# 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/Mus_musculus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-39 132.1 20.0 2.5e-20 72.6 4.3 3.2 3 sp|O70157|TOP3A_MOUSE DNA topoisomerase 3-alpha OS=Mus muscu 3.7e-37 126.5 10.7 9e-21 74.0 0.8 4.5 4 sp|Q8K203|NEIL3_MOUSE Endonuclease 8-like 3 OS=Mus musculus 2.8e-18 66.0 7.9 2.8e-18 66.0 7.9 2.3 2 sp|Q5BKS4|ERI2_MOUSE ERI1 exoribonuclease 2 OS=Mus musculus 8.2e-16 58.1 2.9 8.2e-16 58.1 2.9 2.7 2 sp|Q8BKW4|ZCHC4_MOUSE Zinc finger CCHC domain-containing pro 3.1e-14 53.1 1.4 3.1e-14 53.1 1.4 2.2 2 sp|Q0VGT4|ZGRF1_MOUSE Protein ZGRF1 OS=Mus musculus OX=10090 8.6e-14 51.7 1.2 2.1e-13 50.4 1.2 1.7 1 sp|Q68G58|APEX2_MOUSE DNA-(apurinic or apyrimidinic site) ly 7.4e-07 29.5 2.7 7.4e-07 29.5 2.7 2.7 2 sp|Q5NC05|TTF2_MOUSE Transcription termination factor 2 OS= Domain annotation for each sequence (and alignments): >> sp|O70157|TOP3A_MOUSE DNA topoisomerase 3-alpha OS=Mus musculus OX=10090 GN=Top3a PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.0 0.2 3.2 1e+04 3 15 .. 658 671 .. 657 674 .. 0.69 2 ! 69.1 2.6 9.7e-23 3.1e-19 1 44 [. 813 853 .. 813 854 .. 0.96 3 ! 72.6 4.3 7.9e-24 2.5e-20 2 45 .] 898 941 .. 897 941 .. 0.97 Alignments for each domain: == domain 1 score: -3.0 bits; conditional E-value: 3.2 zf-GRF 3 Ck.cgrlavlltvr 15 C+ c + vl+t + sp|O70157|TOP3A_MOUSE 658 CPqCNKDMVLKTKK 671 77788888877764 PP == domain 2 score: 69.1 bits; conditional E-value: 9.7e-23 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 ++C+cgr+avlltvrk+gpN+GR+FYkC++g+ C+FF Wad+ sp|O70157|TOP3A_MOUSE 813 VTCNCGREAVLLTVRKQGPNQGRHFYKCSNGD---CNFFLWADS 853 58*****************************9...********7 PP == domain 3 score: 72.6 bits; conditional E-value: 7.9e-24 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45 C cg++av++tv+k+gpNkGR+F++C+k++e+qCgFF+W+de+ sp|O70157|TOP3A_MOUSE 898 PCLCGQPAVTRTVQKDGPNKGRQFHTCAKPREQQCGFFQWVDEN 941 6*****************************************96 PP >> sp|Q8K203|NEIL3_MOUSE Endonuclease 8-like 3 OS=Mus musculus OX=10090 GN=Neil3 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.7 0.7 1.3 4e+03 25 36 .. 233 247 .. 228 251 .. 0.73 2 ? -1.7 6.5 1.2 3.9e+03 5 36 .. 255 287 .. 253 289 .. 0.69 3 ! 74.0 0.8 2.8e-24 9e-21 1 44 [. 506 550 .. 506 551 .. 0.96 4 ! 65.4 3.2 1.4e-21 4.3e-18 1 44 [. 553 596 .. 553 597 .. 0.97 Alignments for each domain: == domain 1 score: -1.7 bits; conditional E-value: 1.3 zf-GRF 25 FYkCpkgke...kqC 36 FY+C k+ k+C sp|Q8K203|NEIL3_MOUSE 233 FYRCCKAGSaisKHC 247 999987655455555 PP == domain 2 score: -1.7 bits; conditional E-value: 1.2 zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgke..kqC 36 c + + tv + g+N R Y Cp +++ qC sp|Q8K203|NEIL3_MOUSE 255 CDQCHSKITVCRFGENS-RMTYFCPHCQKenPQC 287 66554445555588885.88899***99866566 PP == domain 3 score: 74.0 bits; conditional E-value: 2.8e-24 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 plCk ++r++vl++vrk+g+NkGR+FY+C++++++qCgFF+Wad sp|Q8K203|NEIL3_MOUSE 506 PLCKmHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADL 550 79**999************************************95 PP == domain 4 score: 65.4 bits; conditional E-value: 1.4e-21 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C +g+++ ++tv k gpN+G++F++Cp+ k+kqC+FF+Wa++ sp|Q8K203|NEIL3_MOUSE 553 PFCRHGKRSIMKTVLKIGPNNGKNFFVCPLEKKKQCNFFQWAEN 596 68***************************************986 PP >> sp|Q5BKS4|ERI2_MOUSE ERI1 exoribonuclease 2 OS=Mus musculus OX=10090 GN=Eri2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.3 0.1 0.47 1.5e+03 33 43 .. 143 154 .. 139 156 .. 0.76 2 ! 66.0 7.9 8.8e-22 2.8e-18 1 44 [. 592 639 .. 592 640 .. 