# 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/Strongylocentrotus_purpuratus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-23 83.3 17.2 4.4e-19 69.0 3.9 2.4 2 tr|W4YDZ2|W4YDZ2_STRPU Uncharacterized protein OS=Strongyloc 5.7e-16 59.0 5.7 1.5e-15 57.6 5.7 1.8 1 tr|W4XZ06|W4XZ06_STRPU Uncharacterized protein OS=Strongyloc 6.2e-15 55.7 5.7 6.2e-15 55.7 5.7 2.0 2 tr|W4YNP2|W4YNP2_STRPU Uncharacterized protein OS=Strongyloc 2.4e-11 44.2 3.5 6e-11 42.9 3.5 1.7 1 tr|W4XGX7|W4XGX7_STRPU DNA-(apurinic or apyrimidinic site) l 1.7e-09 38.3 10.7 1.8e-09 38.2 6.4 3.2 2 tr|W4XYD2|W4XYD2_STRPU Uncharacterized protein OS=Strongyloc 1.6e-06 28.7 13.0 2.5e-06 28.1 4.4 2.7 2 tr|W4Y2I0|W4Y2I0_STRPU Uncharacterized protein OS=Strongyloc 1.8e-06 28.5 1.9 4.6e-06 27.3 1.9 1.7 1 tr|W4XV37|W4XV37_STRPU Uncharacterized protein OS=Strongyloc Domain annotation for each sequence (and alignments): >> tr|W4YDZ2|W4YDZ2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.9 5.4 2.3e-07 0.00093 21 45 .] 75 96 .. 73 96 .. 0.92 2 ! 69.0 3.9 1.1e-22 4.4e-19 1 44 [. 155 198 .. 155 199 .. 0.97 Alignments for each domain: == domain 1 score: 19.9 bits; conditional E-value: 2.3e-07 zf-GRF 21 kGRkFYkCpkgkekqCgFFkWadek 45 +GR+F+kC g C+FF W +e+ tr|W4YDZ2|W4YDZ2_STRPU 75 QGRQFFKCQSGG---CNFFLWSEEN 96 8*******9998...******9985 PP == domain 2 score: 69.0 bits; conditional E-value: 1.1e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 ++C+c av++tv+k+gpN+GR+FY+C k+++kqC +F+Wade tr|W4YDZ2|W4YDZ2_STRPU 155 VMCQCNAAAVQRTVQKEGPNQGRQFYVCGKPRDKQCSYFQWADE 198 69*****************************************8 PP >> tr|W4XZ06|W4XZ06_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 57.6 5.7 3.8e-19 1.5e-15 1 44 [. 707 750 .. 707 751 .. 0.97 Alignments for each domain: == domain 1 score: 57.6 bits; conditional E-value: 3.8e-19 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p Ck+g++a++ v+k+gpNkGR FY+C++ +e+qC FF Wad+ tr|W4XZ06|W4XZ06_STRPU 707 PPCKHGQPAKMVCVKKDGPNKGRMFYACNNQRENQCKFFVWADQ 750 68*****************************************7 PP >> tr|W4YNP2|W4YNP2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -6.1 2.0 7 2.9e+04 3 18 .. 559 576 .. 558 578 .. 0.68 2 ! 55.7 5.7 1.5e-18 6.2e-15 1 44 [. 2381 2424 .. 2381 2425 .. 0.97 Alignments for each domain: == domain 1 score: -6.1 bits; conditional E-value: 7 zf-GRF 3 Ck.cg.rlavlltvrktg 18 Ck c +++ ++ +k+ tr|W4YNP2|W4YNP2_STRPU 559 CKkCKgIRCTCNIPSKDH 576 666766778888777765 PP == domain 2 score: 55.7 bits; conditional E-value: 1.5e-18 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p Ck+g++a++ v+k+gpNkGR FY+C++ +e+qC FF Wad+ tr|W4YNP2|W4YNP2_STRPU 2381 PPCKHGQPAKMVCVKKDGPNKGRMFYACNNQRENQCKFFVWADQ 2424 68*****************************************7 PP >> tr|W4XGX7|W4XGX7_STRPU DNA-(apurinic or apyrimidinic site) lyase OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.9 3.5 1.5e-14 6e-11 1 44 [. 