153280.p2, not unique enough 1177s -skipping training candidate: NM_001586.p2, not unique enough 1177s -skipping training candidate: NM_005183.p3, not unique enough 1177s -skipping training candidate: NM_032591.p3, not unique enough 1177s -skipping training candidate: MSTRG.268.7.p3, not unique enough 1177s -skipping training candidate: NM_001257291.p3, not unique enough 1177s -skipping training candidate: MSTRG.268.2.p2, not unique enough 1177s -skipping training candidate: MSTRG.268.1.p2, not unique enough 1177s -skipping training candidate: MSTRG.268.3.p3, not unique enough 1177s -skipping training candidate: MSTRG.268.6.p2, not unique enough 1177s -skipping training candidate: NM_001143981.p3, not unique enough 1177s -skipping training candidate: MSTRG.876.1.p3, not unique enough 1177s -skipping training candidate: NM_203474.p2, not unique enough 1177s -skipping training candidate: NM_022825.p2, not unique enough 1177s -skipping training candidate: MSTRG.305.8.p3, not unique enough 1177s -skipping training candidate: MSTRG.305.6.p3, not unique enough 1177s -skipping training candidate: NM_203475.p2, not unique enough 1177s -skipping training candidate: NM_203473.p2, not unique enough 1177s -skipping training candidate: MSTRG.305.7.p3, not unique enough 1177s -skipping training candidate: NM_001282167.p3, not unique enough 1177s -skipping training candidate: MSTRG.2.1.p2, not unique enough 1177s -skipping training candidate: NM_007213.p3, not unique enough 1177s -skipping training candidate: MSTRG.68.10.p5, not unique enough 1177s -skipping training candidate: MSTRG.68.5.p4, not unique enough 1177s -skipping training candidate: MSTRG.468.4.p2, not unique enough 1177s -skipping training candidate: NM_032926.p3, not unique enough 1177s -skipping training candidate: NM_016303.p1, not unique enough 1177s -skipping training candidate: NM_001006612.p1, not unique enough 1177s -skipping training candidate: NM_001006614.p1, not unique enough 1177s -skipping training candidate: NM_153280.p3, not unique enough 1177s -skipping training candidate: NM_000533.p2, not unique enough 1177s -skipping training candidate: NM_001145140_dup1.p4, not unique enough 1177s -skipping training candidate: NM_001171184.p2, not unique enough 1177s -skipping training candidate: NM_014927.p3, not unique enough 1177s -skipping training candidate: NM_001168647.p3, not unique enough 1177s -skipping training candidate: NM_024597.p2, not unique enough 1177s -skipping training candidate: MSTRG.17.6.p4, not unique enough 1177s -skipping training candidate: NM_001145139_dup1.p4, not unique enough 1177s -skipping training candidate: NM_001145139.p4, not unique enough 1177s -skipping training candidate: NM_199478.p2, not unique enough 1177s -skipping training candidate: MSTRG.889.17.p2, not unique enough 1177s -skipping training candidate: NM_033215.p3, not unique enough 1177s -skipping training candidate: MSTRG.549.7.p2, not unique enough 1177s -skipping training candidate: NM_017848.p3, not unique enough 1177s -skipping training candidate: NM_001300788.p4, not unique enough 1177s -skipping training candidate: NM_134445.p3, not unique enough 1177s -skipping training candidate: NM_134446.p3, not unique enough 1177s -skipping training candidate: NM_001242614.p3, not unique enough 1177s -skipping training candidate: NM_001184808.p3, not unique enough 1177s -skipping training candidate: NR_029427.p4, not unique enough 1177s -skipping training candidate: MSTRG.325.4.p3, not unique enough 1177s -skipping training candidate: NM_001166426.p4, not unique enough 1177s -skipping training candidate: NM_017883.p4, not unique enough 1177s -skipping training candidate: MSTRG.301.3.p2, not unique enough 1177s -skipping training candidate: MSTRG.301.2.p3, not unique enough 1178s -skipping training candidate: MSTRG.1074.11.p2, not unique enough 1178s -skipping training candidate: MSTRG.1074.9.p2, not unique enough 1178s -skipping training candidate: MSTRG.1074.10.p3, not unique enough 1178s -skipping training candidate: NM_014799.p3, not unique enough 1178s -skipping training candidate: NM_138737.p3, not unique enough 1178s -skipping training candidate: MSTRG.456.2.p3, not unique enough 1178s -skipping training candidate: NM_001040663.p2, not unique enough 1178s -skipping training candidate: MSTRG.862.1.p4, not unique enough 1178s -skipping training candidate: NM_001127197.p3, not unique enough 1178s -skipping training candidate: MSTRG.862.3.p3, not unique enough 1178s -skipping training candidate: NM_001421.p3, not unique enough 1178s -skipping training candidate: MSTRG.862.4.p3, not unique enough 1178s -skipping training candidate: NM_206917.p2, not unique enough 1178s -skipping training candidate: NM_001282157.p2, not unique enough 1178s -skipping training candidate: NM_012280.p2, not unique enough 1178s -skipping training candidate: NM_006013.p2, not unique enough 1178s -skipping training candidate: MSTRG.1025.5.p3, not unique enough 1178s -skipping training candidate: NM_001256577.p2, not unique enough 1178s -skipping training candidate: NM_001303625.p2, not unique enough 1178s -skipping training candidate: NM_001303624.p3, not unique enough 1178s -skipping training candidate: NM_001256580.p2, not unique enough 1178s -skipping training candidate: MSTRG.1025.1.p2, not unique enough 1178s -skipping training candidate: NM_152634.p2, not unique enough 1178s -skipping training candidate: NM_001297563.p2, not unique enough 1178s -skipping training candidate: NM_000513.p2, not unique enough 1178s -skipping training candidate: NM_000513_dup2.p2, not unique enough 1178s -skipping training candidate: NM_001300788.p5, not unique enough 1178s -skipping training candidate: NM_004651.p3, not unique enough 1178s -skipping training candidate: MSTRG.597.1.p2, not unique enough 1178s -skipping training candidate: MSTRG.597.3.p2, not unique enough 1178s -skipping training candidate: NM_001017931.p2, not unique enough 1178s -skipping training candidate: NM_001128835.p2, not unique enough 1178s -skipping training candidate: NM_000451.p2, not unique enough 1178s -skipping training candidate: NM_001114123.p3, not unique enough 1178s -skipping training candidate: MSTRG.907.2.p1, not unique enough 1178s -skipping training candidate: NM_000402.p3, not unique enough 1178s -skipping training candidate: NM_001042351.p2, not unique enough 1178s -skipping training candidate: NM_032539.p2, not unique enough 1178s -skipping training candidate: NM_006013.p3, not unique enough 1178s -skipping training candidate: MSTRG.1025.5.p4, not unique enough 1178s -skipping training candidate: NM_001256577.p3, not unique enough 1178s -skipping training candidate: NM_001303625.p3, not unique enough 1178s -skipping training candidate: NM_001303624.p4, not unique enough 1178s -skipping training candidate: NM_001256580.p3, not unique enough 1178s -skipping training candidate: MSTRG.1025.1.p3, not unique enough 1178s -skipping training candidate: NM_033290.p2, not unique enough 1178s -skipping training candidate: MSTRG.1042.3.p2, not unique enough 1178s -skipping training candidate: MSTRG.1042.1.p3, not unique enough 1178s -skipping training candidate: NM_002637.p2, not unique enough 1178s -skipping training candidate: NM_001172436.p2, not unique enough 1178s -skipping training candidate: MSTRG.306.3.p2, not unique enough 1178s -skipping training candidate: NM_001098624.p2, not unique enough 1178s -skipping training candidate: MSTRG.128.4.p2, not unique enough 1178s -skipping training candidate: MSTRG.1074.5.p3, not unique enough 1178s -skipping training candidate: NM_033289.p2, not unique enough 1178s -skipping training candidate: NM_001145255.p3, not unique enough 1178s -skipping training candidate: MSTRG.1041.6.p4, not unique enough 1178s -skipping training candidate: NM_003639.p2, not unique enough 1178s -skipping training candidate: NM_001099857.p3, not unique enough 1178s -skipping training candidate: MSTRG.1041.7.p3, not unique enough 1178s -skipping training candidate: MSTRG.1041.9.p2, not unique enough 1178s -skipping training candidate: NM_001099856.p2, not unique enough 1178s -skipping training candidate: NM_001303465.p3, not unique enough 1178s -skipping training candidate: MSTRG.1029.3.p4, not unique enough 1178s -skipping training candidate: NM_001193277.p2, not unique enough 1178s -skipping training candidate: NM_147175.p2, not unique enough 1178s -skipping training candidate: NM_198450.p2, not unique enough 1178s -skipping training candidate: MSTRG.108.1.p4, not unique enough 1178s -skipping training candidate: NM_001184835.p2, not unique enough 1178s -skipping training candidate: NM_001079859.p2, not unique enough 1178s -skipping training candidate: NM_032498.p2, not unique enough 1178s -skipping training candidate: NM_001830.p3, not unique enough 1178s -skipping training candidate: MSTRG.961.7.p4, not unique enough 1178s -skipping training candidate: NM_000202.p2, not unique enough 1178s -skipping training candidate: MSTRG.961.3.p2, not unique enough 1178s -skipping training candidate: MSTRG.961.4.p4, not unique enough 1178s -skipping training candidate: NM_001166550.p2, not unique enough 1178s -skipping training candidate: MSTRG.961.1.p3, not unique enough 1178s -skipping training candidate: NM_001163278.p2, not unique enough 1178s -skipping training candidate: NR_109985.p1, not unique enough 1178s -skipping training candidate: NM_001079860.p2, not unique enough 1178s -skipping training candidate: NM_007137.p2, not unique enough 1178s -skipping training candidate: MSTRG.292.4.p2, not unique enough 1178s -skipping training candidate: NM_014253.p2, not unique enough 1178s -skipping training candidate: MSTRG.109.9.p2, not unique enough 1178s -skipping training candidate: NM_001001994.p2, not unique enough 1178s -skipping training candidate: NM_005278.p2, not unique enough 1178s -skipping training candidate: NR_027401.p2, not unique enough 1178s -skipping training candidate: MSTRG.841.1.p3, not unique enough 1178s -skipping training candidate: NM_001079858.p2, not unique enough 1178s -skipping training candidate: NM_001184834.p2, not unique enough 1178s -skipping training candidate: NM_001449.p3, not unique enough 1178s -skipping training candidate: NM_001159703.p3, not unique enough 1178s -skipping training candidate: NM_005756.p2, not unique enough 1178s -skipping training candidate: NM_001099685.p2, not unique enough 1178s -skipping training candidate: NM_001099685_dup1.p2, not unique enough 1178s -skipping training candidate: NM_001141920.p3, not unique enough 1178s -skipping training candidate: NM_001142529.p2, not unique enough 1178s -skipping training candidate: NM_030639.p2, not unique enough 1178s -skipping training candidate: NM_001142528.p2, not unique enough 1178s -skipping training candidate: NM_001142530.p2, not unique enough 1178s -skipping training candidate: NM_001142526.p2, not unique enough 1178s -skipping training candidate: NM_001142527.p2, not unique enough 1178s -skipping training candidate: NM_001142524.p2, not unique enough 1178s -skipping training candidate: NM_001184836.p2, not unique enough 1178s -skipping training candidate: NM_175569.p3, not unique enough 1178s -skipping training candidate: NR_026594.p2, not unique enough 1178s -skipping training candidate: NM_001184837.p2, not unique enough 1178s -skipping training candidate: NM_177537_dup1.p4, not unique enough 1178s -skipping training candidate: NR_103770.p1, not unique enough 1178s -skipping training candidate: MSTRG.945.3.p2, not unique enough 1178s 1178s -redundancy-minimized set includes 1645 / 4259 = 38.62% 1178s 1178s * [Sat Mar 16 21:23:46 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 1179s PCT_GC: 46 1179s * [Sat Mar 16 21:23:47 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores 1188s * [Sat Mar 16 21:23:56 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 1312s * [Sat Mar 16 21:26:00 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 1314s Selecting best orfs 1315s * [Sat Mar 16 21:26:03 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement 1315s Training start codon pattern recognition* [Sat Mar 16 21:26:03 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 1319s * [Sat Mar 16 21:26:07 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 1320s -round: 1 1338s -round: 2 1357s -round: 3 1376s -round: 4 1395s -round: 5 1415s * [Sat Mar 16 21:27:43 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 1415s -parsing scores 1439s * [Sat Mar 16 21:28:07 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 1440s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1440s Execution halted 1440s * [Sat Mar 16 21:28:08 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 1441s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1441s Execution halted 1441s * [Sat Mar 16 21:28:09 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 1441s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1441s Execution halted 1441s * [Sat Mar 16 21:28:09 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 1442s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1442s Execution halted 1442s * [Sat Mar 16 21:28:10 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced 1442s num features: 336 num_incorporate: 100 1442s -feature swap of score: 3.78911079353454 instead of -4.15762669956 1442s -feature swap of score: 4.3075564869904 instead of -3.54241712691985 1442s -feature swap of score: -1.55002091334646 instead of -2.55010664779592 1442s -feature swap of score: 4.83949655109525 instead of -2.24867860418506 1442s -feature swap of score: 0.392270533069581 instead of -2.32345623662297 1442s -feature swap of score: 3.78855323991787 instead of -2.2988029392048 1442s -feature swap of score: 3.99836372804798 instead of -2.19588732342881 1442s -feature swap of score: 3.64835524788969 instead of -2.09663793619562 1442s -feature swap of score: 4.88229074177495 instead of -2.0071137297779 1442s -feature swap of score: -1.8083423728436 instead of -1.93321879934806 1442s -feature swap of score: 3.92879192464595 instead of -1.772614249871 1442s -feature swap of score: -0.465948676008031 instead of -2.00439257184315 1442s -feature swap of score: 0.0546515421473758 instead of -1.60684025496409 1442s -feature swap of score: 0.803622088306608 instead of -1.17227320164039 1442s -feature swap of score: 4.45581598878225 instead of -1.27696269799764 1442s -feature swap of score: 2.07236230159122 instead of -1.40605769767333 1442s -feature swap of score: 4.02245547784082 instead of -1.5805710473436 1442s -feature swap of score: 0.586330906031762 instead of -0.825175240434032 1442s -feature swap of score: 3.96397529913446 instead of -0.871836639747919 1442s -feature swap of score: 1.28205341901886 instead of -0.854499557546068 1442s -feature swap of score: 2.51752465071796 instead of -0.880497045171406 1442s -feature swap of score: 7.60013808606777 instead of -0.651902109016902 1442s -feature swap of score: 5.56752159508171 instead of -0.585113517527429 1442s -feature swap of score: 4.16682533874051 instead of -0.591263924699593 1442s -feature swap of score: 5.98692288702727 instead of -0.550933752346117 1442s -feature swap of score: 2.78461992524222 instead of -0.361642943889318 1442s -feature swap of score: -0.14086687166401 instead of -0.260141330736644 1442s -feature swap of score: 1.30640970749369 instead of -0.208633020456475 1442s -feature swap of score: 0.305536787416525 instead of 0.0104847431676378 1442s -feature swap of score: 3.55759636533095 instead of -0.120486034233916 1442s -feature swap of score: 2.46987628753496 instead of -0.103803542507822 1442s -feature swap of score: 2.0546736913397 instead of 0.0935269368540257 1442s -feature swap of score: 1.31912484703918 instead of 0.229231280733345 1442s -feature swap of score: 1.89359151880524 instead of 0.232351263114116 1442s -feature swap of score: 5.43521751645765 instead of 0.195794099551117 1442s -feature swap of score: 4.33834387795496 instead of -0.054616396540288 1442s -feature swap of score: 6.43704991515938 instead of 0.111124242596921 1442s -feature swap of score: 4.25846830983975 instead of 0.127430589246059 1442s -feature swap of score: 0.771786455336691 instead of 0.285671737045457 1442s -feature swap of score: 6.60911073864081 instead of 0.0418054250163035 1442s -feature swap of score: 6.79809024958936 instead of 0.555671326116825 1443s -feature swap of score: 7.27612094216219 instead of 0.559863976992066 1443s -feature swap of score: 3.36215544495879 instead of 0.702288739001579 1443s -feature swap of score: 4.38866473472805 instead of 0.440911348584446 1443s -feature swap of score: 0.836843797008186 instead of 0.157766373683364 1443s -feature swap of score: 2.13420236534183 instead of 0.949736946003556 1443s -feature swap of score: 1.64354527137561 instead of 0.773162924133292 1443s -feature swap of score: 2.38988424268632 instead of 0.941592652583747 1443s -feature swap of score: 4.91107243910547 instead of 1.09251723189791 1443s -feature swap of score: 2.49264242586391 instead of 0.856412735226522 1443s -feature swap of score: 6.28552706210459 instead of 1.07932791455603 1443s -feature swap of score: 4.67930772689507 instead of 1.27353927782704 1443s -feature swap of score: 7.50973191408739 instead of 1.12100700928058 1443s -feature swap of score: 5.55751937051127 instead of 1.21030026759988 1443s -feature swap of score: 2.60074697345087 instead of 1.47109964978436 1443s -feature swap of score: 3.74655896712747 instead of 1.48225927554747 1443s -feature swap of score: 3.99301668862372 instead of 1.24561259795263 1443s -feature swap of score: 1.72372236527001 instead of 1.02241527158741 1443s -feature swap of score: 6.86300883201794 instead of 1.14563582053961 1443s -feature swap of score: 5.54190533772704 instead of 1.28297492173032 1443s -feature swap of score: 2.51308026289154 instead of 1.4180584754329 1443s -feature swap of score: 3.38846514773249 instead of 1.2857641622143 1443s -feature swap of score: 2.49385651598659 instead of 1.55130322997112 1443s -feature swap of score: 2.65351701617127 instead of 1.23066210648887 1443s -feature swap of score: 2.60425530523188 instead of 1.47665351441682 1443s -feature swap of score: 7.60582369996651 instead of 1.55381032974607 1443s -feature swap of score: 2.9807664000693 instead of 1.59725854839862 1443s -feature swap of score: 4.52648695626297 instead of 1.66034729751211 1443s -feature swap of score: 7.21055045635181 instead of 1.7858663752496 1443s -feature swap of score: 4.25795336260412 instead of 1.84036163713462 1443s -feature swap of score: 9.54168129081765 instead of 1.91931805946798 1443s -feature swap of score: 8.89437210131165 instead of 1.47973460790513 1443s -feature swap of score: 3.3622755750855 instead of 1.94740840499986 1443s -feature swap of score: 6.78489489553093 instead of 1.90264556019824 1443s -feature swap of score: 9.60405031469725 instead of 2.1040236037399 1443s -feature swap of score: 5.57780850222194 instead of 1.85621488376428 1443s -feature swap of score: 3.43303080359017 instead of 0.865435946387495 1443s -feature swap of score: 2.67597182314123 instead of 1.80627212503354 1443s -feature