0.97 Alignments for each domain: == domain 1 score: -0.3 bits; conditional E-value: 0.47 zf-GRF 33 e.kqCgFFkWad 43 e k C F W d sp|Q5BKS4|ERI2_MOUSE 143 EvKLCAFVTWSD 154 4488******98 PP == domain 2 score: 66.0 bits; conditional E-value: 8.8e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke....kqCgFFkWade 44 plCkcgr++++l+v+++gpN+G++FY+Cp+gk+ k+Cg+FkW+++ sp|Q5BKS4|ERI2_MOUSE 592 PLCKCGRRSKRLIVSNNGPNHGKAFYCCPVGKYqqdrKCCGYFKWEQT 639 79*******************************999**********96 PP >> sp|Q8BKW4|ZCHC4_MOUSE Zinc finger CCHC domain-containing protein 4 OS=Mus musculus OX=10090 GN=Zcchc4 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 58.1 2.9 2.6e-19 8.2e-16 1 45 [] 37 81 .. 37 81 .. 0.96 2 ? -8.1 7.2 7 2.2e+04 21 36 .. 402 415 .. 391 430 .. 0.73 Alignments for each domain: == domain 1 score: 58.1 bits; conditional E-value: 2.6e-19 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45 plC++g +l++++++ +g++++RkFY+C+++++ k+C+FF+W+dek sp|Q8BKW4|ZCHC4_MOUSE 37 PLCPHGpTLLFVKVN--QGKEETRKFYACSACRDrKDCNFFQWEDEK 81 79************9..6***************************95 PP == domain 2 score: -8.1 bits; conditional E-value: 7 zf-GRF 21 kGRkFYkCpkgkekqC 36 GRk+ C ++k+ C sp|Q8BKW4|ZCHC4_MOUSE 402 DGRKWSHCFLCKK--C 415 5777777777665..4 PP >> sp|Q0VGT4|ZGRF1_MOUSE Protein ZGRF1 OS=Mus musculus OX=10090 GN=Zgrf1 PE=1 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.5 0.1 2.3 7.2e+03 3 14 .. 713 724 .. 712 729 .. 0.75 2 ! 53.1 1.4 9.6e-18 3.1e-14 1 44 [. 1109 1152 .. 1109 1153 .. 0.96 Alignments for each domain: == domain 1 score: -2.5 bits; conditional E-value: 2.3 zf-GRF 3 Ckcgrlavlltv 14 C+c +a+++ v sp|Q0VGT4|ZGRF1_MOUSE 713 CPCEHRASQQPV 724 ****88887766 PP == domain 2 score: 53.1 bits; conditional E-value: 9.6e-18 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C + ++a+l v+k+gpNkGR FY+C k k++qC FFkW +e sp|Q0VGT4|ZGRF1_MOUSE 1109 PSCHHNQPAKLVMVKKEGPNKGRLFYTCDKSKDNQCKFFKWLEE 1152 68***************************************987 PP >> sp|Q68G58|APEX2_MOUSE DNA-(apurinic or apyrimidinic site) lyase 2 OS=Mus musculus OX=10090 GN=Apex2 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 50.4 1.2 6.7e-17 2.1e-13 1 42 [. 465 513 .. 465 515 .. 0.94 Alignments for each domain: == domain 1 score: 50.4 bits; conditional E-value: 6.7e-17 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42 plC + +++v++tv+ktgpN GR+FY C+ +++ + C+FF W sp|Q68G58|APEX2_MOUSE 465 PLCGgHREPCVMRTVKKTGPNFGRQFYMCARPRGppsdpsSRCNFFLWS 513 6899777**************************999999999******5 PP >> sp|Q5NC05|TTF2_MOUSE Transcription termination factor 2 OS=Mus musculus OX=10090 GN=Ttf2 PE=1 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.5 2.7 2.3e-10 7.4e-07 2 40 .. 5 41 .. 4 44 .. 0.92 2 ? 1.0 1.7 0.19 5.9e+02 22 43 .. 72 96 .. 66 98 .. 0.78 Alignments for each domain: == domain 1 score: 29.5 bits; conditional E-value: 2.3e-10 zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFk 40 C+ +g ++l+t ++gpNkG+ FY+C + CgF + sp|Q5NC05|TTF2_MOUSE 5 KCPeHGDACFLKTGVRDGPNKGKSFYVCRTNT---CGFVQ 41 6999*********999************9988...**966 PP == domain 2 score: 1.0 bits; conditional E-value: 0.19 zf-GRF 22 GRkFYkCpkgke...kqCgFFkWad 43 R F++C+ k + Cg W + sp|Q5NC05|TTF2_MOUSE 72 WRLFFRCARTKAegkQWCGNVPWRQ 96 599*****99887877799887766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 22289 (11757923 residues searched) Passed MSV filter: 1158 (0.0519539); expected 445.8 (0.02) Passed bias filter: 430 (0.019292); expected 445.8 (0.02) Passed Vit filter: 27 (0.00121136); expected 22.3 (0.001) Passed Fwd filter: 7 (0.000314056); expected 0.2 (1e-05) Initial search space (Z): 22289 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.08 # Mc/sec: 6613.83 // [ok]