# 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_savignyi.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-30 104.7 0.0 6e-30 103.7 0.0 1.5 2 tr|H2YWT1|H2YWT1_CIOSA Uncharacterized protein OS=Ciona savi 1.1e-09 38.0 0.0 2e-09 37.2 0.0 1.4 1 tr|H2YFV4|H2YFV4_CIOSA Uncharacterized protein OS=Ciona savi 4.2e-05 23.1 0.0 6.2e-05 22.6 0.0 1.3 1 tr|H2YLA3|H2YLA3_CIOSA Uncharacterized protein OS=Ciona savi ------ inclusion threshold ------ 0.014 14.9 0.0 1.1 8.8 0.0 2.3 2 tr|H2YY31|H2YY31_CIOSA Uncharacterized protein OS=Ciona savi Domain annotation for each sequence (and alignments): >> tr|H2YWT1|H2YWT1_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.0 0.0 1.6 4.7e+03 58 85 .. 190 217 .. 181 236 .. 0.62 2 ! 103.7 0.0 2.1e-33 6e-30 2 141 .. 246 387 .. 245 388 .. 0.90 Alignments for each domain: == domain 1 score: -3.0 bits; conditional E-value: 1.6 EEEESSHHHHHHHHCCCTEEEEEESTT- CS SpoU_methylase 58 lkvvdsleealkelkeegfalvatslkg 85 + v+++++ l++lk +++ ++ ++++ tr|H2YWT1|H2YWT1_CIOSA 190 WIPVQNIRNNLRDLKSSNWVAMGNKKSE 217 5567888888888888855555544443 PP == domain 2 score: 103.7 bits; conditional E-value: 2.1e-33 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEES..SHHHHHHHHCCCTEEEEEESTT-S CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvd..sleealkelkeegfalvatslkgk 86 l++v i++p NlG + Rt+++fga+++v+ + ++ +++ ++ +++ a+++l + +v+ +le++l+++k+eg+alvat++ ++ tr|H2YWT1|H2YWT1_CIOSA 246 LVLVASLIDKPSNLGGLSRTCEVFGAERMVVHNLSCV--NDKLFQSLSVTAHKWLVMSEVKrwDLEKYLEAMKREGYALVATEQTEQ 330 6889999************************998888..777777788888888777777522789******************888 PP EGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 87 sls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 s++ ++++++k+++++GnE++G++++ll+l+d v+Ip+ g v+SLNv+v+ +i + tr|H2YWT1|H2YWT1_CIOSA 331 SVCltQYKFSSKCVVLLGNEKEGIPPNLLRLCDASVEIPQVGVVRSLNVHVSGGITV 387 8887799999*******************************************9975 PP >> tr|H2YFV4|H2YFV4_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 37.2 0.0 6.8e-13 2e-09 2 62 .. 165 223 .. 164 228 .] 0.87 Alignments for each domain: == domain 1 score: 37.2 bits; conditional E-value: 6.8e-13 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEES CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvd 62 l v+l++i dp+N+G+i+Rt+ +g+ e+ ++ ++a +++p++ +a++ga ev++l+ + tr|H2YFV4|H2YFV4_CIOSA 165 LWVLLYDIIDPMNIGNILRTCHFLGV-EVPIMTSQCA-PISPTTSKASSGAVEVMQLYSTN 223 6799**********************.6666666998.*****************987665 PP >> tr|H2YLA3|H2YLA3_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.6 0.0 2.2e-08 6.2e-05 2 76 .. 45 117 .. 44 152 .. 0.83 Alignments for each domain: == domain 1 score: 22.6 bits; conditional E-value: 2.2e-08 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTE CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegf 76 +++++++i+d++ +G ++ +a g++++++++ +++++n+ +++ aa a++++++ +++e++ k + +e f tr|H2YLA3|H2YLA3_CIOSA 45 ITLICDGIKDAKIMGDVLKVALSSGCQQVYVME-GCVNIWNSSVLKRAAAAHFKIPILPNQQWENMEKLVSHE-F 117 68999**************************98.9*********************99999999976666655.3 PP >> tr|H2YY31|H2YY31_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.8 0.0 0.00037 1.1 16 38 .. 87 109 .. 86 144 .. 0.83 2 ? 3.6 0.0 0.016 45 62 102 .. 255 301 .. 244 307 .. 0.75 Alignments for each domain: == domain 1 score: 8.8 bits; conditional E-value: 0.00037 HHHHHHHHHTT-SEEEEESGSSC CS SpoU_methylase 16 GaiaRtakafgaselvlvkprsa 38 G iaR++ +f+++e+++ ++ + tr|H2YY31|H2YY31_CIOSA 87 GQIARACVIFQVDEIIVFDESAS 109 99***************996554 PP == domain 2 score: 3.6 bits; conditional E-value: 0.016 SSHHHHHHHHCCC..T.EEE.EEESTT-SEGCCSHHH..TTEEEEEE CS SpoU_methylase 62 dsleealkelkee..g.fal.vatslkgkslseidlk..ekvalvfG 102 +sl++a+ e+ + g ++l ++ts+kg+++s+++++ ++ ++vfG tr|H2YY31|H2YY31_CIOSA 255 NSLSSAIVECPYSdtGkYDLtIGTSEKGNPVSKFKMPkfKHLLIVFG 301 55666666655442223555589999******999998899*****9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 11592 (4231397 residues searched) Passed MSV filter: 248 (0.0213941); expected 231.8 (0.02) Passed bias filter: 217 (0.0187198); expected 231.8 (0.02) Passed Vit filter: 23 (0.00198413); expected 11.6 (0.001) Passed Fwd filter: 4 (0.000345066); expected 0.1 (1e-05) Initial search space (Z): 11592 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.03 # Mc/sec: 20028.61 // [ok]