# 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/Mus_musculus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-30 106.8 0.0 4.6e-30 104.9 0.0 2.0 2 tr|E9Q368|E9Q368_MOUSE TAR RNA-binding protein 1 OS=Mus musc 7.1e-28 97.9 0.0 9.5e-28 97.4 0.0 1.2 1 sp|Q99J25|MRM1_MOUSE rRNA methyltransferase 1, mitochondri 4.6e-23 82.3 0.0 6.9e-22 78.5 0.0 2.1 1 sp|Q5ND52|MRM3_MOUSE rRNA methyltransferase 3, mitochondri 0.0097 16.4 0.1 0.013 16.0 0.1 1.1 1 sp|Q9JKP7|DPOE3_MOUSE DNA polymerase epsilon subunit 3 OS=M Domain annotation for each sequence (and alignments): >> tr|E9Q368|E9Q368_MOUSE TAR RNA-binding protein 1 OS=Mus musculus OX=10090 GN=Tarbp1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.8 0.0 0.7 3.9e+03 42 92 .. 927 977 .. 905 989 .. 0.75 2 ! 104.9 0.0 8.3e-34 4.6e-30 2 141 .. 1422 1563 .. 1421 1564 .. 0.91 Alignments for each domain: == domain 1 score: -1.8 bits; conditional E-value: 0.7 SHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSH CS SpoU_methylase 42 npeakraaagalevlelkvvdsleealkelkeegfalvatslkgkslseid 92 + ++++ ++l+ +l+ +++l+++++ + ++++ ++a++lkg+ + +i+ tr|E9Q368|E9Q368_MOUSE 927 SFDVAWKIISSLSNTQLTFWPNLKAFVHFVFDHEILTIAAKLKGQVYFKIK 977 55555666677888889999*********9999999999999999888764 PP == domain 2 score: 104.9 bits; conditional E-value: 8.3e-34 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEEST. CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatsl. 83 livv i++p+NlG ++Rt+++fga lv+ + +++ ++++++++++a+++l+l++v ++l ++l++ k eg++++++++ tr|E9Q368|E9Q368_MOUSE 1422 LIVVASLIDKPTNLGGLCRTCEVFGAAVLVVGSLQCV--SDRQFQHLSVSAEQWLPLVEVrpSQLMNYLQQKKAEGYTVIGVEQt 1504 799***********************66666665665..9****************77776789******************996 PP .T-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 84 .kgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 ++++l +++++ek +l++GnE++G++ +l++++d +v+Ip++g ++SLNv+v+ a+l+ tr|E9Q368|E9Q368_MOUSE 1505 aQSSDLAQYRFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLI 1563 6666777************************************************9987 PP >> sp|Q99J25|MRM1_MOUSE rRNA methyltransferase 1, mitochondrial OS=Mus musculus OX=10090 GN=Mrm1 PE=2 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 97.4 0.0 1.7e-31 9.5e-28 2 142 .] 144 299 .. 143 299 .. 0.87 Alignments for each domain: == domain 1 score: 97.4 bits; conditional E-value: 1.7e-31 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST.T-SEGC CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl.kgksls 89 l +vl++++dp+NlGa++R+a +g+++++ ++++s +l+p + +a+aga ev+++ ++l +l++ ++g+ +v+t + g ++s sp|Q99J25|MRM1_MOUSE 144 LWLVLEGLQDPRNLGAVMRSAHFLGVDRVITSQRNSC-PLTPVVSKASAGAMEVMDVFATPDLPGFLQAKAQQGWLVVGTVGcPGPEIS 231 569****************************997776.******************************************999787777 PP ...........CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....---TTSSS--HHHHHHHHHH CS SpoU_methylase 90 ...........eidlkekvalvfGnEdkGlsnelleladrlvkI....pmsgeveSLNvavAvailly 142 e+ ++++++lv+G+E++Gls+e+ + ++ l++I + eSLNv+vA++ill+ sp|Q99J25|MRM1_MOUSE 232 qsskvpitsclEFVWDRPTLLVLGSEGSGLSQEVFASCQLLLTIlprrHLPPGLESLNVSVATGILLH 299 4443333344444777***********************999995444457889***********985 PP >> sp|Q5ND52|MRM3_MOUSE rRNA methyltransferase 3, mitochondrial OS=Mus musculus OX=10090 GN=Mrm3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.5 0.0 1.2e-25 6.9e-22 2 142 .] 210 398 .. 209 398 .. 0.84 Alignments for each domain: == domain 1 score: 78.5 bits; conditional E-value: 1.2e-25 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-SEG CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl..kgksl 88 l++++++++dpgNlG+i+R+a+ +g+s+++l+k ++d ++p+++ra++ga+++++++ ++e + ++l ++++++++ + ++ sp|Q5ND52|MRM3_MOUSE 210 LVLICDNLRDPGNLGTILRSAAGAGCSKVLLTK-GCVDAWEPKVLRAGMGAHFQVPIVNNVEWETVPNHLPPD-TRVYVADNcgHYAQV 296 789****************************88.**********************99*************99.******997533333 PP C..CS................HHH...........................TTEEEEEEBTTTBS-HHHHCTSS....EEEE----TTS CS SpoU_methylase 89 s..ei................dlk...........................ekvalvfGnEdkGlsnellelad....rlvkIpmsgev 128 + + + ++a+v+G E++G+s e l+la+ + + Ip+ + v sp|Q5ND52|MRM3_MOUSE 297 QmsDKtgdrdwacdrrflkfhK-YeedldtktrkdwlpklevqsydldwtgAPAAVVIGGETHGVSLESLQLAEstggKRLLIPVVPGV 384 3332246665555555555551.056666667777778888888899999*********************99955556899******* PP SS--HHHHHHHHHH CS SpoU_methylase 129 eSLNvavAvailly 142 +SLN a+A++ill+ sp|Q5ND52|MRM3_MOUSE 385 DSLNSAMAASILLF 398 ***********985 PP >> sp|Q9JKP7|DPOE3_MOUSE DNA polymerase epsilon subunit 3 OS=Mus musculus OX=10090 GN=Pole3 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.0 0.1 2.3e-06 0.013 8 89 .. 22 102 .. 16 119 .. 0.85 Alignments for each domain: == domain 1 score: 16.0 bits; conditional E-value: 2.3e-06 S-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS SpoU_methylase 8 eiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89 + d N+++ aR+a as vl ++ +a+ + + kr +++a +vl + + ++++++++ lke+ ++ + +++kgk+ sp|Q9JKP7|DPOE3_MOUSE 22 ALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFITPLKEA-LEAYRRDEKGKKEA 102 55667799999****9999999*********************************************.******99665433 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 22289 (11757923 residues searched) Passed MSV filter: 403 (0.0180807); expected 445.8 (0.02) Passed bias filter: 379 (0.0170039); expected 445.8 (0.02) Passed Vit filter: 28 (0.00125623); expected 22.3 (0.001) Passed Fwd filter: 4 (0.000179461); expected 0.2 (1e-05) Initial search space (Z): 22289 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.15u 0.01s 00:00:00.16 Elapsed: 00:00:00.09 # Mc/sec: 18551.39 // [ok]