# 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/Danio_rerio.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-36 122.8 28.9 6.5e-19 68.3 1.9 4.1 4 tr|A0A2R8RKD0|A0A2R8RKD0_DANRE Nei-like DNA glycosylase 3 OS=Da 4.1e-35 120.1 14.0 4.5e-17 62.4 1.9 2.9 2 tr|X1WCF3|X1WCF3_DANRE DNA topoisomerase OS=Danio rerio 2.6e-14 53.5 4.3 2.6e-14 53.5 4.3 2.2 2 sp|Q502M8|ERI2_DANRE ERI1 exoribonuclease 2 OS=Danio 4.9e-14 52.6 2.2 1.5e-13 51.1 2.2 1.9 1 tr|F1Q865|F1Q865_DANRE DNA-(apurinic or apyrimidinic si 1.6e-13 51.0 3.2 9.4e-13 48.5 3.2 2.4 1 tr|A0A0R4IVN4|A0A0R4IVN4_DANRE Zinc finger, CCHC domain-contain 3.1e-09 37.3 9.0 1.3e-08 35.3 1.7 3.0 2 tr|A0A0R4IFG3|A0A0R4IFG3_DANRE Transcription termination factor Domain annotation for each sequence (and alignments): >> tr|A0A2R8RKD0|A0A2R8RKD0_DANRE Nei-like DNA glycosylase 3 OS=Danio rerio OX=7955 GN=neil3 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.5 0.0 0.91 3.9e+03 24 30 .. 209 215 .. 201 217 .. 0.83 2 ? 2.1 3.0 0.07 3e+02 4 32 .. 231 258 .. 229 263 .. 0.85 3 ! 65.6 5.6 1.1e-21 4.5e-18 1 43 [. 468 511 .. 468 513 .. 0.95 4 ! 68.3 1.9 1.5e-22 6.5e-19 1 44 [. 515 558 .. 515 559 .. 0.97 Alignments for each domain: == domain 1 score: -1.5 bits; conditional E-value: 0.91 zf-GRF 24 kFYkCpk 30 FYkC k tr|A0A2R8RKD0|A0A2R8RKD0_DANRE 209 LFYKCRK 215 59***65 PP == domain 2 score: 2.1 bits; conditional E-value: 0.07 zf-GRF 4 kcgrlavlltvrktgpNkGRkFYkCpkgk 32 +cg+ + + tv + g N GR Y C ++ tr|A0A2R8RKD0|A0A2R8RKD0_DANRE 231 NCGQCSGTVTVCRLGDN-GRMTYYCQRCQ 258 7**********988876.99999998877 PP == domain 3 score: 65.6 bits; conditional E-value: 1.1e-21 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 p Ck ++r++++++v k+g+NkGR+FY+C++++e qC+FF+Wad tr|A0A2R8RKD0|A0A2R8RKD0_DANRE 468 PCCKsHHRPCTQRVVTKEGENKGRQFYTCSLPRETQCNFFEWAD 511 5799899************************************9 PP == domain 4 score: 68.3 bits; conditional E-value: 1.5e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C +g++ v++tv k gpN+GR+FY+Cp+ +kqC+FF+Wa++ tr|A0A2R8RKD0|A0A2R8RKD0_DANRE 515 PMCHHGKRTVMKTVLKLGPNNGRNFYTCPVKMGKQCNFFQWAEN 558 79***************************************986 PP >> tr|X1WCF3|X1WCF3_DANRE DNA topoisomerase OS=Danio rerio OX=7955 GN=top3a PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 62.4 1.9 1.1e-20 4.5e-17 2 44 .. 814 853 .. 813 854 .. 0.96 2 ! 62.2 4.6 1.1e-20 4.9e-17 2 45 .] 901 944 .. 900 944 .. 0.97 Alignments for each domain: == domain 1 score: 62.4 bits; conditional E-value: 1.1e-20 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 C+cg+ a lltvrk+gpN+GR+FYkC++g+ C FF Wad+ tr|X1WCF3|X1WCF3_DANRE 814 VCNCGQDALLLTVRKEGPNQGRQFYKCNTGD---CKFFLWADQ 853 7*****************************9...********7 PP == domain 2 score: 62.2 bits; conditional E-value: 1.1e-20 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45 +C+c +++v++tv k+gpNkGR F++C k++++qCgFF+Wa+e+ tr|X1WCF3|X1WCF3_DANRE 901 MCNCNEPSVTRTVMKEGPNKGRMFHTCGKPRDQQCGFFQWANEN 944 8****************************************986 PP >> sp|Q502M8|ERI2_DANRE ERI1 exoribonuclease 2 OS=Danio rerio OX=7955 GN=eri2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.7 0.1 0.52 2.2e+03 32 43 .. 