# 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/Petromyzon_marinus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-34 115.5 6.7 1.2e-17 63.3 0.7 3.0 2 tr|S4RC13|S4RC13_PETMA DNA topoisomerase OS=Petromyzon marin 1.7e-31 107.6 28.4 2.2e-18 65.7 1.5 4.6 5 tr|S4RD41|S4RD41_PETMA Nei-like DNA glycosylase 3 OS=Petromy Domain annotation for each sequence (and alignments): >> tr|S4RC13|S4RC13_PETMA DNA topoisomerase OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 54.3 0.8 1.2e-18 7.8e-15 2 44 .. 810 849 .. 809 850 .. 0.95 2 ! 63.3 0.7 1.8e-21 1.2e-17 1 42 [. 877 918 .. 877 922 .. 0.95 Alignments for each domain: == domain 1 score: 54.3 bits; conditional E-value: 1.2e-18 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 C+cg +a+lltv+k+g NkGR FYkC+ C+FF Wad+ tr|S4RC13|S4RC13_PETMA 810 VCNCGIEATLLTVKKEGINKGRMFYKCSSSV---CNFFLWADQ 849 7***************************998...********7 PP == domain 2 score: 63.3 bits; conditional E-value: 1.8e-21 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWa 42 ++C c ++av++t k+gpNkGR+FY+C+k++++qCgFF W tr|S4RC13|S4RC13_PETMA 877 VMCSCNNPAVMRTIVKDGPNKGRQFYTCSKPRDEQCGFFLWM 918 69***************************************6 PP >> tr|S4RD41|S4RD41_PETMA Nei-like DNA glycosylase 3 OS=Petromyzon marinus OX=7757 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.1 0.29 2e+03 25 32 .. 24 31 .. 21 41 .. 0.72 2 ! 5.9 2.6 0.0015 10 5 33 .. 46 73 .. 43 75 .. 0.73 3 ? -3.2 0.1 1.1 7.4e+03 12 22 .. 273 283 .. 270 283 .. 0.65 4 ! 52.7 1.4 3.7e-18 2.5e-14 3 43 .. 301 342 .. 299 344 .. 0.95 5 ! 65.7 1.5 3.2e-22 2.2e-18 1 43 [. 346 388 .. 346 390 .. 0.97 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.29 zf-GRF 25 FYkCpkgk 32 FY+C k tr|S4RD41|S4RD41_PETMA 24 FYQCRKTG 31 9***8765 PP == domain 2 score: 5.9 bits; conditional E-value: 0.0015 zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgke 33 cg+ ++ +v + g+ +GR Y Cp ++ tr|S4RD41|S4RD41_PETMA 46 CGQCRTRVVVCRLGE-NGRMTYFCPHCQH 73 777555555555665.5*********986 PP == domain 3 score: -3.2 bits; conditional E-value: 1.1 zf-GRF 12 ltvrktgpNkG 22 +t ++ g+N G tr|S4RD41|S4RD41_PETMA 273 RTPNNRGQNSG 283 56667777766 PP == domain 4 score: 52.7 bits; conditional E-value: 3.7e-18 zf-GRF 3 Ck.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 C + r++ l +v+k gpN+GR+F++C++++++qC F+Wad tr|S4RD41|S4RD41_PETMA 301 CRgHDRPCALHVVQKAGPNRGRHFHACALPQKQQCQHFEWAD 342 99788************************************9 PP == domain 5 score: 65.7 bits; conditional E-value: 3.2e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 p C +g ++v++tv k gpN+GR+FY+C++g+++qC FF+Wad tr|S4RD41|S4RD41_PETMA 346 PECDHGLRCVMRTVLKLGPNNGRNFYACAQGRDRQCAFFQWAD 388 57****************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 13539 (5048892 residues searched) Passed MSV filter: 561 (0.0414359); expected 270.8 (0.02) Passed bias filter: 259 (0.0191299); expected 270.8 (0.02) Passed Vit filter: 17 (0.00125563); expected 13.5 (0.001) Passed Fwd filter: 2 (0.000147721); expected 0.1 (1e-05) Initial search space (Z): 13539 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 7573.34 // [ok]