swap of score: 6.43244682385697 instead of 1.78041450678908 1443s -feature swap of score: 3.95962793695356 instead of 1.84794334938432 1443s -feature swap of score: 3.98432173082736 instead of 1.875580806845 1443s -feature swap of score: 3.21236503540814 instead of 2.21808523494257 1443s -feature swap of score: 7.03718379305501 instead of 2.08706655299514 1443s -feature swap of score: 5.90582904633149 instead of 1.87026115503397 1443s -feature swap of score: 5.79478155363706 instead of 1.80883534807753 1443s -feature swap of score: 5.36619160368881 instead of 1.98766010735596 1443s -feature swap of score: 6.07858328906771 instead of 2.06576129141207 1443s -feature swap of score: 5.86937251981998 instead of 1.90511689506347 1443s -feature swap of score: 3.38462816070108 instead of 2.13933881189727 1443s -feature swap of score: 6.37449231938971 instead of 2.82058094033957 1443s -feature swap of score: 6.72646305674668 instead of 2.83352026076865 1443s -feature swap of score: 4.82560543584288 instead of 2.70443214397618 1443s -feature swap of score: 4.42177781286965 instead of 2.8151180947157 1443s -feature swap of score: 8.98279247275997 instead of 2.94679407717209 1443s -feature swap of score: 4.60893969392588 instead of 2.9477877072234 1443s -feature swap of score: 7.85133157245333 instead of 1.91369736378323 1443s -feature swap of score: 5.99853031964839 instead of 2.93641177087966 1443s -feature swap of score: 4.29682354807149 instead of 3.14449015818142 1443s -feature swap of score: 3.52291944162443 instead of 3.13111126617467 1443s -feature swap of score: 4.76551376672987 instead of 3.16811466075655 1443s -num feature swaps: 100 1443s * [Sat Mar 16 21:28:11 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 1443s -round: 1 1462s -round: 2 1481s -round: 3 1498s -round: 4 1516s -round: 5 1534s * [Sat Mar 16 21:29:42 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1534s -parsing scores 1555s * [Sat Mar 16 21:30:03 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 1556s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1556s Execution halted 1556s * [Sat Mar 16 21:30:04 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1556s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1556s Execution halted 1556s * [Sat Mar 16 21:30:04 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 1557s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1557s Execution halted 1557s * [Sat Mar 16 21:30:05 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 1560s Refining start codon selections. 1561s -number of revised start positions: 247 1561s * [Sat Mar 16 21:30:09 2024] Running CMD: cp /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 1561s copying output to final output file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Sat Mar 16 21:30:09 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 1563s Making bed file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed 1563s * [Sat Mar 16 21:30:11 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 1566s Making pep file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep 1569s * [Sat Mar 16 21:30:16 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/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.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 1572s Making cds file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds 1574s transdecoder is finished. See output files /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* 1574s 1574s 1574s 1574s 1574s ## convert to genome coordinates 1574s ../../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 1578s 1583s 1583s 1583s Done. 3037 / 3037 transcript orfs could be propagated to the genome 1583s 1583s 1583s 1583s ## make bed files for viewing with GenomeView 1583s 1583s # covert cufflinks gtf to bed 1583s ../../util/gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed 1588s 1588s # convert the genome-based gene-gff3 file to bed 1588s ../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed 1593s 1593s 1593s 1593s ../../util/fasta_prot_checker.pl stringtie_merged.transcripts.fasta.transdecoder.pep 1594s make[1]: Leaving directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/stringtie_example' 1594s Running example in $... 1594s 1594s # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* 1594s 1594s 1594s exit 0 1594s make[1]: Entering directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 1594s ./runMe.sh 1594s + ../../util/gtf_to_alignment_gff3.pl supertranscripts.gtf 1594s + ../../util/gtf_genome_to_cdna_fasta.pl supertranscripts.gtf supertranscripts.fasta 1594s -parsing cufflinks output: supertranscripts.gtf 1594s -parsing genome fasta: supertranscripts.fasta 1594s -done parsing genome. 1594s // processing ADD1 1594s // processing ATPsyn-d 1594s // processing AdipoR 1594s // processing Aldh-III 1594s // processing CG10082 1594s // processing CG10237 1594s // processing CG12581 1594s // processing CG13255 1594s // processing CG13284 1594s // processing CG13887 1595s // processing CG14995 1595s // processing CG15715 1595s // processing CG30438 1595s // processing CG31639 1595s // processing CG31948 1595s // processing CG32082 1595s // processing CG33125 1595s // processing CG33970 1595s // processing CG3530 1595s // processing CG6024 1595s // processing CG6091 1595s // processing CG6145 1595s // processing CG6424 1595s // processing CG6852 1595s // processing CG7564 1595s // processing CG8136 1595s // processing CG8312 1595s // processing Calx 1595s // processing CanB2 1595s // processing Cdep 1595s // processing Cnx99A 1595s // processing Dat 1595s // processing Dgk 1595s // processing Eno 1595s // processing Est-6 1595s // processing Gale 1595s // processing Galk 1595s // processing His4r 1595s // processing Hsc70-1 1595s // processing IP3K1 1595s // processing Irk2 1595s // processing Klp10A 1595s // processing Lip4 1595s // processing Mgstl 1595s // processing Myo61F 1595s // processing Npl4 1595s // processing RpL15 1595s // processing S-Lap3 1595s // processing Sec16 1595s // processing Tm1 1595s // processing bdg 1595s // processing bic 1595s // processing cdi 1595s // processing ctp 1595s // processing eIF5B 1595s // processing eff 1595s // processing gukh 1595s // processing hrg 1595s // processing kto 1595s // processing l(1)G0193 1595s // processing l(3)05822 1595s // processing mGluR 1595s // processing mge 1595s // processing nmo 1595s // processing ogre 1595s // processing regucalcin 1595s // processing sqd 1595s // processing stas 1595s // processing trc 1595s + ../../TransDecoder.LongOrfs -t transcripts.fasta 1595s CMD: mkdir -p /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir 1595s * [Sat Mar 16 21:30:43 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/compute_base_probs.pl transcripts.fasta 0 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat 1595s 1595s 1595s -first extracting base frequencies, we'll need them later. 1595s 1595s 1595s - extracting ORFs from transcripts. 1595s -total transcripts to examine: 279 1600s [100/279] = 35.84% done [200/279] = 71.68% done CMD: touch /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok 1600s 1600s 1600s ################################# 1600s ### Done preparing long ORFs. ### 1600s ################################## 1600s 1600s Use file: /tmp/autopkgtest.x2gTgS/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. 1600s 1600s Then, run TransDecoder.Predict for your final coding region predictions. 1600s 1600s 1600s + cmd='../../TransDecoder.Predict -t transcripts.fasta' 1600s + '[' ']' 1600s + eval ../../TransDecoder.Predict -t transcripts.fasta 1600s ++ ../../TransDecoder.Predict -t transcripts.fasta 1600s * [Sat Mar 16 21:30:48 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 1600s * [Sat Mar 16 21:30:48 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/exclude_similar_proteins.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 1600s -skipping training candidate: bdg_i4.p1, not unique enough 1600s -skipping training candidate: bdg_i2.p1, not unique enough 1600s -skipping training candidate: bdg_i1.p1, not unique enough 1600s -skipping training candidate: Dgk_i7.p1, not unique enough 1600s -skipping training candidate: Cdep_i1.p1, not unique enough 1600s -skipping training candidate: eIF5B_i3.p1, not unique enough 1600s -skipping training candidate: eIF5B_i2.p1, not unique enough 1600s -skipping training candidate: Dgk_i1.p1, not unique enough 1600s -skipping training candidate: eIF5B_i5.p1, not unique enough 1600s -skipping training candidate: Dgk_i3.p1, not unique enough 1600s -skipping training candidate: Dgk_i6.p1, not unique enough 1600s -skipping training candidate: eIF5B_i1.p1, not unique enough 1600s -skipping training candidate: Myo61F_i3.p1, not unique enough 1600s -skipping training candidate: Myo61F_i2.p1, not unique enough 1600s -skipping training candidate: Myo61F_i4.p1, not unique enough 1600s -skipping training candidate: ADD1_i3.p1, not unique enough 1601s -skipping training candidate: mGluR_i3.p1, not unique enough 1601s -skipping training candidate: Calx_i3.p1, not unique enough 1601s -skipping training candidate: Calx_i9.p1, not unique enough 1601s -skipping training candidate: Calx_i8.p1, not unique enough 1601s -skipping training candidate: Calx_i1.p1, not unique enough 1601s -skipping training candidate: Calx_i2.p1, not unique enough 1601s -skipping training candidate: Calx_i5.p1, not unique enough 1601s -skipping training candidate: Calx_i4.p1, not unique enough 1601s -skipping training candidate: cdi_i1.p1, not unique enough 1601s -skipping training