# 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/Thermococcus_kodakarensis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-35 117.8 0.0 7.8e-35 117.2 0.0 1.3 1 tr|Q5JGC0|Q5JGC0_THEKO Probable tRNA/rRNA methyltransferase, 4.8e-07 27.1 0.0 0.0016 15.7 0.0 2.2 2 tr|Q5JDI9|Q5JDI9_THEKO Uncharacterized protein OS=Thermococc 0.00084 16.6 0.0 0.0011 16.2 0.0 1.2 1 sp|Q5JEG5|TRM56_THEKO tRNA (cytidine(56)-2'-O)-methyltransf Domain annotation for each sequence (and alignments): >> tr|Q5JGC0|Q5JGC0_THEKO Probable tRNA/rRNA methyltransferase, SpoU family OS=Thermococcus kodakarensis (strain ATCC B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.2 0.0 1e-37 7.8e-35 2 142 .] 2 150 .. 1 150 [. 0.91 Alignments for each domain: == domain 1 score: 117.2 bits; conditional E-value: 1e-37 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEEST.T-S CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvatsl.kgk 86 + vvlve+e p N+G+iaRt+k+fg+s+lvl++p+ ++e ++ a++a++vle + + ds+e+al+ ++ + v+t++ gk tr|Q5JGC0|Q5JGC0_THEKO 2 ISVVLVEPEGPANIGMIARTMKNFGFSRLVLINPNL----TEESYAYAVHARDVLEnALILDSFEKALELFDFT----VGTTGkPGK 80 78*******************************776....699*****************************99....888887777 PP EGCCS..............HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 87 slsei..............dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142 ++ + d++++v ++fG+E+ Gl+ne+l+++d +++Ip+s+e++ +N+a+A+a++ly tr|Q5JGC0|Q5JGC0_THEKO 81 RFIPHraplmpwelvglikDYPGEVGIFFGRESIGLKNEELDAMDVTLTIPTSEEYPVMNLAQAAAVVLY 150 6663333556667788888888**********************************************99 PP >> tr|Q5JDI9|Q5JDI9_THEKO Uncharacterized protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.4 0.0 0.00018 0.14 15 42 .. 25 49 .. 19 77 .. 0.80 2 ! 15.7 0.0 2.1e-06 0.0016 59 110 .. 158 213 .. 113 232 .. 0.78 Alignments for each domain: == domain 1 score: 9.4 bits; conditional E-value: 0.00018 HHHHHHHHHHTT-SEEEEESGSSCTCGS CS SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadlln 42 +G +aR++++fg++++++ + + + tr|Q5JDI9|Q5JDI9_THEKO 25 VGQVARACSIFGVEHIWIYRAGGR---D 49 8**************999775444...4 PP == domain 2 score: 15.7 bits; conditional E-value: 2.1e-06 EEESSHHHHHHHHCCCTEEE.EEESTT-SEGCCSHHH...TTEEEEEEBTTTBS-H CS SpoU_methylase 59 kvvdsleealkelkeegfal.vatslkgkslseidlk...ekvalvfGnEdkGlsn 110 +v+ + +++ k lk++g++l +ats+kg++++e++++ ++v +vfG+ +kG+ + tr|Q5JDI9|Q5JDI9_THEKO 158 RVHLTRKSLAKTLKKAGLDLvIATSRKGRDIREVEIPpleGEVGFVFGSPRKGVME 213 56666677778888899777477777******99777777***********99976 PP >> sp|Q5JEG5|TRM56_THEKO tRNA (cytidine(56)-2'-O)-methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.2 0.0 1.5e-06 0.0011 18 122 .. 24 132 .. 18 145 .. 0.77 Alignments for each domain: == domain 1 score: 16.2 bits; conditional E-value: 1.5e-06 HHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCS......HHH..TTE CS SpoU_methylase 18 iaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgkslsei......dlk..ekv 97 +a ta+afga+++++ +++ + ++ + + +e++ +s++++l+e+k++g+ + ++ +g +++++ +lk + sp|Q5JEG5|TRM56_THEKO 24 VALTARAFGADKIIIAAEEDE-HVKESVEDVVNRWGGPFEIEFNPSWKKILREWKDRGIIV-HLTMYGIHIDDAiprikdELKsgKDL 109 56699**********996665.888889999888888889999**************6555.44466776665445444433366*** PP EEEEEBTTTBS-HHHHCTSSEEEE- CS SpoU_methylase 98 alvfGnEdkGlsnelleladrlvkI 122 ++v+G E+ +++e+ e ad+ v + sp|Q5JEG5|TRM56_THEKO 110 LIVVGAEK--VPREVYEMADYNVAV 132 *******7..788888888887766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 77 (0.0334637); expected 46.0 (0.02) Passed bias filter: 74 (0.0321599); expected 46.0 (0.02) Passed Vit filter: 13 (0.00564972); expected 2.3 (0.001) Passed Fwd filter: 3 (0.00130378); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9055.06 // [ok]