# 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/Macaca_mulatta.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-37 128.2 10.4 4.6e-20 71.7 0.7 4.3 5 tr|F6T3Q0|F6T3Q0_MACMU Nei like DNA glycosylase 3 OS=Macaca 1.7e-36 124.3 20.9 1.9e-19 69.7 4.0 3.3 3 tr|F6Z6P9|F6Z6P9_MACMU DNA topoisomerase OS=Macaca mulatta O 2e-17 63.2 8.2 2e-17 63.2 8.2 2.4 2 tr|F7APV0|F7APV0_MACMU ERI1 exoribonuclease family member 2 3.2e-15 56.2 2.2 3.2e-15 56.2 2.2 2.9 2 tr|F6Q4X7|F6Q4X7_MACMU Zinc finger CCHC domain-containing pr 1.9e-13 50.5 0.3 4.8e-13 49.2 0.3 1.7 1 tr|F7HFN8|F7HFN8_MACMU Zinc finger GRF-type containing 1 OS= 4.9e-13 49.2 0.5 1.4e-12 47.7 0.5 1.8 1 tr|F6VBU4|F6VBU4_MACMU DNA-(apurinic or apyrimidinic site) l 6.3e-06 26.4 3.1 6.3e-06 26.4 3.1 2.5 2 tr|F7CPX6|F7CPX6_MACMU Uncharacterized protein OS=Macaca mul Domain annotation for each sequence (and alignments): >> tr|F6T3Q0|F6T3Q0_MACMU Nei like DNA glycosylase 3 OS=Macaca mulatta OX=9544 GN=NEIL3 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.4 0.1 4.3 1.3e+04 25 30 .. 229 234 .. 228 235 .. 0.80 2 ? -1.6 7.1 1.2 3.5e+03 4 33 .. 250 278 .. 248 282 .. 0.75 3 ? -2.4 0.1 2.1 6.4e+03 28 37 .. 469 478 .. 468 493 .. 0.87 4 ! 71.7 0.7 1.5e-23 4.6e-20 2 44 .. 503 546 .. 502 547 .. 0.93 5 ! 69.4 3.2 7.9e-23 2.4e-19 1 44 [. 549 592 .. 549 593 .. 0.97 Alignments for each domain: == domain 1 score: -3.4 bits; conditional E-value: 4.3 zf-GRF 25 FYkCpk 30 FY+C k tr|F6T3Q0|F6T3Q0_MACMU 229 FYRCRK 234 9***65 PP == domain 2 score: -1.6 bits; conditional E-value: 1.2 zf-GRF 4 kcg.rlavlltvrktgpNkGRkFYkCpkgke 33 +cg +++ + r g N+ R Y Cp +++ tr|F6T3Q0|F6T3Q0_MACMU 250 NCGqCHCRITVCR-FGDNN-RMTYFCPRCQK 278 6994456666665.99997.888889*9986 PP == domain 3 score: -2.4 bits; conditional E-value: 2.1 zf-GRF 28 CpkgkekqCg 37 C+ ++ k+C+ tr|F6T3Q0|F6T3Q0_MACMU 469 CSSPDLKSCN 478 8899889997 PP == domain 4 score: 71.7 bits; conditional E-value: 1.5e-23 zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 C + rl+vl++vrk+g+NkGR+FY+Cp+++e+qCgFF+Wad tr|F6T3Q0|F6T3Q0_MACMU 503 RCSkHSRLCVLRVVRKDGENKGRQFYACPLPREAQCGFFEWADL 546 688577************************************95 PP == domain 5 score: 69.4 bits; conditional E-value: 7.9e-23 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C++g+++ ++tv k gpN+G++F++Cp+gkekqC+FF+Wa++ tr|F6T3Q0|F6T3Q0_MACMU 549 PFCNHGKRSIMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAEN 592 68***************************************986 PP >> tr|F6Z6P9|F6Z6P9_MACMU DNA topoisomerase OS=Macaca mulatta OX=9544 GN=TOP3A PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.3 1 3.1e+03 3 16 .. 658 672 .. 656 675 .. 0.75 2 ! 64.0 3.4 3.8e-21 1.1e-17 1 44 [. 811 851 .. 811 852 .. 0.96 3 ! 69.7 4.0 6.3e-23 1.9e-19 2 45 .] 896 939 .. 895 939 .. 0.97 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 1 zf-GRF 3 Ck.cgrlavlltvrk 16 C+ c + vl+t ++ tr|F6Z6P9|F6Z6P9_MACMU 658 CPqCNKDMVLKTKKN 672 888889999988864 PP == domain 2 score: 64.0 bits; conditional E-value: 3.8e-21 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 ++C+cg++avlltvrk+gpN+GR+F+kC+ g+ C+FF Wad+ tr|F6Z6P9|F6Z6P9_MACMU 811 VTCNCGQEAVLLTVRKEGPNQGRQFFKCNGGS---CNFFLWADS 851 58****************************99...********7 PP == domain 3 score: 69.7 bits; conditional E-value: 6.3e-23 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45 +C c ++av++tv+k+gpNkGR+F++C+k++e+qCgFF+W+de+ tr|F6Z6P9|F6Z6P9_MACMU 896 SCLCSQPAVTRTVQKDGPNKGRQFHTCAKPREQQCGFFQWVDEN 939 7*****************************************96 PP >> tr|F7APV0|F7APV0_MACMU ERI1 exoribonuclease family member 2 OS=Macaca mulatta OX=9544 GN=ERI2 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.1 0.1 0.4 1.2e+03 33 43 .. 