candidate: CG8312_i2.p1, not unique enough 1601s -skipping training candidate: CG8312_i4.p1, not unique enough 1601s -skipping training candidate: Klp10A_i2.p1, not unique enough 1601s -skipping training candidate: Klp10A_i4.p1, not unique enough 1601s -skipping training candidate: Klp10A_i5.p1, not unique enough 1601s -skipping training candidate: Klp10A_i3.p1, not unique enough 1601s -skipping training candidate: Klp10A_i1.p1, not unique enough 1601s -skipping training candidate: CG6424_i4.p1, not unique enough 1601s -skipping training candidate: CG6424_i3.p1, not unique enough 1601s -skipping training candidate: CG6424_i1.p1, not unique enough 1601s -skipping training candidate: Dgk_i4.p1, not unique enough 1601s -skipping training candidate: CG33970_i1.p1, not unique enough 1601s -skipping training candidate: Dgk_i5.p1, not unique enough 1601s -skipping training candidate: CG33125_i1.p1, not unique enough 1601s -skipping training candidate: CG3530_i2.p1, not unique enough 1601s -skipping training candidate: CG10082_i2.p1, not unique enough 1601s -skipping training candidate: CG12581_i1.p1, not unique enough 1601s -skipping training candidate: CG6091_i3.p1, not unique enough 1601s -skipping training candidate: hrg_i3.p1, not unique enough 1601s -skipping training candidate: hrg_i4.p1, not unique enough 1601s -skipping training candidate: hrg_i2.p1, not unique enough 1601s -skipping training candidate: Calx_i7.p1, not unique enough 1601s -skipping training candidate: CG32082_i1.p1, not unique enough 1601s -skipping training candidate: Npl4_i3.p1, not unique enough 1601s -skipping training candidate: Npl4_i1.p1, not unique enough 1601s -skipping training candidate: CG3530_i3.p1, not unique enough 1601s -skipping training candidate: CG32082_i3.p1, not unique enough 1601s -skipping training candidate: CG32082_i2.p1, not unique enough 1601s -skipping training candidate: l(3)05822_i3.p1, not unique enough 1601s -skipping training candidate: Cnx99A_i3.p1, not unique enough 1601s -skipping training candidate: Cnx99A_i4.p1, not unique enough 1601s -skipping training candidate: Cnx99A_i2.p1, not unique enough 1601s -skipping training candidate: l(3)05822_i1.p1, not unique enough 1601s -skipping training candidate: l(3)05822_i4.p1, not unique enough 1601s -skipping training candidate: CG6091_i4.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i5.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i12.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i1.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i9.p1, not unique enough 1601s -skipping training candidate: Hsc70-1_i3.p1, not unique enough 1601s -skipping training candidate: Hsc70-1_i2.p1, not unique enough 1601s -skipping training candidate: Est-6_i1.p1, not unique enough 1601s -skipping training candidate: S-Lap3_i1.p1, not unique enough 1601s -skipping training candidate: S-Lap3_i3.p1, not unique enough 1601s -skipping training candidate: gukh_i4.p1, not unique enough 1601s -skipping training candidate: mGluR_i2.p1, not unique enough 1601s -skipping training candidate: CG30438_i5.p1, not unique enough 1601s -skipping training candidate: CG30438_i2.p1, not unique enough 1601s -skipping training candidate: CG30438_i1.p1, not unique enough 1601s -skipping training candidate: CG6145_i4.p1, not unique enough 1601s -skipping training candidate: CG33970_i3.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i11.p1, not unique enough 1601s -skipping training candidate: mGluR_i1.p1, not unique enough 1601s -skipping training candidate: Eno_i5.p1, not unique enough 1601s -skipping training candidate: Eno_i1.p1, not unique enough 1601s -skipping training candidate: Eno_i3.p1, not unique enough 1601s -skipping training candidate: CG6091_i2.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i7.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i6.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i3.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i4.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i10.p1, not unique enough 1601s -skipping training candidate: Aldh-III_i8.p1, not unique enough 1601s -skipping training candidate: Galk_i4.p1, not unique enough 1601s -skipping training candidate: Galk_i3.p1, not unique enough 1601s -skipping training candidate: Galk_i1.p1, not unique enough 1601s -skipping training candidate: CG6145_i1.p1, not unique enough 1601s -skipping training candidate: CG6145_i2.p1, not unique enough 1601s -skipping training candidate: Eno_i4.p2, not unique enough 1601s -skipping training candidate: Eno_i5.p2, not unique enough 1601s -skipping training candidate: Eno_i1.p2, not unique enough 1601s -skipping training candidate: Eno_i6.p1, not unique enough 1601s -skipping training candidate: Eno_i3.p2, not unique enough 1601s -skipping training candidate: CG6424_i3.p2, not unique enough 1601s -skipping training candidate: CG6424_i2.p2, not unique enough 1601s -skipping training candidate: CG6424_i1.p2, not unique enough 1601s -skipping training candidate: Eno_i6.p2, not unique enough 1601s -skipping training candidate: Eno_i2.p2, not unique enough 1601s -skipping training candidate: trc_i2.p1, not unique enough 1601s -skipping training candidate: Irk2_i1.p1, not unique enough 1601s -skipping training candidate: Irk2_i4.p1, not unique enough 1601s -skipping training candidate: Lip4_i2.p1, not unique enough 1601s -skipping training candidate: CG8312_i1.p1, not unique enough 1601s -skipping training candidate: AdipoR_i5.p1, not unique enough 1601s -skipping training candidate: AdipoR_i4.p1, not unique enough 1601s -skipping training candidate: AdipoR_i2.p1, not unique enough 1601s -skipping training candidate: Tm1_i14.p1, not unique enough 1601s -skipping training candidate: Tm1_i5.p1, not unique enough 1601s -skipping training candidate: CG8136_i4.p1, not unique enough 1601s -skipping training candidate: kto_i2.p3, not unique enough 1601s -skipping training candidate: CG30438_i4.p1, not unique enough 1601s -skipping training candidate: Lip4_i1.p1, not unique enough 1601s -skipping training candidate: nmo_i1.p1, not unique enough 1601s -skipping training candidate: nmo_i6.p1, not unique enough 1601s -skipping training candidate: nmo_i7.p1, not unique enough 1601s -skipping training candidate: CG8136_i1.p1, not unique enough 1601s -skipping training candidate: CG8136_i3.p1, not unique enough 1601s -skipping training candidate: CG6145_i3.p1, not unique enough 1601s -skipping training candidate: CG7564_i3.p1, not unique enough 1601s -skipping training candidate: CG7564_i1.p1, not unique enough 1601s -skipping training candidate: CG7564_i2.p3, not unique enough 1601s -skipping training candidate: CG14995_i7.p1, not unique enough 1601s -skipping training candidate: nmo_i5.p1, not unique enough 1601s -skipping training candidate: nmo_i2.p1, not unique enough 1601s -skipping training candidate: nmo_i4.p1, not unique enough 1601s -skipping training candidate: CG14995_i3.p1, not unique enough 1601s -skipping training candidate: Cdep_i4.p1, not unique enough 1601s -skipping training candidate: CG14995_i2.p1, not unique enough 1601s -skipping training candidate: CG6024_i2.p1, not unique enough 1601s -skipping training candidate: gukh_i4.p2, not unique enough 1601s -skipping training candidate: AdipoR_i1.p1, not unique enough 1601s -skipping training candidate: CG14995_i4.p1, not unique enough 1601s -skipping training candidate: ogre_i3.p1, not unique enough 1601s -skipping training candidate: ogre_i5.p1, not unique enough 1601s -skipping training candidate: ogre_i6.p1, not unique enough 1601s -skipping training candidate: ogre_i2.p1, not unique enough 1601s -skipping training candidate: ogre_i1.p1, not unique enough 1601s -skipping training candidate: IP3K1_i2.p1, not unique enough 1601s -skipping training candidate: CG14995_i1.p1, not unique enough 1601s -skipping training candidate: Gale_i1.p1, not unique enough 1601s -skipping training candidate: CG33125_i1.p2, not unique enough 1601s -skipping training candidate: CG13284_i3.p1, not unique enough 1601s -skipping training candidate: CG13284_i1.p1, not unique enough 1601s -skipping training candidate: CG13284_i4.p1, not unique enough 1601s -skipping training candidate: CG13284_i2.p1, not unique enough 1601s -skipping training candidate: sqd_i4.p1, not unique enough 1601s -skipping training candidate: Klp10A_i2.p2, not unique enough 1601s -skipping training candidate: Klp10A_i4.p2, not unique enough 1601s -skipping training candidate: Klp10A_i5.p2, not unique enough 1601s -skipping training candidate: Klp10A_i3.p2, not unique enough 1601s -skipping training candidate: Klp10A_i1.p2, not unique enough 1601s -skipping training candidate: Calx_i7.p2, not unique enough 1601s -skipping training candidate: sqd_i1.p1, not unique enough 1601s -skipping training candidate: sqd_i2.p1, not unique enough 1601s -skipping training candidate: CG10237_i4.p1, not unique enough 1601s -skipping training candidate: CG10237_i5.p1, not unique enough 1601s -skipping training candidate: CG31948_i2.p1, not unique enough 1601s -skipping training candidate: regucalcin_i4.p1, not unique enough 1601s -skipping training candidate: regucalcin_i2.p1, not unique enough 1601s -skipping training candidate: regucalcin_i1.p1, not unique enough 1601s -skipping training candidate: CG10237_i3.p1, not unique enough 1601s -skipping training candidate: CG10237_i1.p1, not unique enough 1601s -skipping training candidate: l(3)05822_i3.p2, not unique enough 1601s -skipping training candidate: l(3)05822_i2.p2, not unique enough 1601s -skipping training