# 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/Monosiga_brevicollis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-29 99.8 0.0 2.3e-28 98.2 0.0 2.0 1 tr|A9US19|A9US19_MONBE Predicted protein OS=Monosiga brevico 6.5e-21 74.1 0.0 1.3e-20 73.1 0.0 1.5 1 tr|A9UYT1|A9UYT1_MONBE Predicted protein OS=Monosiga brevico ------ inclusion threshold ------ 0.032 13.4 0.0 0.15 11.3 0.0 1.9 2 tr|A9URY6|A9URY6_MONBE Predicted protein (Fragment) OS=Monos Domain annotation for each sequence (and alignments): >> tr|A9US19|A9US19_MONBE Predicted protein OS=Monosiga brevicollis OX=81824 GN=22775 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 98.2 0.0 7.5e-32 2.3e-28 2 142 .] 1386 1529 .. 1385 1529 .. 0.87 Alignments for each domain: == domain 1 score: 98.2 bits; conditional E-value: 7.5e-32 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEESTT- CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvatslkg 85 liv+ +++p NlG + Rt+++f+a++lv+ ++r + + + + ++++ + +++ +k d+l e+l + ++eg+++v++++ + tr|A9US19|A9US19_MONBE 1386 LIVAASFVNIPYNLGGLTRTCEIFNADRLVMPDNRVLQSKEYKGVSVSSERWMHFDiVKPEDELVEYLVRKRREGYTIVGLEQTA 1470 67888889***********************9988775566666666666667777666679999999999999*********55 PP SEGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 86 ksls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142 +s+ e++++e+++lv+G+E++G+s+++l+ +dr+v+Ip+ g ++SLNv+v++ai++y tr|A9US19|A9US19_MONBE 1471 ESVPlqEYTFPERTVLVLGEERRGISPKVLAVIDRCVEIPQFGVTRSLNVHVSAAIAIY 1529 554444***************************************************98 PP >> tr|A9UYT1|A9UYT1_MONBE Predicted protein OS=Monosiga brevicollis OX=81824 GN=36980 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 73.1 0.0 4.1e-24 1.3e-20 3 141 .. 391 536 .. 390 537 .. 0.77 Alignments for each domain: == domain 1 score: 73.1 bits; conditional E-value: 4.1e-24 EEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCT.EEEEEEST.... CS SpoU_methylase 3 ivvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeeg.falvatsl.... 83 ++v+v +dp+N+G+i+Rta afga+++++ + +a++l+ +++a+ag+ + + l + l++a + e+ +l+++ + tr|A9UYT1|A9UYT1_MONBE 391 RLVVVAAQDPHNVGSIVRTALAFGADAICVWD-GAAQPLTAATIKASAGHVFAGRfLSPTEVLRAARSTASEVApSTLWTAAEahap 476 6899*********************9999977.8888*************9888844444444444444444432233333222222 PP ...T-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 84 ...kgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 + ++l++++++ + +lv+G E++G++++l ++ v+I +++ veSL va A+ail+ tr|A9UYT1|A9UYT1_MONBE 477 sswSHRQLEDVAWPHRRVLVLGHETRGVPRDLQPFCQP-VHIAIHPGVESLSVAAAAAILC 536 22222244488*************************96.********************97 PP >> tr|A9URY6|A9URY6_MONBE Predicted protein (Fragment) OS=Monosiga brevicollis OX=81824 GN=14566 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.3 0.0 4.9e-05 0.15 15 40 .. 24 49 .. 23 74 .. 0.82 2 ? -0.7 0.0 0.24 7.4e+02 58 102 .. 195 246 .. 176 247 .. 0.72 Alignments for each domain: == domain 1 score: 11.3 bits; conditional E-value: 4.9e-05 HHHHHHHHHHTT-SEEEEESGSSCTC CS SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadl 40 +G iaR+a +f a+e+v+ k+++ ++ tr|A9URY6|A9URY6_MONBE 24 VGQIARAAVIFRADEIVIFKDKCTQP 49 79******************999833 PP == domain 2 score: -0.7 bits; conditional E-value: 0.24 EEEESSHHHHHHHHCCC.TEEE.EEESTT-SEGCCSHHH.....TTEEEEEE CS SpoU_methylase 58 lkvvdsleealkelkee.gfal.vatslkgkslseidlk.....ekvalvfG 102 ++ ++++e+++k+ g++l +++s kg++l+++ l+ ++ ++vfG tr|A9URY6|A9URY6_MONBE 195 VRLAEDIEQVFKQSPYPgGYDLtIGISDKGSPLNKLHLHkhaayNHLLVVFG 246 5566777777777777734777578888999999886665556677788887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 9188 (5511963 residues searched) Passed MSV filter: 246 (0.0267741); expected 183.8 (0.02) Passed bias filter: 220 (0.0239443); expected 183.8 (0.02) Passed Vit filter: 10 (0.00108838); expected 9.2 (0.001) Passed Fwd filter: 3 (0.000326513); expected 0.1 (1e-05) Initial search space (Z): 9188 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.04 # Mc/sec: 19567.47 // [ok]