# 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/SpoU_methylase.hmm.txt # target sequence database: proteomes/Xenopus_tropicalis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoU_methylase [M=142] Accession: PF00588.18 Description: SpoU rRNA Methylase family 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-23 81.8 0.0 5.8e-21 75.6 0.0 2.2 1 sp|A4QNL8|MRM3_XENTR rRNA methyltransferase 3, mitochondri 1e-22 81.2 0.0 1.9e-22 80.4 0.0 1.5 1 tr|F6ULL7|F6ULL7_XENTR TAR (HIV-1) RNA-binding protein 1 OS= 0.0076 16.8 0.1 0.01 16.4 0.1 1.2 1 tr|Q28J93|Q28J93_XENTR Polymerase (DNA directed), epsilon 3 ------ inclusion threshold ------ 0.088 13.4 0.0 13 6.4 0.0 2.4 2 tr|F6ZQ62|F6ZQ62_XENTR SPOUT domain-containing methyltransfe Domain annotation for each sequence (and alignments): >> sp|A4QNL8|MRM3_XENTR rRNA methyltransferase 3, mitochondrial OS=Xenopus tropicalis OX=8364 GN=mrm3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 75.6 0.0 9.6e-25 5.8e-21 2 142 .] 205 401 .. 204 401 .. 0.79 Alignments for each domain: == domain 1 score: 75.6 bits; conditional E-value: 9.6e-25 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST.T-SEGC CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl.kgksls 89 l +++++i+dpgNlG+i+R+a+ +g+++++l+k ++d ++p+++ra++ga++ l++ +++ + + l +g++++ +++ + +++ sp|A4QNL8|MRM3_XENTR 205 LSLICDNIRDPGNLGTILRCAAGAGCNKVLLTK-GCVDAWEPKVLRAGMGAHFRLPVISSLDWDIVPNYLS-AGTKVFLADNfR-PDMK 290 6799***************************88.**********************888888877666666.56******9953.4444 PP ....CS...................HHH................................TTEEEEEEBTTTBS-HHHHCTSS....EE CS SpoU_methylase 90 ....ei...................dlk................................ekvalvfGnEdkGlsnellelad....rl 119 ++ + + +++a+v+G E++Gls e l la+ + sp|A4QNL8|MRM3_XENTR 291 hktgDVsekasdygwvstnprriliT-EegyesssdeednadklyipglevqsyfeswaqSPCAIVIGGETHGLSIESLLLAEksngKR 378 33343344455556665555555550.055556666667777778888888888999999***************99986665333569 PP EE----TTSSS--HHHHHHHHHH CS SpoU_methylase 120 vkIpmsgeveSLNvavAvailly 142 ++Ip+ ++++SLN a+A++ill+ sp|A4QNL8|MRM3_XENTR 379 LYIPVVPDIDSLNSAMAASILLF 401 ********************985 PP >> tr|F6ULL7|F6ULL7_XENTR TAR (HIV-1) RNA-binding protein 1 OS=Xenopus tropicalis OX=8364 GN=tarbp1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 80.4 0.0 3.1e-26 1.9e-22 2 141 .. 1208 1347 .. 1207 1348 .. 0.93 Alignments for each domain: == domain 1 score: 80.4 bits; conditional E-value: 3.1e-26 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEESTT CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatslk 84 livv i++p+NlG ++Rt+++fgas+lv+ + + ++++++++ ++++a+++l+l +v ++l e+l+e k++g+ l+ + ++ tr|F6ULL7|F6ULL7_XENTR 1208 LIVVASLIDKPTNLGGLCRTCEIFGASALVVDS-LH-HVNDKQFQYLSVSAEQWLPLIEVkpTQLLEYLQERKQQGYSLLNIGGR 1290 799***********************9999955.33.479****************8888567999****************999 PP -SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 85 gkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 ++ +++d ek + + nE++G++ +l++++d +v+Ip++g ++SLNv+v+ a+l+ tr|F6ULL7|F6ULL7_XENTR 1291 LQTEKDTDSCEKNWGRLRNEREGIPANLIQHLDVCVEIPQQGIIRSLNVHVSGAVLI 1347 99999**************************************************97 PP >> tr|Q28J93|Q28J93_XENTR Polymerase (DNA directed), epsilon 3 (P17 subunit) OS=Xenopus tropicalis OX=8364 GN=pole3 PE= # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.4 0.1 1.7e-06 0.01 13 91 .. 27 105 .. 16 118 .. 0.84 Alignments for each domain: == domain 1 score: 16.4 bits; conditional E-value: 1.7e-06 HHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC.CS CS SpoU_methylase 13 gNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls.ei 91 N+++ aR+a as vl ++ +a+ + + kr +++a +vl + + ++++++l+ lke+ ++++ ++kgk+ e tr|Q28J93|Q28J93_XENTR 27 VNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNATDVLAAMEEMEFQRFLTPLKES-LEVYRQDQKGKKEAtEQ 105 699999999999999999999*****************************************.******99555433233 PP >> tr|F6ZQ62|F6ZQ62_XENTR SPOUT domain-containing methyltransferase 1 OS=Xenopus tropicalis OX=8364 GN=spout1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 6.4 0.0 0.0021 13 16 37 .. 104 125 .. 103 163 .. 0.86 2 ? 4.7 0.0 0.007 42 40 102 .. 251 317 .. 229 359 .. 0.84 Alignments for each domain: == domain 1 score: 6.4 bits; conditional E-value: 0.0021 HHHHHHHHHTT-SEEEEESGSS CS SpoU_methylase 16 GaiaRtakafgaselvlvkprs 37 G iaR++++f ++e+v+ ++ + tr|F6ZQ62|F6ZQ62_XENTR 104 GQIARACAIFCIDEIVIFDETG 125 99***************98755 PP == domain 2 score: 4.7 bits; conditional E-value: 0.007 CGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCC.TEEE.EEESTT-SEGCCSHHH..TTEEEEEE CS SpoU_methylase 40 llnpeakraaagalevlelkvvdsleealkelkee.gfal.vatslkgkslseidlk..ekvalvfG 102 + +p+ r+a+g +++ ++ l+++++e+ + g++l ++ts++g+s+++++l+ +++++vfG tr|F6ZQ62|F6ZQ62_XENTR 251 VVSPQHPRTASGLYWGYRVRLASCLSAVFTECPFKdGYDLtIGTSERGSSVETVSLPdfRHAMIVFG 317 5677777777777777778888889999999999967988689999********999999******9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 24182 (11782085 residues searched) Passed MSV filter: 553 (0.0228682); expected 483.6 (0.02) Passed bias filter: 434 (0.0179472); expected 483.6 (0.02) Passed Vit filter: 33 (0.00136465); expected 24.2 (0.001) Passed Fwd filter: 4 (0.000165412); expected 0.2 (1e-05) Initial search space (Z): 24182 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.07 # Mc/sec: 23900.80 // [ok]