candidate: l(3)05822_i4.p2, not unique enough 1601s -skipping training candidate: Tm1_i3.p1, not unique enough 1601s -skipping training candidate: Tm1_i6.p1, not unique enough 1601s -skipping training candidate: Tm1_i2.p1, not unique enough 1601s -skipping training candidate: Tm1_i4.p1, not unique enough 1601s -skipping training candidate: Tm1_i9.p1, not unique enough 1601s -skipping training candidate: Tm1_i11.p1, not unique enough 1601s -skipping training candidate: Npl4_i2.p2, not unique enough 1601s -skipping training candidate: Npl4_i1.p2, not unique enough 1601s -skipping training candidate: Sec16_i1.p2, not unique enough 1601s -skipping training candidate: Sec16_i5.p2, not unique enough 1601s -skipping training candidate: Sec16_i2.p2, not unique enough 1601s -skipping training candidate: CG8312_i2.p2, not unique enough 1601s -skipping training candidate: CG8312_i4.p2, not unique enough 1601s -skipping training candidate: Dgk_i7.p2, not unique enough 1601s -skipping training candidate: eIF5B_i1.p2, not unique enough 1601s -skipping training candidate: eIF5B_i5.p2, not unique enough 1601s -skipping training candidate: eIF5B_i3.p2, not unique enough 1601s -skipping training candidate: eIF5B_i2.p2, not unique enough 1601s -skipping training candidate: Dgk_i3.p2, not unique enough 1601s -skipping training candidate: Dgk_i6.p2, not unique enough 1601s -skipping training candidate: Dgk_i2.p2, not unique enough 1601s -skipping training candidate: l(1)G0193_i1.p2, not unique enough 1601s -skipping training candidate: Tm1_i12.p1, not unique enough 1601s -skipping training candidate: Dgk_i1.p3, not unique enough 1601s -skipping training candidate: Dgk_i7.p3, not unique enough 1601s -skipping training candidate: Dat_i1.p1, not unique enough 1601s -skipping training candidate: Dgk_i3.p3, not unique enough 1601s -skipping training candidate: Dgk_i6.p3, not unique enough 1601s -skipping training candidate: Dgk_i2.p3, not unique enough 1601s -skipping training candidate: Dgk_i4.p3, not unique enough 1601s -skipping training candidate: l(3)05822_i3.p3, not unique enough 1601s -skipping training candidate: l(3)05822_i2.p3, not unique enough 1601s -skipping training candidate: l(3)05822_i4.p3, not unique enough 1601s -skipping training candidate: CG14995_i5.p1, not unique enough 1601s -skipping training candidate: CG6024_i2.p2, not unique enough 1601s -skipping training candidate: Sec16_i5.p3, not unique enough 1601s -skipping training candidate: Sec16_i2.p3, not unique enough 1601s -skipping training candidate: CG13887_i1.p1, not unique enough 1601s -skipping training candidate: CG13887_i4.p1, not unique enough 1601s -skipping training candidate: CG14995_i7.p2, not unique enough 1601s -skipping training candidate: Dgk_i5.p3, not unique enough 1601s -skipping training candidate: nmo_i2.p2, not unique enough 1601s -skipping training candidate: nmo_i4.p2, not unique enough 1601s -skipping training candidate: nmo_i3.p2, not unique enough 1601s -skipping training candidate: nmo_i1.p2, not unique enough 1601s -skipping training candidate: nmo_i6.p2, not unique enough 1601s -skipping training candidate: nmo_i7.p2, not unique enough 1601s -skipping training candidate: RpL15_i6.p1, not unique enough 1601s -skipping training candidate: regucalcin_i1.p2, not unique enough 1601s -skipping training candidate: Hsc70-1_i3.p2, not unique enough 1601s -skipping training candidate: RpL15_i7.p1, not unique enough 1601s -skipping training candidate: regucalcin_i3.p2, not unique enough 1601s -skipping training candidate: regucalcin_i2.p2, not unique enough 1601s -skipping training candidate: gukh_i3.p2, not unique enough 1601s -skipping training candidate: gukh_i4.p3, not unique enough 1601s -skipping training candidate: cdi_i1.p2, not unique enough 1601s -skipping training candidate: Hsc70-1_i2.p2, not unique enough 1601s -skipping training candidate: RpL15_i4.p1, not unique enough 1601s -skipping training candidate: RpL15_i2.p1, not unique enough 1601s -skipping training candidate: RpL15_i1.p1, not unique enough 1601s -skipping training candidate: RpL15_i5.p1, not unique enough 1601s -skipping training candidate: RpL15_i3.p1, not unique enough 1601s -skipping training candidate: Npl4_i2.p3, not unique enough 1601s -skipping training candidate: Npl4_i1.p3, not unique enough 1601s -skipping training candidate: trc_i2.p2, not unique enough 1601s -skipping training candidate: Hsc70-1_i2.p3, not unique enough 1601s -skipping training candidate: Hsc70-1_i1.p3, not unique enough 1601s -skipping training candidate: CG14995_i5.p2, not unique enough 1601s -skipping training candidate: CG14995_i4.p2, not unique enough 1601s -skipping training candidate: CG14995_i2.p2, not unique enough 1601s -skipping training candidate: CG14995_i1.p2, not unique enough 1601s -skipping training candidate: CG10237_i3.p2, not unique enough 1601s -skipping training candidate: CG10237_i5.p2, not unique enough 1601s -skipping training candidate: CG10237_i2.p2, not unique enough 1601s -skipping training candidate: CG10237_i1.p2, not unique enough 1601s -skipping training candidate: Eno_i5.p3, not unique enough 1601s -skipping training candidate: Eno_i1.p3, not unique enough 1601s -skipping training candidate: Eno_i2.p3, not unique enough 1601s -skipping training candidate: Eno_i6.p3, not unique enough 1601s -skipping training candidate: Eno_i3.p3, not unique enough 1601s -skipping training candidate: Sec16_i1.p3, not unique enough 1601s -skipping training candidate: Sec16_i3.p2, not unique enough 1601s -skipping training candidate: CG14995_i3.p3, not unique enough 1601s -skipping training candidate: CG14995_i7.p3, not unique enough 1601s -skipping training candidate: CG13887_i3.p1, not unique enough 1601s -skipping training candidate: gukh_i2.p2, not unique enough 1601s -skipping training candidate: ATPsyn-d_i1.p1, not unique enough 1601s -skipping training candidate: ATPsyn-d_i3.p1, not unique enough 1601s -skipping training candidate: CG10082_i1.p2, not unique enough 1601s -skipping training candidate: sqd_i5.p1, not unique enough 1601s -skipping training candidate: CG14995_i6.p3, not unique enough 1601s -skipping training candidate: CG14995_i5.p3, not unique enough 1601s -skipping training candidate: CG30438_i3.p2, not unique enough 1601s -skipping training candidate: CG30438_i5.p2, not unique enough 1601s -skipping training candidate: CG30438_i2.p2, not unique enough 1601s -skipping training candidate: CG30438_i1.p2, not unique enough 1601s -skipping training candidate: CG14995_i5.p4, not unique enough 1601s -skipping training candidate: stas_i1.p1, not unique enough 1601s -skipping training candidate: cdi_i1.p3, not unique enough 1601s -skipping training candidate: CG14995_i4.p3, not unique enough 1601s -skipping training candidate: CG14995_i2.p3, not unique enough 1601s -skipping training candidate: CG14995_i1.p3, not unique enough 1601s -skipping training candidate: CanB2_i2.p1, not unique enough 1601s -skipping training candidate: ADD1_i3.p2, not unique enough 1601s -skipping training candidate: Sec16_i1.p4, not unique enough 1601s -skipping training candidate: Sec16_i3.p3, not unique enough 1601s -skipping training candidate: bic_i1.p1, not unique enough 1601s -skipping training candidate: CG12581_i1.p2, not unique enough 1601s -skipping training candidate: Mgstl_i1.p1, not unique enough 1601s -skipping training candidate: ctp_i1.p1, not unique enough 1601s -skipping training candidate: ctp_i4.p1, not unique enough 1601s -skipping training candidate: ctp_i2.p1, not unique enough 1601s -skipping training candidate: hrg_i3.p2, not unique enough 1601s -skipping training candidate: hrg_i4.p2, not unique enough 1601s -skipping training candidate: Eno_i5.p4, not unique enough 1601s -skipping training candidate: Eno_i1.p4, not unique enough 1601s -skipping training candidate: Eno_i2.p4, not unique enough 1601s -skipping training candidate: Eno_i6.p4, not unique enough 1601s -skipping training candidate: Eno_i3.p4, not unique enough 1601s -skipping training candidate: Klp10A_i2.p4, not unique enough 1601s -skipping training candidate: Klp10A_i4.p3, not unique enough 1601s -skipping training candidate: Klp10A_i5.p3, not unique enough 1601s -skipping training candidate: Klp10A_i3.p3, not unique enough 1601s -skipping training candidate: Klp10A_i1.p3, not unique enough 1601s -skipping training candidate: Calx_i8.p2, not unique enough 1601s -skipping training candidate: Calx_i9.p2, not unique enough 1601s -skipping training candidate: Calx_i7.p3, not unique enough 1601s -skipping training candidate: Calx_i2.p2, not unique enough 1601s -skipping training candidate: Calx_i6.p2, not unique enough 1601s -skipping training candidate: Calx_i3.p2, not unique enough 1601s -skipping training candidate: Calx_i5.p2, not unique enough 1601s -skipping training candidate: Calx_i4.p2, not unique enough 1601s -skipping training candidate: CG7564_i4.p2, not unique enough 1601s -skipping training candidate: CG7564_i3.p3, not unique enough 1601s -skipping training candidate: CG7564_i1.p2, not unique enough 1601s -skipping training candidate: CG7564_i1.p3, not unique enough 1601s -skipping training candidate: CG7564_i2.p4, not unique enough 1601s -skipping training candidate: CG7564_i2.p5, not unique enough 1601s -skipping training candidate: Gale_i1.p2, not unique enough 1601s -skipping training candidate: eIF5B_i1.p3, not unique enough 1601s -skipping training candidate: eIF5B_i5.p3, not unique enough 1601s -skipping training candidate: eIF5B_i3.p3, not unique enough 1601s -skipping training candidate: eIF5B_i2.p3, not unique enough 1601s -skipping training candidate: Dgk_i7.p4, not unique enough 1601s -skipping training candidate: Mgstl_i3.p2, not unique enough 1601s -skipping training candidate: AdipoR_i4.p2, not unique enough 1601s -skipping training candidate: CG6424_i3.p3, not unique enough 1601s -skipping training candidate: CG6424_i2.p3, not unique enough 1601s -skipping training candidate: CG6424_i1.p3, not unique enough 1601s -skipping training candidate: CG6424_i1.p4, not unique enough 1601s -skipping training candidate: Tm1_i13.p2, not unique enough 1601s -skipping training candidate: Tm1_i14.p2, not unique enough 1601s -skipping training candidate: Tm1_i5.p2, not unique enough 1601s -skipping training candidate: Dgk_i1.p4, not unique enough 1601s -skipping training candidate: Dgk_i7.p5, not unique enough 1601s -skipping training candidate: Dgk_i6.p4, not unique enough 1601s -skipping training candidate: Dgk_i2.p5, not unique enough 1601s -skipping training candidate: cdi_i1.p4, not unique enough 1601s -skipping training candidate: eff_i3.p1, not unique enough 1601s -skipping training candidate: eff_i1.p1, not unique enough 1601s -skipping training candidate: CG6852_i2.p1, not unique enough 1601s -skipping training candidate: eIF5B_i1.p4, not unique enough 1601s -skipping training candidate: eIF5B_i5.p4, not unique enough 1601s -skipping training candidate: eIF5B_i3.p4, not unique enough 1601s -skipping training candidate: eIF5B_i2.p4, not unique enough 1601s -skipping training candidate: Sec16_i6.p3, not unique enough 1601s -skipping training candidate: Sec16_i1.p5, not unique enough 1601s -skipping training candidate: Sec16_i5.p4, not unique enough 1601s -skipping training candidate: Sec16_i2.p5, not unique enough 1601s -skipping training candidate: Sec16_i3.p4, not unique enough 1601s -skipping training candidate: CG32082_i1.p2, not unique enough 1601s -skipping training candidate: CG32082_i3.p2, not unique enough 1601s -skipping training candidate: CG32082_i4.p2, not unique enough 1601s -skipping training candidate: CG3530_i2.p2, not unique enough 1601s -skipping training candidate: CG3530_i3.p2, not unique enough 1601s -skipping training candidate: Dgk_i2.p6, not unique enough 1601s -skipping training candidate: l(3)05822_i3.p4, not unique enough 1601s -skipping training candidate: l(3)05822_i2.p4, not unique enough 1601s -skipping training candidate: l(3)05822_i4.p4, not unique enough 1601s -skipping training candidate: sqd_i2.p2, not unique enough 1601s -skipping training candidate: CG7564_i3.p4, not unique enough 1601s -skipping training candidate: CG7564_i1.p4, not unique enough 1601s -skipping training candidate: CG7564_i2.p6, not unique enough 1601s -skipping training candidate: S-Lap3_i1.p2, not unique enough 1601s -skipping training candidate: S-Lap3_i3.p2, not unique enough 1601s -skipping training candidate: cdi_i1.p5, not unique enough 1601s -skipping training candidate: CG6091_i1.p2, not unique enough 1601s -skipping training candidate: CG6091_i4.p2, not unique enough 1601s -skipping training candidate: CG6091_i3.p2, not unique enough 1601s -skipping training candidate: Cdep_i1.p2, not unique enough 1601s -skipping training candidate: Cdep_i3.p2, not unique enough 1601s -skipping training candidate: Cnx99A_i4.p2, not unique enough 1601s -skipping training candidate: Cnx99A_i2.p2, not unique enough 1601s -skipping training candidate: Cnx99A_i1.p2, not unique enough 1601s -skipping training candidate: Sec16_i1.p6, not unique enough 1601s -skipping training candidate: Sec16_i5.p5, not unique enough 1601s -skipping training candidate: Sec16_i3.p5, not unique enough 1601s -skipping training candidate: ogre_i6.p2, not unique enough 1601s -skipping training candidate: CG6024_i2.p3, not unique enough 1601s -skipping training candidate: hrg_i3.p3, not unique enough 1601s -skipping training candidate: hrg_i4.p3, not unique enough 1601s -skipping training candidate: ATPsyn-d_i3.p2, not unique enough 1601s -skipping training candidate: CG6091_i4.p3, not unique enough 1601s -skipping training candidate: CG6091_i3.p3, not unique enough 1601s -skipping training candidate: ATPsyn-d_i2.p2, not unique enough 1601s -skipping training candidate: CG33970_i2.p2, not unique enough 1601s -skipping training candidate: CG33970_i1.p2, not unique enough 1601s -skipping training candidate: eIF5B_i1.p5, not unique enough 1601s -skipping training candidate: eIF5B_i5.p5, not unique enough 1601s -skipping training candidate: eIF5B_i3.p5, not unique enough 1601s -skipping training candidate: Aldh-III_i8.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i11.p2, not unique enough 1601s -skipping training candidate: CG13284_i5.p2, not unique enough 1601s -skipping training candidate: CG13284_i3.p2, not unique enough 1601s -skipping training candidate: CG13284_i1.p2, not unique enough 1601s -skipping training candidate: CG13284_i2.p2, not unique enough 1601s -skipping training candidate: Lip4_i2.p2, not unique enough 1601s -skipping training candidate: Lip4_i1.p2, not unique enough 1601s -skipping training candidate: Dgk_i1.p5, not unique enough 1601s -skipping training candidate: Dgk_i7.p7, not unique enough 1601s -skipping training candidate: Dgk_i6.p5, not unique enough 1601s -skipping training candidate: Dgk_i2.p7, not unique enough 1601s -skipping training candidate: Dgk_i5.p4, not unique enough 1601s -skipping training candidate: Dgk_i4.p4, not unique enough 1601s -skipping training candidate: Tm1_i13.p3, not unique enough 1601s -skipping training candidate: Tm1_i14.p3, not unique enough 1601s -skipping training candidate: Tm1_i5.p3, not unique enough 1601s -skipping training candidate: CG8312_i2.p3, not unique enough 1601s -skipping training candidate: CG8312_i2.p4, not unique enough 1601s -skipping training candidate: CG8312_i3.p3, not unique enough 1601s -skipping training candidate: CG8312_i3.p4, not unique enough 1601s -skipping training candidate: CG8312_i4.p3, not unique enough 1601s -skipping training candidate: CG8312_i4.p4, not unique enough 1601s -skipping training candidate: Klp10A_i2.p6, not unique enough 1601s -skipping training candidate: Klp10A_i4.p4, not unique enough 1601s -skipping training candidate: Klp10A_i5.p4, not unique enough 1601s -skipping training candidate: Klp10A_i3.p4, not unique enough 1601s -skipping training candidate: Klp10A_i1.p4, not unique enough 1601s -skipping training candidate: eff_i3.p2, not unique enough 1601s -skipping training candidate: eff_i1.p2, not unique enough 1601s -skipping training candidate: CG14995_i6.p4, not unique enough 1601s -skipping training candidate: CG14995_i5.p5, not unique enough 1601s -skipping training candidate: CG14995_i3.p4, not unique enough 1601s -skipping training candidate: CG14995_i1.p4, not unique enough 1601s -skipping training candidate: CG14995_i7.p4, not unique enough 1601s -skipping training candidate: CG6424_i3.p5, not unique enough 1601s -skipping training candidate: CG6424_i2.p4, not unique enough 1601s -skipping training candidate: CG6424_i1.p5, not unique enough 1601s -skipping training candidate: CG12581_i1.p3, not unique enough 1601s -skipping training candidate: CG32082_i1.p3, not unique enough 1601s -skipping training candidate: CG32082_i3.p3, not unique enough 1601s -skipping training candidate: CG32082_i4.p5, not unique enough 1601s -skipping training candidate: Cnx99A_i2.p3, not unique enough 1601s -skipping training candidate: Cnx99A_i1.p3, not unique enough 1601s -skipping training candidate: Cdep_i4.p2, not unique enough 1601s -skipping training candidate: Cdep_i3.p3, not unique enough 1601s -skipping training candidate: Sec16_i2.p6, not unique enough 1601s -skipping training candidate: CG33970_i2.p3, not unique enough 1601s -skipping training candidate: CG33970_i1.p3, not unique enough 1601s -skipping training candidate: Sec16_i4.p7, not unique enough 1601s -skipping training candidate: Sec16_i6.p5, not unique enough 1601s -skipping training candidate: Sec16_i1.p7, not unique enough 1601s -skipping training candidate: Sec16_i5.p6, not unique enough 1601s -skipping training candidate: Sec16_i2.p7, not unique enough 1601s -skipping training candidate: Sec16_i3.p6, not unique enough 1601s -skipping training candidate: mge_i3.p1, not unique enough 1601s -skipping training candidate: CG6024_i2.p4, not unique enough 1601s -skipping training candidate: Myo61F_i3.p2, not unique enough 1601s -skipping training candidate: Myo61F_i2.p2, not unique enough 1601s -skipping training candidate: Myo61F_i1.p2, not unique enough 1601s -skipping training candidate: Cdep_i1.p3, not unique enough 1601s -skipping training candidate: Cnx99A_i2.p4, not unique enough 1601s -skipping training candidate: Cnx99A_i1.p4, not unique enough 1601s -skipping training candidate: CG13887_i1.p2, not unique enough 1601s -skipping training candidate: CG13887_i4.p2, not unique enough 1601s -skipping training candidate: CG6145_i5.p2, not unique enough 1601s -skipping training candidate: CG6145_i4.p2, not unique enough 1601s -skipping training candidate: CG6145_i2.p2, not unique enough 1601s -skipping training candidate: CG6145_i1.p2, not unique enough 1601s -skipping training candidate: Calx_i8.p3, not unique enough 1601s -skipping training candidate: Calx_i9.p3, not unique enough 1601s -skipping training candidate: Calx_i7.p5, not unique enough 1601s -skipping training candidate: Calx_i2.p3, not unique enough 1601s -skipping training candidate: Calx_i6.p3, not unique enough 1601s -skipping training candidate: Calx_i3.p3, not unique enough 1601s -skipping training candidate: Calx_i5.p3, not unique enough 1601s -skipping training candidate: Calx_i4.p3, not unique enough 1601s -skipping training candidate: mge_i1.p2, not unique enough 1601s -skipping training candidate: AdipoR_i5.p2, not unique enough 1601s -skipping training candidate: AdipoR_i4.p3, not unique enough 1601s -skipping training candidate: AdipoR_i2.p2, not unique enough 1601s -skipping training candidate: AdipoR_i1.