# 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/Drosophila_melanogaster.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-38 130.2 18.6 4.6e-21 74.3 2.1 3.0 3 sp|Q9NG98|TOP3A_DROME DNA topoisomerase 3-alpha OS=Drosophi ------ inclusion threshold ------ 0.04 13.6 0.2 0.098 12.4 0.2 1.7 1 tr|A8DY89|A8DY89_DROME Uncharacterized protein OS=Drosophila Domain annotation for each sequence (and alignments): >> sp|Q9NG98|TOP3A_DROME DNA topoisomerase 3-alpha OS=Drosophila melanogaster OX=7227 GN=Top3alpha PE=2 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -4.2 0.4 2 1.4e+04 26 33 .. 656 663 .. 656 664 .. 0.79 2 ! 66.3 2.8 2.1e-22 1.4e-18 1 44 [. 1033 1075 .. 1033 1076 .. 0.97 3 ! 74.3 2.1 6.6e-25 4.6e-21 1 44 [. 1150 1192 .. 1150 1193 .. 0.95 Alignments for each domain: == domain 1 score: -4.2 bits; conditional E-value: 2 zf-GRF 26 YkCpkgke 33 ++Cpk++e sp|Q9NG98|TOP3A_DROME 656 FQCPKCNE 663 68999986 PP == domain 2 score: 66.3 bits; conditional E-value: 2.1e-22 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 +lC+ c+++a+++tvrk+gpN GR +YkCpk++e C+FF+Wade sp|Q9NG98|TOP3A_DROME 1033 VLCTgCQQPARQNTVRKNGPNLGRLYYKCPKPDE--CNFFQWADE 1075 68*******************************9..********8 PP == domain 3 score: 74.3 bits; conditional E-value: 6.6e-25 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 ++C+cg+la++ltvrk+gpN+GR FY+Cp++++ +CgFFkW de sp|Q9NG98|TOP3A_DROME 1150 VMCNCGQLASQLTVRKDGPNQGRPFYACPTREK-SCGFFKWGDE 1192 69*****************************95.9********8 PP >> tr|A8DY89|A8DY89_DROME Uncharacterized protein OS=Drosophila melanogaster OX=7227 GN=CG34220 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.4 0.2 1.4e-05 0.098 5 43 .. 668 706 .. 665 708 .. 0.82 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 1.4e-05 zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgke..kqCgFFkWad 43 c ++a +v + pN+ R +Y C +g+ ++C W d tr|A8DY89|A8DY89_DROME 668 CAGRADGSIV--QDPNHCRRYYECRAGRRllRKCRAGLWYD 706 7788888999..59*************99887786666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 13786 (7394964 residues searched) Passed MSV filter: 629 (0.045626); expected 275.7 (0.02) Passed bias filter: 290 (0.0210358); expected 275.7 (0.02) Passed Vit filter: 21 (0.00152328); expected 13.8 (0.001) Passed Fwd filter: 2 (0.000145075); expected 0.1 (1e-05) Initial search space (Z): 13786 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.05 # Mc/sec: 6655.47 // [ok]