139 150 .. 135 152 .. 0.79 2 ! 53.5 4.3 6.1e-18 2.6e-14 1 42 [. 486 531 .. 486 534 .. 0.95 Alignments for each domain: == domain 1 score: -0.7 bits; conditional E-value: 0.52 zf-GRF 32 kekqCgFFkWad 43 + + C F W d sp|Q502M8|ERI2_DANRE 139 SAQLCAFVTWSD 150 4567******98 PP == domain 2 score: 53.5 bits; conditional E-value: 6.1e-18 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke....kqCgFFkWa 42 plC cgr+a++ltv + gpN+GR FY+Cp ++ + C FF+W+ sp|Q502M8|ERI2_DANRE 486 PLCVCGRRARRLTVGNGGPNHGRVFYCCPRRRSnthtHTCDFFQWE 531 79*****************************99999999******8 PP >> tr|F1Q865|F1Q865_DANRE DNA-(apurinic or apyrimidinic site) lyase OS=Danio rerio OX=7955 GN=apex2 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 51.1 2.2 3.6e-17 1.5e-13 1 44 [. 506 556 .. 506 557 .. 0.93 Alignments for each domain: == domain 1 score: 51.1 bits; conditional E-value: 3.6e-17 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWade 44 plCk + +++vl+tv+k gpN GR+F++C+ +++ + C+FF W+++ tr|F1Q865|F1Q865_DANRE 506 PLCKsHNEPCVLRTVKKAGPNLGRQFFVCARPQGhasnpqARCNFFAWVEK 556 79**777*************************9999999999******986 PP >> tr|A0A0R4IVN4|A0A0R4IVN4_DANRE Zinc finger, CCHC domain-containing 4 OS=Danio rerio OX=7955 GN=zcchc4 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.5 3.2 2.2e-16 9.4e-13 1 45 [] 27 72 .. 27 72 .. 0.94 Alignments for each domain: == domain 1 score: 48.5 bits; conditional E-value: 2.2e-16 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45 p C++g l++ +t + ++kGR FY+C+++++ k+C+FF+Wadek tr|A0A0R4IVN4|A0A0R4IVN4_DANRE 27 PRCPHGpALLFEKTGH-GEEEKGRRFYACSACRDrKDCNFFQWADEK 72 57****99*******7.8899************************95 PP >> tr|A0A0R4IFG3|A0A0R4IFG3_DANRE Transcription termination factor, RNA polymerase II OS=Danio rerio OX=7955 GN=ttf2 PE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 35.3 1.7 3.1e-12 1.3e-08 1 38 [. 4 42 .. 4 43 .. 0.97 2 ! 5.1 0.9 0.0082 35 13 44 .. 67 100 .. 53 101 .. 0.81 Alignments for each domain: == domain 1 score: 35.3 bits; conditional E-value: 3.1e-12 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38 +lC+ +g + l+t k+gpNkG+ FY+C +++ C+F tr|A0A0R4IFG3|A0A0R4IFG3_DANRE 4 VLCErHGSTCLLKTGVKEGPNKGKSFYVCTARDATPCNF 42 58*99*********************************9 PP == domain 2 score: 5.1 bits; conditional E-value: 0.0082 zf-GRF 13 tvrktgpNkGRkFYkCpkgke...kqCgFFkWade 44 + + + ++k + FY+C +gk k Cg W ++ tr|A0A0R4IFG3|A0A0R4IFG3_DANRE 67 IYN-KKQDKYKLFYRCMLGKTegqKWCGCVPWKEK 100 554.6678889********9988899998888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 25687 (13798380 residues searched) Passed MSV filter: 1301 (0.0506482); expected 513.7 (0.02) Passed bias filter: 485 (0.0188811); expected 513.7 (0.02) Passed Vit filter: 41 (0.00159614); expected 25.7 (0.001) Passed Fwd filter: 7 (0.000272511); expected 0.3 (1e-05) Initial search space (Z): 25687 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.09 # Mc/sec: 6899.19 // [ok]