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i10.p3, not unique enough 1601s -skipping training candidate: Aldh-III_i6.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i1.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i2.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i9.p2, not unique enough 1601s -skipping training candidate: Aldh-III_i4.p2, not unique enough 1601s -skipping training candidate: Cdep_i1.p4, not unique enough 1601s -skipping training candidate: Cdep_i4.p3, not unique enough 1601s -skipping training candidate: Cdep_i3.p4, not unique enough 1601s -skipping training candidate: hrg_i3.p4, not unique enough 1601s -skipping training candidate: hrg_i4.p4, not unique enough 1601s -skipping training candidate: hrg_i2.p2, not unique enough 1601s -skipping training candidate: CG33125_i1.p3, not unique enough 1601s -skipping training candidate: Calx_i9.p4, not unique enough 1601s -skipping training candidate: mge_i3.p2, not unique enough 1601s -skipping training candidate: CG12581_i1.p4, not unique enough 1601s -skipping training candidate: Sec16_i6.p6, not unique enough 1601s -skipping training candidate: Sec16_i6.p7, not unique enough 1601s -skipping training candidate: Sec16_i1.p8, not unique enough 1601s -skipping training candidate: Sec16_i1.p9, not unique enough 1601s -skipping training candidate: Sec16_i5.p7, not unique enough 1601s -skipping training candidate: Sec16_i5.p8, not unique enough 1601s -skipping training candidate: Sec16_i2.p8, not unique enough 1601s -skipping training candidate: Sec16_i2.p9, not unique enough 1601s -skipping training candidate: Sec16_i3.p7, not unique enough 1601s -skipping training candidate: Sec16_i3.p8, not unique enough 1601s -skipping training candidate: Aldh-III_i4.p3, not unique enough 1601s -skipping training candidate: l(3)05822_i2.p5, not unique enough 1601s -skipping training candidate: CG6091_i1.p4, not unique enough 1601s -skipping training candidate: CG6091_i4.p4, not unique enough 1601s -skipping training candidate: CG6091_i3.p4, not unique enough 1601s -skipping training candidate: CanB2_i2.p2, not unique enough 1601s -skipping training candidate: IP3K1_i2.p2, not unique enough 1601s -skipping training candidate: Klp10A_i2.p8, not unique enough 1601s -skipping training candidate: Klp10A_i4.p5, not unique enough 1601s -skipping training candidate: Klp10A_i5.p5, not unique enough 1601s -skipping training candidate: Klp10A_i3.p5, not unique enough 1601s -skipping training candidate: Klp10A_i1.p6, not unique enough 1601s -skipping training candidate: AdipoR_i2.p3, not unique enough 1601s -skipping training candidate: Cdep_i1.p5, not unique enough 1601s -skipping training candidate: Cdep_i4.p4, not unique enough 1601s -skipping training candidate: Cdep_i3.p5, not unique enough 1601s -skipping training candidate: Est-6_i1.p2, not unique enough 1601s -skipping training candidate: Klp10A_i2.p9, not unique enough 1601s -skipping training candidate: Klp10A_i4.p6, not unique enough 1601s -skipping training candidate: Klp10A_i5.p6, not unique enough 1601s -skipping training candidate: Klp10A_i3.p6, not unique enough 1601s -skipping training candidate: Klp10A_i1.p7, not unique enough 1601s -skipping training candidate: l(3)05822_i3.p5, not unique enough 1601s -skipping training candidate: ADD1_i3.p4, not unique enough 1601s -skipping training candidate: AdipoR_i5.p3, not unique enough 1601s -skipping training candidate: Cnx99A_i4.p3, not unique enough 1601s -skipping training candidate: Cnx99A_i2.p5, not unique enough 1601s -skipping training candidate: Cnx99A_i1.p5, not unique enough 1601s -skipping training candidate: Myo61F_i3.p3, not unique enough 1601s -skipping training candidate: Myo61F_i2.p3, not unique enough 1601s -skipping training candidate: Myo61F_i1.p3, not unique enough 1601s -skipping training candidate: Myo61F_i3.p4, not unique enough 1601s -skipping training candidate: Myo61F_i2.p4, not unique enough 1601s -skipping training candidate: Myo61F_i1.p4, not unique enough 1601s -skipping training candidate: bic_i1.p3, not unique enough 1601s -skipping training candidate: CG10082_i1.p5, not unique enough 1601s -skipping training candidate: CG32082_i1.p4, not unique enough 1601s -skipping training candidate: CG32082_i3.p4, not unique enough 1601s -skipping training candidate: CG32082_i4.p6, not unique enough 1601s -skipping training candidate: Eno_i5.p6, not unique enough 1601s -skipping training candidate: Eno_i1.p6, not unique enough 1601s -skipping training candidate: Eno_i2.p5, not unique enough 1601s -skipping training candidate: Eno_i6.p5, not unique enough 1601s -skipping training candidate: Eno_i3.p5, not unique enough 1601s -skipping training candidate: Sec16_i4.p10, not unique enough 1601s -skipping training candidate: Sec16_i1.p10, not unique enough 1601s -skipping training candidate: Sec16_i3.p9, not unique enough 1601s -skipping training candidate: Dgk_i1.p6, not unique enough 1601s -skipping training candidate: Dgk_i7.p8, not unique enough 1601s -skipping training candidate: Dgk_i6.p6, not unique enough 1601s -skipping training candidate: Dgk_i2.p8, not unique enough 1601s -skipping training candidate: Dgk_i5.p5, not unique enough 1601s -skipping training candidate: Dgk_i4.p5, not unique enough 1601s -skipping training candidate: nmo_i6.p3, not unique enough 1601s -skipping training candidate: CG33970_i1.p4, not unique enough 1601s -skipping training candidate: sqd_i5.p3, not unique enough 1601s -skipping training candidate: Dgk_i1.p7, not unique enough 1601s -skipping training candidate: Dgk_i6.p7, not unique enough 1601s -skipping training candidate: His4r_i3.p1, not unique enough 1601s -skipping training candidate: His4r_i1.p1, not unique enough 1601s -skipping training candidate: His4r_i4.p1, not unique enough 1601s -skipping training candidate: Hsc70-1_i2.p5, not unique enough 1601s -skipping training candidate: Hsc70-1_i1.p4, not unique enough 1601s -skipping training candidate: hrg_i3.p5, not unique enough 1601s -skipping training candidate: hrg_i4.p6, not unique enough 1601s -skipping training candidate: CG8136_i1.p2, not unique enough 1601s -skipping training candidate: CG8136_i4.p2, not unique enough 1601s -skipping training candidate: CG8136_i3.p2, not unique enough 1601s -skipping training candidate: Myo61F_i3.p5, not unique enough 1601s -skipping training candidate: Myo61F_i2.p5, not unique enough 1601s -skipping training candidate: Myo61F_i1.p5, not unique enough 1601s -skipping training candidate: CG6091_i1.p5, not unique enough 1601s -skipping training candidate: CG6091_i4.p5, not unique enough 1601s -skipping training candidate: CG6091_i3.p5, not unique enough 1601s -skipping training candidate: CG6145_i5.p3, not unique enough 1601s -skipping training candidate: CG6145_i4.p3, not unique enough 1601s -skipping training candidate: CG6145_i2.p3, not unique enough 1601s -skipping training candidate: CG6145_i1.p3, not unique enough 1601s -skipping training candidate: gukh_i2.p3, not unique enough 1601s -skipping training candidate: sqd_i5.p4, not unique enough 1601s -skipping training candidate: CG33125_i1.p4, not unique enough 1601s -skipping training candidate: gukh_i2.p4, not unique enough 1601s 1601s -redundancy-minimized set includes 286 / 856 = 33.41% 1601s 1601s * [Sat Mar 16 21:30:49 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/get_top_longest_fasta_entries.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 1601s PCT_GC: 49.4 1601s * [Sat Mar 16 21:30:49 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores 1604s * [Sat Mar 16 21:30:52 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores 1623s * [Sat Mar 16 21:31:11 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 1624s Selecting best orfs 1624s * [Sat Mar 16 21:31:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement 1624s Training start codon pattern recognition* [Sat Mar 16 21:31:12 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 1625s * [Sat Mar 16 21:31:13 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores 1625s -round: 1 1643s -round: 2 1661s -round: 3 1679s -round: 4 1697s -round: 5 1715s * [Sat Mar 16 21:32:43 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 1715s -parsing scores 1737s * [Sat Mar 16 21:33:05 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : 1737s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1737s Execution halted 1737s * [Sat Mar 16 21:33:05 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc 1738s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1738s Execution halted 1738s * [Sat Mar 16 21:33:06 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : 1739s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1739s Execution halted 1739s * [Sat Mar 16 21:33:07 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : 1739s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1739s Execution halted 1739s * [Sat Mar 16 21:33:07 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/deplete_feature_noise.