50 61 .. 46 63 .. 0.76 2 ! 63.2 8.2 6.6e-21 2e-17 1 44 [. 501 548 .. 501 549 .. 0.97 Alignments for each domain: == domain 1 score: -0.1 bits; conditional E-value: 0.4 zf-GRF 33 e.kqCgFFkWad 43 e k C F W d tr|F7APV0|F7APV0_MACMU 50 EvKLCAFVTWSD 61 4488******98 PP == domain 2 score: 63.2 bits; conditional E-value: 6.6e-21 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke....kqCgFFkWade 44 plCkcgr++++l+v+++gpN+G+ FY+Cp gk+ k+Cg+FkW+++ tr|F7APV0|F7APV0_MACMU 501 PLCKCGRRSKRLVVSNNGPNHGKVFYCCPIGKYqenrKCCGYFKWEQT 548 79******************************999***********96 PP >> tr|F6Q4X7|F6Q4X7_MACMU Zinc finger CCHC domain-containing protein 4 OS=Macaca mulatta OX=9544 GN=ZCCHC4 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 56.2 2.2 1.1e-18 3.2e-15 1 45 [] 38 82 .. 38 82 .. 0.96 2 ? -5.1 4.2 7 2.1e+04 21 36 .. 404 417 .. 393 422 .. 0.78 Alignments for each domain: == domain 1 score: 56.2 bits; conditional E-value: 1.1e-18 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45 plC++g +l+++++ +g++++R FY+C+++++ k+C+FF+W+dek tr|F6Q4X7|F6Q4X7_MACMU 38 PLCPHGpTLLFVKVT--QGKEETRRFYACSACRDrKDCNFFQWEDEK 82 79*************..6***************************95 PP == domain 2 score: -5.1 bits; conditional E-value: 7 zf-GRF 21 kGRkFYkCpkgkekqC 36 GRk+ C ++k+ C tr|F6Q4X7|F6Q4X7_MACMU 404 DGRKWNHCFLCKK--C 417 6888888888886..5 PP >> tr|F7HFN8|F7HFN8_MACMU Zinc finger GRF-type containing 1 OS=Macaca mulatta OX=9544 GN=ZGRF1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 49.2 0.3 1.6e-16 4.8e-13 1 43 [. 1346 1388 .. 1346 1390 .. 0.95 Alignments for each domain: == domain 1 score: 49.2 bits; conditional E-value: 1.6e-16 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 p+C + ++a+l v+k+gpNkGR FY+C +k C FFkW + tr|F7HFN8|F7HFN8_MACMU 1346 PSCHHSQPAKLVMVKKEGPNKGRLFYTCDGPKADRCKFFKWLE 1388 68***************************************87 PP >> tr|F6VBU4|F6VBU4_MACMU DNA-(apurinic or apyrimidinic site) lyase OS=Macaca mulatta OX=9544 GN=APEX2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 47.7 0.5 4.7e-16 1.4e-12 1 42 [. 467 515 .. 467 517 .. 0.94 Alignments for each domain: == domain 1 score: 47.7 bits; conditional E-value: 4.7e-16 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42 plC + +++v++tv+k gpN GR FY C+ +++ + C+FF W tr|F6VBU4|F6VBU4_MACMU 467 PLCGgHREPCVMRTVKKPGPNLGRRFYMCARPRGpptdpsSRCNFFLWS 515 6899777***************************99999999******5 PP >> tr|F7CPX6|F7CPX6_MACMU Uncharacterized protein OS=Macaca mulatta OX=9544 GN=TTF2 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.4 3.1 2.1e-09 6.3e-06 2 38 .. 5 39 .. 4 41 .. 0.89 2 ? -0.5 0.4 0.52 1.6e+03 22 43 .. 72 96 .. 66 98 .. 0.73 Alignments for each domain: == domain 1 score: 26.4 bits; conditional E-value: 2.1e-09 zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38 C+ +g++++l+t ++gpNkG+ FY+C + C F tr|F7CPX6|F7CPX6_MACMU 5 RCPeHGTFCFLKTGVRDGPNKGKSFYVCRADT---CSF 39 6999*********999************8765...776 PP == domain 2 score: -0.5 bits; conditional E-value: 0.52 zf-GRF 22 GRkFYkCpkgke...kqCgFFkWad 43 R F++C k + Cg W d tr|F7CPX6|F7CPX6_MACMU 72 YRLFFRCIRSKAegkHWCGSIPWQD 96 599****766655566799888877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 21211 (10888574 residues searched) Passed MSV filter: 1081 (0.0509641); expected 424.2 (0.02) Passed bias filter: 402 (0.0189524); expected 424.2 (0.02) Passed Vit filter: 21 (0.000990052); expected 21.2 (0.001) Passed Fwd filter: 7 (0.000330017); expected 0.2 (1e-05) Initial search space (Z): 21211 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.10u 0.01s 00:00:00.11 Elapsed: 00:00:00.06 # Mc/sec: 8166.43 // [ok]