# 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/Ciona_intestinalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-31 107.5 0.0 9.9e-31 106.7 0.0 1.4 2 tr|F6YVG2|F6YVG2_CIOIN Uncharacterized protein OS=Ciona inte ------ inclusion threshold ------ 0.02 15.0 0.0 1.9 8.5 0.0 2.3 2 tr|F6QCQ5|F6QCQ5_CIOIN putative methyltransferase C9orf114 O Domain annotation for each sequence (and alignments): >> tr|F6YVG2|F6YVG2_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.4 0.0 1.1 9e+03 65 83 .. 50 68 .. 39 89 .. 0.53 2 ! 106.7 0.0 1.2e-34 9.9e-31 2 141 .. 101 242 .. 100 243 .. 0.92 Alignments for each domain: == domain 1 score: -3.4 bits; conditional E-value: 1.1 HHHHHHHCCCTEEEEEEST CS SpoU_methylase 65 eealkelkeegfalvatsl 83 +++l++l+ +++ ++ ++ tr|F6YVG2|F6YVG2_CIOIN 50 RSILRDLNSSNWIAMGSKK 68 4445555555443333333 PP == domain 2 score: 106.7 bits; conditional E-value: 1.2e-34 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEES..SHHHHHHHHCCCTEEEEEESTT-S CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvd..sleealkelkeegfalvatslkgk 86 l++v i++p NlG + Rt+++fga+++++ + + ++ ++ +++ a+++l++ +v+ +lee+l+ +k++g+alvat++ ++ tr|F6YVG2|F6YVG2_CIOIN 101 LVLVASLIDKPSNLGGLTRTCEVFGAEQMIVHSLSCT--SDKLFQSLSVTAHKWLKMSEVKrwELEEYLESMKRQGYALVATEQTEQ 185 6789999*******************99999887776..889999***********9999722568******************888 PP EGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 87 sls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 s++ e++++ k+++++GnE++G++++ll+ ++ +++Ip+ g v+SLNv+v+ +i + tr|F6YVG2|F6YVG2_CIOIN 186 SVCltEYKFPPKCVILLGNEKEGIPPNLLRMCSACIEIPQVGVVRSLNVHVSGGITV 242 8888899**********************************************9975 PP >> tr|F6QCQ5|F6QCQ5_CIOIN putative methyltransferase C9orf114 OS=Ciona intestinalis OX=7719 GN=LOC100187134 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.5 0.0 0.00023 1.9 16 38 .. 84 106 .. 83 121 .. 0.85 2 ? 3.9 0.0 0.0064 53 60 102 .. 251 299 .. 238 308 .. 0.78 Alignments for each domain: == domain 1 score: 8.5 bits; conditional E-value: 0.00023 HHHHHHHHHTT-SEEEEESGSSC CS SpoU_methylase 16 GaiaRtakafgaselvlvkprsa 38 G iaR++ +f+++e+++ ++ + tr|F6QCQ5|F6QCQ5_CIOIN 84 GQIARACVVFQVDEIIVFDESAS 106 99***************986554 PP == domain 2 score: 3.9 bits; conditional E-value: 0.0064 EESSHHHHHHHHCCC..T.EEE.EEESTT-SEGCCSHHH..TTEEEEEE CS SpoU_methylase 60 vvdsleealkelkee..g.fal.vatslkgkslseidlk..ekvalvfG 102 ++sl++a+ ++ + g +++ ++ts kg+++ +++++ ++ ++vfG tr|F6QCQ5|F6QCQ5_CIOIN 251 LANSLSSAIVDCPYSdtGkYDItIGTSDKGEPVADFKMPtfKHLLIVFG 299 5667777777766553234666589999******9999999*******9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 16678 (5370518 residues searched) Passed MSV filter: 361 (0.0216453); expected 333.6 (0.02) Passed bias filter: 322 (0.0193069); expected 333.6 (0.02) Passed Vit filter: 25 (0.00149898); expected 16.7 (0.001) Passed Fwd filter: 2 (0.000119918); expected 0.2 (1e-05) Initial search space (Z): 16678 [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: 00:00:00.03 # Mc/sec: 25420.45 // [ok]