# 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/Caenorhabditis_elegans.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-14 52.3 4.2 1e-13 51.2 4.2 1.6 1 sp|O61660|TOP3_CAEEL DNA topoisomerase 3 OS=Caenorhabditis e Domain annotation for each sequence (and alignments): >> sp|O61660|TOP3_CAEEL DNA topoisomerase 3 OS=Caenorhabditis elegans OX=6239 GN=top-3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 51.2 4.2 5.2e-18 1e-13 2 42 .. 715 759 .] 714 759 .] 0.91 Alignments for each domain: == domain 1 score: 51.2 bits; conditional E-value: 5.2e-18 zf-GRF 2 lCkcg..rlavlltvrktgpNkGRkFYkCpkgke..kqCgFFkWa 42 +C+c +av+++v+k+gpNkG+kFY+C+++ ++C+FFkWa sp|O61660|TOP3_CAEEL 715 FCQCPepMRAVTKVVQKEGPNKGKKFYTCSLPYTssEKCNFFKWA 759 688876689**********************9888889******7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 20008 (8229220 residues searched) Passed MSV filter: 1032 (0.0515794); expected 400.2 (0.02) Passed bias filter: 444 (0.0221911); expected 400.2 (0.02) Passed Vit filter: 32 (0.00159936); expected 20.0 (0.001) Passed Fwd filter: 1 (4.998e-05); expected 0.2 (1e-05) Initial search space (Z): 20008 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.06 # Mc/sec: 6171.91 // [ok]