# 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/Petromyzon_marinus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-21 74.7 0.0 4.6e-14 52.4 0.0 2.3 2 tr|S4R976|S4R976_PETMA Uncharacterized protein OS=Petromyzon 6.3e-16 58.4 0.0 9.6e-16 57.8 0.0 1.3 1 tr|S4R5Q8|S4R5Q8_PETMA Mitochondrial rRNA methyltransferase Domain annotation for each sequence (and alignments): >> tr|S4R976|S4R976_PETMA Uncharacterized protein OS=Petromyzon marinus OX=7757 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 52.4 0.0 6.8e-18 4.6e-14 2 65 .. 122 184 .. 121 219 .. 0.88 2 ! 20.2 0.0 5.7e-08 0.00038 94 142 .] 274 326 .. 222 326 .. 0.78 Alignments for each domain: == domain 1 score: 52.4 bits; conditional E-value: 6.8e-18 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHH CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsle 65 + +v+++++dpgN+G+i+R+a+a+g+s+++l+k ++d+++p+++ra+aga++ ++l ++ tr|S4R976|S4R976_PETMA 122 ISLVCDNVRDPGNMGTIIRSAAAVGCSKVLLIK-GCVDVWEPKVLRAGAGAHFRVPLLPCLRWK 184 679*****************************9.********************9976555554 PP == domain 2 score: 20.2 bits; conditional E-value: 5.7e-08 HTTEEEEEEBTTTBS-HHHHCTSS....EEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 94 kekvalvfGnEdkGlsnellelad....rlvkIpmsgeveSLNvavAvailly 142 ++++alv+ E +Gl e+l+la+ r +++ m+ veSLNv vA+++ll+ tr|S4R976|S4R976_PETMA 274 ARETALVVSGEAQGLGVEALRLAEgtggRRLHVGMAAGVESLNVGVAASVLLF 326 3899*******************9666679********************985 PP >> tr|S4R5Q8|S4R5Q8_PETMA Mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae) OS=Petromyzon marinus OX=7757 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 57.8 0.0 1.4e-19 9.6e-16 2 102 .. 110 219 .] 109 219 .] 0.88 Alignments for each domain: == domain 1 score: 57.8 bits; conditional E-value: 1.4e-19 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEG CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksl 88 l vv+ e++dp+NlGa++R+ + +g+++++++k++s l+p++ +a+ag+ ev+++++ + l ++l+e ++g+++v+t +++ks+ tr|S4R5Q8|S4R5Q8_PETMA 110 LWVVINEVNDPMNLGAVLRSTYFMGVETVLITKQNSSCSLTPTVSKASAGTVEVMDIYTTGRLPQVLQEKAKQGWQIVGTVGYAKST 196 579*******************************99999*****************************************9977755 PP C.........CSHHHTTEEEEEE CS SpoU_methylase 89 s.........eidlkekvalvfG 102 +++lk +++l++G tr|S4R5Q8|S4R5Q8_PETMA 197 GsavpvvpcdQYQLKAPTILLIG 219 43233334445588899999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 13539 (5048892 residues searched) Passed MSV filter: 235 (0.0173573); expected 270.8 (0.02) Passed bias filter: 217 (0.0160278); expected 270.8 (0.02) Passed Vit filter: 9 (0.000664746); expected 13.5 (0.001) Passed Fwd filter: 2 (0.000147721); expected 0.1 (1e-05) Initial search space (Z): 13539 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.04 # Mc/sec: 17923.57 // [ok]