# 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/Trichoplax_adhaerens.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-15 54.0 1.0 2.4e-14 52.5 1.0 1.8 1 tr|B3RI89|B3RI89_TRIAD DNA-(apurinic or apyrimidinic site) l 1.9e-08 33.6 3.3 1.9e-08 33.6 3.3 3.8 4 tr|B3S3K0|B3S3K0_TRIAD Uncharacterized protein OS=Trichoplax Domain annotation for each sequence (and alignments): >> tr|B3RI89|B3RI89_TRIAD DNA-(apurinic or apyrimidinic site) lyase OS=Trichoplax adhaerens OX=10228 GN=TRIADDRAFT_1941 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 52.5 1.0 4.1e-18 2.4e-14 1 43 [. 478 527 .] 478 527 .] 0.94 Alignments for each domain: == domain 1 score: 52.5 bits; conditional E-value: 4.1e-18 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWad 43 plC + ++v++tv+k gpN+GR FY+C ++++ + C+FF+Wa+ tr|B3RI89|B3RI89_TRIAD 478 PLCSgHKVPSVMRTVKKSGPNQGRRFYVCTLPEGrrgnpnARCNFFQWAN 527 6899788***********************999999999999******96 PP >> tr|B3S3K0|B3S3K0_TRIAD Uncharacterized protein OS=Trichoplax adhaerens OX=10228 GN=TRIADDRAFT_28284 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 33.6 3.3 3.4e-12 1.9e-08 1 44 [. 7 50 .. 7 51 .. 0.90 2 ? 2.1 0.4 0.024 1.4e+02 32 39 .. 147 154 .. 141 155 .. 0.82 3 ? -2.1 0.3 0.47 2.7e+03 26 32 .. 364 370 .. 357 374 .. 0.80 4 ? -4.3 5.4 2 1.2e+04 19 36 .. 371 386 .. 363 387 .. 0.73 Alignments for each domain: == domain 1 score: 33.6 bits; conditional E-value: 3.4e-12 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWade 44 p C++g +l++ + + R F++C+++++ k+C FF+Wade tr|B3S3K0|B3S3K0_TRIAD 7 PYCPHGpTLLFERFYK--SHKTSRRFFACSACRDrKDCSFFQWADE 50 579***9999999985..88899**********************8 PP == domain 2 score: 2.1 bits; conditional E-value: 0.024 zf-GRF 32 kekqCgFF 39 ++k C+FF tr|B3S3K0|B3S3K0_TRIAD 147 SDKTCNFF 154 5689**** PP == domain 3 score: -2.1 bits; conditional E-value: 0.47 zf-GRF 26 YkCpkgk 32 YkC+++ tr|B3S3K0|B3S3K0_TRIAD 364 YKCNNCP 370 9999875 PP == domain 4 score: -4.3 bits; conditional E-value: 2 zf-GRF 19 pNkGRkFYkCpkgkekqC 36 GR + C +k+ C tr|B3S3K0|B3S3K0_TRIAD 371 SKDGRTYIHCDECKK--C 386 557999999998886..6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 11518 (5222075 residues searched) Passed MSV filter: 453 (0.0393297); expected 230.4 (0.02) Passed bias filter: 242 (0.0210106); expected 230.4 (0.02) Passed Vit filter: 19 (0.00164959); expected 11.5 (0.001) Passed Fwd filter: 2 (0.000173641); expected 0.1 (1e-05) Initial search space (Z): 11518 [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: 7833.11 // [ok]