# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/zf-GRF.hmm.txt # target sequence database: proteomes/Amphimedon_queenslandica.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: zf-GRF [M=45] Accession: PF06839.12 Description: GRF zinc finger Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-30 105.3 10.2 9.1e-15 55.7 0.9 3.0 2 tr|A0A1X7UTP9|A0A1X7UTP9_AMPQE DNA topoisomerase OS=Amphimedon 2.1e-12 48.2 2.7 4.8e-12 47.0 2.7 1.7 1 tr|A0A1X7VD76|A0A1X7VD76_AMPQE DNA-(apurinic or apyrimidinic si ------ inclusion threshold ------ 0.011 17.1 0.7 0.016 16.5 0.7 1.2 1 tr|A0A1X7TBK2|A0A1X7TBK2_AMPQE Uncharacterized protein OS=Amphi 0.025 15.9 0.7 0.05 14.9 0.7 1.5 1 tr|A0A1X7T2K3|A0A1X7T2K3_AMPQE Uncharacterized protein OS=Amphi 0.035 15.4 0.0 0.053 14.9 0.0 1.2 1 tr|A0A1X7VSR7|A0A1X7VSR7_AMPQE Uncharacterized protein OS=Amphi 0.062 14.6 0.7 0.15 13.4 0.7 1.6 1 tr|A0A1X7TBJ0|A0A1X7TBJ0_AMPQE Uncharacterized protein OS=Amphi 0.099 14.0 0.5 0.14 13.5 0.5 1.2 1 tr|A0A1X7UY93|A0A1X7UY93_AMPQE Uncharacterized protein OS=Amphi 0.63 11.4 0.5 1.3 10.4 0.5 1.5 1 tr|A0A1X7UGJ6|A0A1X7UGJ6_AMPQE Uncharacterized protein OS=Amphi Domain annotation for each sequence (and alignments): >> tr|A0A1X7UTP9|A0A1X7UTP9_AMPQE DNA topoisomerase OS=Amphimedon queenslandica OX=400682 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 55.7 0.9 1.7e-18 9.1e-15 2 44 .. 806 850 .. 805 851 .. 0.90 2 ! 53.1 2.7 1.1e-17 6.1e-14 2 44 .. 909 950 .. 908 951 .. 0.97 Alignments for each domain: == domain 1 score: 55.7 bits; conditional E-value: 1.7e-18 zf-GRF 2 lCkcgrlavlltvrk.tgpNkGRkFYkCpkgke.kqCgFFkWade 44 C+cg +a lltvr+ + NkGR+FYkC+k++e +C+FF Wade tr|A0A1X7UTP9|A0A1X7UTP9_AMPQE 806 VCNCGIEAILLTVRNeQSINKGRQFYKCAKRDEeGKCNFFLWADE 850 7************982456*************9999********8 PP == domain 2 score: 53.1 bits; conditional E-value: 1.1e-17 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 +C cg +av++tv+ g N+GR F +Cpk++++qCgFF+W d+ tr|A0A1X7UTP9|A0A1X7UTP9_AMPQE 909 TCRCGLPAVQRTVQ-SGNNQGRLFRTCPKPRDEQCGFFEWMDN 950 7************8.**************************97 PP >> tr|A0A1X7VD76|A0A1X7VD76_AMPQE DNA-(apurinic or apyrimidinic site) lyase OS=Amphimedon queenslandica OX=400682 PE=3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 47.0 2.7 8.8e-16 4.8e-12 1 42 [. 389 437 .. 389 438 .] 0.93 Alignments for each domain: == domain 1 score: 47.0 bits; conditional E-value: 8.8e-16 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42 plC + ++avl++v+k gpN+ RkFY+C +++ ++C+FFkW+ tr|A0A1X7VD76|A0A1X7VD76_AMPQE 389 PLCSgHKEPAVLRVVKKPGPNHNRKFYVCGRPDGskhdpnASCNFFKWC 437 69*9888**********************9999888999999******9 PP >> tr|A0A1X7TBK2|A0A1X7TBK2_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 16.5 0.7 2.9e-06 0.016 2 23 .. 