539 589 .. 539 590 .. 0.92 Alignments for each domain: == domain 1 score: 42.9 bits; conditional E-value: 1.5e-14 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWade 44 p+Ck +++++ l+tv+k gpN G++F++C +++ + C+ F+W+ + tr|W4XGX7|W4XGX7_STRPU 539 PMCKgHQEPCLLRTVKKAGPNLGKQFFVCKRPEGhknnpeARCNHFEWVSK 589 79**999**********************9999888999999******865 PP >> tr|W4XYD2|W4XYD2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.7 0.1 0.61 2.5e+03 34 43 .. 152 161 .. 143 163 .. 0.79 2 ! 38.2 6.4 4.5e-13 1.8e-09 1 42 [. 533 587 .. 533 590 .. 0.92 Alignments for each domain: == domain 1 score: -0.7 bits; conditional E-value: 0.61 zf-GRF 34 kqCgFFkWad 43 k C F W d tr|W4XYD2|W4XYD2_STRPU 152 KLCTFVTWSD 161 78******98 PP == domain 2 score: 38.2 bits; conditional E-value: 4.5e-13 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke.............kqCgFFkWa 42 p+Ckc r+++++++ + gpN+GR+FY Cp k CgFF W+ tr|W4XYD2|W4XYD2_STRPU 533 PMCKCARRSKRRVAARPGPNQGRAFYSCPGLKRrsggglkdttnakMGCGFFSWE 587 79***************************9888889999989888778******8 PP >> tr|W4Y2I0|W4Y2I0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 28.1 4.4 6.2e-10 2.5e-06 1 39 [. 4 43 .. 4 45 .. 0.95 2 ! 5.4 1.3 0.0077 31 21 38 .. 45 65 .. 43 66 .. 0.84 Alignments for each domain: == domain 1 score: 28.1 bits; conditional E-value: 6.2e-10 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFF 39 ++Ck +g+ ++l+t +gp kG+ FY C e++C+F tr|W4Y2I0|W4Y2I0_STRPU 4 VQCKgHGETCFLKTGVSEGPRKGKSFYICGSTAEQKCNFV 43 68**9*********999**********************6 PP == domain 2 score: 5.4 bits; conditional E-value: 0.0077 zf-GRF 21 kGRkFYkCpkgke...kqCgF 38 ++R++Y+C + k+ Cg+ tr|W4Y2I0|W4Y2I0_STRPU 45 ETRQYYRCTTSKQegkGWCGY 65 79*******999877667887 PP >> tr|W4XV37|W4XV37_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.3 1.9 1.1e-09 4.6e-06 1 40 [. 25 64 .. 25 67 .. 0.93 Alignments for each domain: == domain 1 score: 27.3 bits; conditional E-value: 1.1e-09 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFk 40 p C++g +l++ + g++ + +Y+C+++++ k+CgFF+ tr|W4XV37|W4XV37_STRPU 25 PHCPHGpTLLFERFT--PGKDTSQRYYACSACRDrKDCGFFQ 64 57****999999999..6***********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 28594 (14266044 residues searched) Passed MSV filter: 1160 (0.040568); expected 571.9 (0.02) Passed bias filter: 551 (0.0192698); expected 571.9 (0.02) Passed Vit filter: 35 (0.00122403); expected 28.6 (0.001) Passed Fwd filter: 8 (0.000279779); expected 0.3 (1e-05) Initial search space (Z): 28594 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.13u 0.01s 00:00:00.14 Elapsed: 00:00:00.09 # Mc/sec: 7133.02 // [ok]