# 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/Ciona_intestinalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-35 119.2 13.6 2.9e-18 65.6 3.5 2.4 2 tr|H2XWS4|H2XWS4_CIOIN Uncharacterized protein OS=Ciona inte 2.5e-12 46.6 2.9 5.6e-12 45.4 2.9 1.6 1 tr|H2Y1C1|H2Y1C1_CIOIN Uncharacterized protein OS=Ciona inte Domain annotation for each sequence (and alignments): >> tr|H2XWS4|H2XWS4_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 59.0 2.6 3.8e-20 3.2e-16 1 45 [] 27 70 .. 27 70 .. 0.95 2 ! 65.6 3.5 3.5e-22 2.9e-18 1 44 [. 94 137 .. 94 138 .. 0.97 Alignments for each domain: == domain 1 score: 59.0 bits; conditional E-value: 3.8e-20 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45 p C+cg+ + +ltvrk+gpN GR+FYkC k ++ C FF W+d++ tr|H2XWS4|H2XWS4_CIOIN 27 PACQCGEVSIVLTVRKDGPNTGREFYKCGKQNG-GCDFFMWVDNN 70 67****************************997.8********86 PP == domain 2 score: 65.6 bits; conditional E-value: 3.5e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 ++Ckc +a+++tv+k+g NkGR FY+C k++++qCgFF+W+d+ tr|H2XWS4|H2XWS4_CIOIN 94 VMCKCDIPATQRTVQKEGANKGRMFYTCDKPRDAQCGFFEWCDS 137 69*****************************************7 PP >> tr|H2Y1C1|H2Y1C1_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.4 2.9 6.8e-16 5.6e-12 1 43 [. 91 131 .. 91 133 .. 0.95 Alignments for each domain: == domain 1 score: 45.4 bits; conditional E-value: 6.8e-16 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 p C + ++++++ v+k+gpN GR FY C+ ++ C FFkWa+ tr|H2Y1C1|H2Y1C1_CIOIN 91 PYCDHDTPCRMNRVKKEGPNIGRIFYSCARKRK--CKFFKWAE 131 57******************************7..******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 16678 (5370518 residues searched) Passed MSV filter: 750 (0.0449694); expected 333.6 (0.02) Passed bias filter: 322 (0.0193069); expected 333.6 (0.02) Passed Vit filter: 14 (0.000839429); expected 16.7 (0.001) Passed Fwd filter: 2 (0.000119918); expected 0.2 (1e-05) Initial search space (Z): 16678 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.03 # Mc/sec: 8055.78 // [ok]