69 90 .. 68 91 .. 0.94 Alignments for each domain: == domain 1 score: 16.5 bits; conditional E-value: 2.9e-06 zf-GRF 2 lCkcgrlavlltvrktgpNkGR 23 C c ++++ +v+++g+N+G+ tr|A0A1X7TBK2|A0A1X7TBK2_AMPQE 69 YCLCKHRSTTHVVQRNGKNQGQ 90 5*******************96 PP >> tr|A0A1X7T2K3|A0A1X7T2K3_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 14.9 0.7 9.2e-06 0.05 2 23 .. 176 197 .. 175 198 .. 0.94 Alignments for each domain: == domain 1 score: 14.9 bits; conditional E-value: 9.2e-06 zf-GRF 2 lCkcgrlavlltvrktgpNkGR 23 C c ++++ +v+++g+N+G+ tr|A0A1X7T2K3|A0A1X7T2K3_AMPQE 176 YCLCKHRSTTHVVQRNGKNQGQ 197 5*******************96 PP >> tr|A0A1X7VSR7|A0A1X7VSR7_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 14.9 0.0 9.8e-06 0.053 10 29 .. 59 78 .. 55 84 .. 0.88 Alignments for each domain: == domain 1 score: 14.9 bits; conditional E-value: 9.8e-06 zf-GRF 10 vlltvrktgpNkGRkFYkCp 29 +l+vrk+++ R FY+C tr|A0A1X7VSR7|A0A1X7VSR7_AMPQE 59 NVLVVRKEREQTNRDFYVCR 78 689****************6 PP >> tr|A0A1X7TBJ0|A0A1X7TBJ0_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.4 0.7 2.7e-05 0.15 2 23 .. 446 467 .. 445 468 .. 0.94 Alignments for each domain: == domain 1 score: 13.4 bits; conditional E-value: 2.7e-05 zf-GRF 2 lCkcgrlavlltvrktgpNkGR 23 C c ++++ +v+++g+N+G+ tr|A0A1X7TBJ0|A0A1X7TBJ0_AMPQE 446 YCLCKHRSTTHVVQRNGKNQGQ 467 5*******************96 PP >> tr|A0A1X7UY93|A0A1X7UY93_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.5 0.5 2.5e-05 0.14 15 44 .. 28 53 .. 26 54 .. 0.87 Alignments for each domain: == domain 1 score: 13.5 bits; conditional E-value: 2.5e-05 zf-GRF 15 rktgpNkGRkFYkCpkgkekqCgFFkWade 44 +++g NkG ++kC g F W d+ tr|A0A1X7UY93|A0A1X7UY93_AMPQE 28 KNDGSNKGMTYFKCKDKH----GVFVWRDK 53 689***********9888....68999886 PP >> tr|A0A1X7UGJ6|A0A1X7UGJ6_AMPQE Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.4 0.5 0.00024 1.3 26 44 .. 478 493 .. 477 494 .. 0.90 Alignments for each domain: == domain 1 score: 10.4 bits; conditional E-value: 0.00024 zf-GRF 26 YkCpkgkekqCgFFkWade 44 ++Cp g++ gFFkW d+ tr|A0A1X7UGJ6|A0A1X7UGJ6_AMPQE 478 WRCPEGRK---GFFKWTDS 493 58*****9...******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 43435 (14716620 residues searched) Passed MSV filter: 1789 (0.041188); expected 868.7 (0.02) Passed bias filter: 859 (0.0197767); expected 868.7 (0.02) Passed Vit filter: 68 (0.00156556); expected 43.4 (0.001) Passed Fwd filter: 10 (0.000230229); expected 0.4 (1e-05) Initial search space (Z): 43435 [actual number of targets] Domain search space (domZ): 8 [number of targets reported over threshold] # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.09 # Mc/sec: 7358.31 // [ok]