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced 1739s num features: 253 num_incorporate: 75 1739s -feature swap of score: -1.15948703606228 instead of -3.44783733338203 1739s -feature swap of score: -1.64858868703877 instead of -3.15957369506248 1739s -feature swap of score: -1.84921682631439 instead of -2.64654195516221 1739s -feature swap of score: -1.32478452245366 instead of -1.71607938531798 1739s -feature swap of score: -0.576054137577056 instead of -1.45490518944522 1739s -feature swap of score: -0.575478749559333 instead of -1.19342279146535 1739s -feature swap of score: 2.03844684531066 instead of -1.03000036539794 1739s -feature swap of score: -0.450648696691341 instead of -1.27874143919474 1739s -feature swap of score: 2.83932109321603 instead of -1.00316472450472 1739s -feature swap of score: -0.552801026020784 instead of -2.44641174097196 1739s -feature swap of score: 2.46051232407935 instead of -1.29172766987212 1739s -feature swap of score: -0.815281305010109 instead of -1.33368888759649 1739s -feature swap of score: 0.319578014495981 instead of -1.67750341369932 1739s -feature swap of score: 1.18877051299198 instead of -1.05655797642049 1739s -feature swap of score: 2.04992984581715 instead of -1.18205179352451 1739s -feature swap of score: -0.146380048193006 instead of -0.958178767498348 1739s -feature swap of score: -0.639348640102213 instead of -1.26256379792973 1740s -feature swap of score: 0.515412459881242 instead of -1.23223400925953 1740s -feature swap of score: 0.237731009296898 instead of -0.89353486597709 1740s -feature swap of score: 0.767267564522656 instead of -0.874091061267222 1740s -feature swap of score: 3.60868186324452 instead of -0.434352908397648 1740s -feature swap of score: 1.34535297233448 instead of -0.434191961906409 1740s -feature swap of score: 0.142472073141975 instead of -0.474200102026679 1740s -feature swap of score: 2.84585164444569 instead of -0.590780120723625 1740s -feature swap of score: -0.493030515906422 instead of -0.597134536274646 1740s -feature swap of score: -0.208441045685527 instead of -0.415994805783018 1740s -feature swap of score: 0.177796454310818 instead of -0.119336900093732 1740s -feature swap of score: 1.63409051831367 instead of 0.0237135555528417 1740s -feature swap of score: 1.53490812444396 instead of -0.174805217876581 1740s -feature swap of score: 0.772608644742238 instead of -0.0777520242693992 1740s -feature swap of score: 2.30977801064524 instead of -0.252594567355857 1740s -feature swap of score: 0.530017014035564 instead of -0.180540611181672 1740s -feature swap of score: 0.728823950783197 instead of -0.179164611406895 1740s -feature swap of score: -0.238122215542939 instead of -0.390565499559854 1740s -feature swap of score: 0.00975091295376107 instead of -0.651445354627928 1740s -feature swap of score: 1.00018450756267 instead of -0.618003482837443 1740s -feature swap of score: 0.661525185369691 instead of -0.153214546710276 1740s -feature swap of score: 1.99281736973102 instead of -0.317186480322445 1740s -feature swap of score: 0.39665422378862 instead of -0.00931803955118399 1740s -feature swap of score: 2.15556164753785 instead of -0.068164086340615 1740s -feature swap of score: 1.70804906992696 instead of -0.0193624773591394 1740s -feature swap of score: 0.72392116725844 instead of -1.24786135221253 1740s -feature swap of score: 1.77264258890623 instead of 0.313978376329229 1740s -feature swap of score: 1.26974261924121 instead of 0.321354733467996 1740s -feature swap of score: 0.696968658755029 instead of 0.304353599451399 1740s -feature swap of score: 3.80729793896385 instead of 0.254824884392955 1740s -feature swap of score: 1.52105297406327 instead of 0.39615137272736 1740s -feature swap of score: 2.68936341482088 instead of 0.475931278347427 1740s -feature swap of score: 1.56851760234112 instead of 0.5329874918689 1740s -feature swap of score: 2.10645017637443 instead of 0.40119220919184 1740s -feature swap of score: 4.06776868711762 instead of 0.257180581795856 1740s -feature swap of score: 1.48965911662099 instead of 0.559865838652429 1740s -feature swap of score: 5.47576986838788 instead of 0.799272762185617 1740s -feature swap of score: 3.19517813485205 instead of 0.785921534404079 1740s -num feature swaps: 54 1740s * [Sat Mar 16 21:33:08 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scoring.+-.pl --features_plus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores 1740s -round: 1 1758s -round: 2 1775s -round: 3 1792s -round: 4 1809s -round: 5 1827s * [Sat Mar 16 21:34:35 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/feature_scores_to_ROC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1827s -parsing scores 1847s * [Sat Mar 16 21:34:55 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/plot_ROC.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : 1848s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1848s Execution halted 1848s * [Sat Mar 16 21:34:56 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/compute_AUC.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc 1849s Error in library(ggplot2) : there is no package called ‘ggplot2’ 1849s Execution halted 1849s * [Sat Mar 16 21:34:57 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/PWM/make_seqLogo.Rscript /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : 1849s Error in library(seqLogo) : there is no package called ‘seqLogo’ 1849s Execution halted 1849s * [Sat Mar 16 21:34:57 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 1850s Refining start codon selections. 1850s -number of revised start positions: 13 1850s * [Sat Mar 16 21:34:58 2024] Running CMD: cp /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 1850s copying output to final output file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Sat Mar 16 21:34:58 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_bed.pl /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 1850s Making bed file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed 1850s * [Sat Mar 16 21:34:58 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 1851s Making pep file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep 1851s * [Sat Mar 16 21:34:59 2024] Running CMD: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/util/gff3_file_to_proteins.pl --gff3 /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 1852s Making cds file: /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds 1852s transdecoder is finished. See output files /tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* 1852s 1852s 1852s + ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 supertranscripts.gff3 transcripts.fasta 1852s 1852s -Warning [1], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG10082_i1.p3. 1852s -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i1.p3. 1852s -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i2.p3. 1852s -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i3.p3. 1852s -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i4.p5. 1852s -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6091_i4.p2. 1852s -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. 1852s -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. 1852s -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. 1852s -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. 1852s -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. 1852s -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. 1852s -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. 1852s -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. 1852s -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. 1852s -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i3.p5. 1852s -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i4.p4. 1852s -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Galk_i4.p2. 1852s -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Klp10A_i2.p3. 1852s -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Tm1_i14.p4. 1852s -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry bic_i2.p3. 1852s -Warning [22], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i1.p2. 1852s -Warning [23], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i3.p2. 1852s -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i4.p2. 1852s -Warning [25], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i1.p2. 1852s -Warning [26], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i2.p2. 1852s -Warning [27], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i3.p2. 1852s -Warning [28], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i3.p2. 1852s -Warning [29], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i6.p2. 1853s 1853s 1853s Done. 305 / 334 transcript orfs could be propagated to the genome 1853s 1853s + ../../util/gff3_file_to_bed.pl supertranscripts.wOrfs.gff3 1853s 1853s + ../../util/gff3_gene_to_gtf_format.pl supertranscripts.wOrfs.gff3 supertranscripts.fasta 1853s -missing faidx file: supertranscripts.fasta.fai, extracting positions directly. 1853s -Fasta_retriever:: begin initializing for supertranscripts.fasta 1853s -Fasta_retriever:: done initializing for supertranscripts.fasta 1853s 1855s + echo Done 1855s Done 1855s make[1]: Leaving directory '/tmp/autopkgtest.x2gTgS/autopkgtest_tmp/transdecoder/sample_data/supertranscripts_example' 1855s autopkgtest [21:35:03]: test run-tests: -----------------------] 1856s autopkgtest [21:35:04]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 1856s run-tests PASS 1857s autopkgtest [21:35:05]: @@@@@@@@@@@@@@@@@@@@ summary 1857s run-tests PASS 1867s Creating nova instance adt-noble-arm64-transdecoder-20240316-210408-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...