# 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/Trichomonas_vaginalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.46 12.0 0.2 6.4 8.4 0.0 2.5 2 tr|A2GAQ6|A2GAQ6_TRIVA DDE superfamily endonuclease containi 1.5 10.4 0.1 1.5 10.4 0.1 4.0 7 tr|A2DAD1|A2DAD1_TRIVA Surface antigen BspA-like OS=Trichomo 2.6 9.6 5.9 17 7.0 2.2 2.5 2 tr|A2EA27|A2EA27_TRIVA Uncharacterized protein OS=Trichomona Domain annotation for each sequence (and alignments): >> tr|A2GAQ6|A2GAQ6_TRIVA DDE superfamily endonuclease containing protein OS=Trichomonas vaginalis OX=5722 GN=TVAG_3236 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.4 0.0 0.00038 6.4 22 36 .. 81 95 .. 74 96 .. 0.86 2 ? 0.8 0.0 0.092 1.5e+03 21 31 .. 165 175 .. 158 179 .. 0.76 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 0.00038 zf-GRF 22 GRkFYkCpkgkekqC 36 GR FY Cpk + C tr|A2GAQ6|A2GAQ6_TRIVA 81 GRRFYLCPKDDSDLC 95 9********987666 PP == domain 2 score: 0.8 bits; conditional E-value: 0.092 zf-GRF 21 kGRkFYkCpkg 31 + + +++Cp tr|A2GAQ6|A2GAQ6_TRIVA 165 EPKRYFACPGE 175 6699*****76 PP >> tr|A2DAD1|A2DAD1_TRIVA Surface antigen BspA-like OS=Trichomonas vaginalis OX=5722 GN=TVAG_477080 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.6 0.1 1 1.7e+04 23 32 .. 29 38 .. 27 44 .. 0.75 2 ? 10.4 0.1 9e-05 1.5 22 38 .. 51 69 .. 49 71 .. 0.92 3 ? -3.7 0.0 2.3 3.8e+04 24 31 .. 99 106 .. 98 108 .. 0.73 4 ? -1.9 0.1 0.62 1e+04 2 8 .. 146 152 .. 145 160 .. 0.76 5 ? -1.9 0.1 0.61 1e+04 24 30 .. 168 174 .. 165 177 .. 0.81 6 ? -2.1 0.1 0.73 1.2e+04 24 30 .. 191 197 .. 191 200 .. 0.76 7 ? -2.1 0.1 0.73 1.2e+04 24 30 .. 214 220 .. 214 223 .. 0.76 Alignments for each domain: == domain 1 score: -2.6 bits; conditional E-value: 1 zf-GRF 23 RkFYkCpkgk 32 R+F C++ tr|A2DAD1|A2DAD1_TRIVA 29 RAFQYCSNLT 38 7888898765 PP == domain 2 score: 10.4 bits; conditional E-value: 9e-05 zf-GRF 22 GRkFYkCpkgke..kqCgF 38 G +FY Cp +e +C+F tr|A2DAD1|A2DAD1_TRIVA 51 GHAFYGCPSIQEftLNCNF 69 899*********9989**9 PP == domain 3 score: -3.7 bits; conditional E-value: 2.3 zf-GRF 24 kFYkCpkg 31 +F Cp+ tr|A2DAD1|A2DAD1_TRIVA 99 AFNNCPLL 106 58889976 PP == domain 4 score: -1.9 bits; conditional E-value: 0.62 zf-GRF 2 lCkcgrl 8 +C+c l tr|A2DAD1|A2DAD1_TRIVA 146 FCNCKSL 152 7999855 PP == domain 5 score: -1.9 bits; conditional E-value: 0.61 zf-GRF 24 kFYkCpk 30 +FY C tr|A2DAD1|A2DAD1_TRIVA 168 AFYDCKS 174 6****75 PP == domain 6 score: -2.1 bits; conditional E-value: 0.73 zf-GRF 24 kFYkCpk 30 +FY C tr|A2DAD1|A2DAD1_TRIVA 191 AFYDCKS 197 59***75 PP == domain 7 score: -2.1 bits; conditional E-value: 0.73 zf-GRF 24 kFYkCpk 30 +FY C tr|A2DAD1|A2DAD1_TRIVA 214 AFYDCKS 220 59***75 PP >> tr|A2EA27|A2EA27_TRIVA Uncharacterized protein OS=Trichomonas vaginalis OX=5722 GN=TVAG_483840 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 3.5 0.1 0.013 2.2e+02 17 29 .. 90 102 .. 78 108 .. 0.79 2 ? 7.0 2.2 0.001 17 20 38 .. 294 315 .. 284 317 .. 0.89 Alignments for each domain: == domain 1 score: 3.5 bits; conditional E-value: 0.013 zf-GRF 17 tgpNkGRkFYkCp 29 ++N++ FY+C tr|A2EA27|A2EA27_TRIVA 90 FPENETATFYRCH 102 579*********6 PP == domain 2 score: 7.0 bits; conditional E-value: 0.001 zf-GRF 20 NkGRkFYkCpkgke...kqCgF 38 Nk F+ Cp++++ k C+F tr|A2EA27|A2EA27_TRIVA 294 NKFNFFFNCPTPSNvifKGCNF 315 55566****************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 50190 (17055200 residues searched) Passed MSV filter: 1572 (0.031321); expected 1003.8 (0.02) Passed bias filter: 937 (0.0186691); expected 1003.8 (0.02) Passed Vit filter: 54 (0.00107591); expected 50.2 (0.001) Passed Fwd filter: 4 (7.96972e-05); expected 0.5 (1e-05) Initial search space (Z): 50190 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.11 # Mc/sec: 6977.13 // [ok]