# 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/Ciona_savignyi.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-34 114.8 15.8 2.2e-17 62.3 3.2 3.2 3 tr|H2Z235|H2Z235_CIOSA DNA topoisomerase OS=Ciona savignyi O 1.1e-11 44.0 1.2 3.4e-11 42.4 1.2 1.9 1 tr|H2YY54|H2YY54_CIOSA DNA-(apurinic or apyrimidinic site) l Domain annotation for each sequence (and alignments): >> tr|H2Z235|H2Z235_CIOSA DNA topoisomerase OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.7 0.2 1.5 8.7e+03 22 32 .. 449 459 .. 449 461 .. 0.78 2 ! 60.7 0.9 1.2e-20 6.9e-17 1 44 [. 838 880 .. 838 881 .. 0.96 3 ! 62.3 3.2 3.8e-21 2.2e-17 2 44 .. 909 951 .. 908 952 .. 0.97 Alignments for each domain: == domain 1 score: -3.7 bits; conditional E-value: 1.5 zf-GRF 22 GRkFYkCpkgk 32 +R+F +C ++ tr|H2Z235|H2Z235_CIOSA 449 TRHFLACCHRD 459 69999998776 PP == domain 2 score: 60.7 bits; conditional E-value: 1.2e-20 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C+c ++av+ltvr++gpN GR+FYkC+k ++ C FF Wad+ tr|H2Z235|H2Z235_CIOSA 838 PMCNCSEMAVVLTVRREGPNTGRQFYKCSKQSG-GCDFFLWADD 880 79******************************8.8*******97 PP == domain 3 score: 62.3 bits; conditional E-value: 3.8e-21 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 +Ckc av++tv+k+gpNkGR FY+C k++ +qCgFF+W+d+ tr|H2Z235|H2Z235_CIOSA 909 MCKCNIQAVQRTVQKDGPNKGRVFYTCDKPRAEQCGFFEWEDA 951 8****************************************97 PP >> tr|H2YY54|H2YY54_CIOSA DNA-(apurinic or apyrimidinic site) lyase OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.4 1.2 5.9e-15 3.4e-11 1 42 [. 422 470 .. 422 472 .] 0.93 Alignments for each domain: == domain 1 score: 42.4 bits; conditional E-value: 5.9e-15 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42 plC+ + ++av ++v+k+g N GRkFY+C+ +++ + C +F+W+ tr|H2YY54|H2YY54_CIOSA 422 PLCPgHNEPAVERVVKKEGLNLGRKFYCCARPDGlksnpeARCQYFEWV 470 79**888*************************9999999999******7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 11592 (4231397 residues searched) Passed MSV filter: 545 (0.0470152); expected 231.8 (0.02) Passed bias filter: 226 (0.0194962); expected 231.8 (0.02) Passed Vit filter: 18 (0.0015528); expected 11.6 (0.001) Passed Fwd filter: 2 (0.000172533); expected 0.1 (1e-05) Initial search space (Z): 11592 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 3808.26 // [ok]