# 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/TrmO.hmm.txt # target sequence database: proteomes/Thermococcus_kodakarensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TrmO [M=119] Accession: PF01980.16 Description: tRNA-methyltransferase O 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-41 136.4 0.0 8e-41 136.1 0.0 1.1 1 tr|Q5JG53|Q5JG53_THEKO Uncharacterized protein OS=Thermococc 5.2e-26 88.3 0.0 9e-26 87.6 0.0 1.3 1 tr|Q5JED3|Q5JED3_THEKO Uncharacterized protein OS=Thermococc Domain annotation for each sequence (and alignments): >> tr|Q5JG53|Q5JG53_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 ! 136.1 0.0 6.9e-44 8e-41 1 119 [] 29 141 .. 29 141 .. 0.97 Alignments for each domain: == domain 1 score: 136.1 bits; conditional E-value: 6.9e-44 TS-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEE CS TrmO 1 giPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvvkl 87 ++P+q++ a+ +++++ ++pe+ ee+l+++e+fsh++l+++fh++ ++k++++ p +++n + GvfatR+p Rpnpig+s+v+l tr|Q5JG53|Q5JG53_THEKO 29 DVPIQASAARGIRGTVDVFPEF--EEGLKDIEGFSHVILIYHFHRA---RFKSLLVRPYMDENYH-GVFATRAPARPNPIGISIVRL 109 58********************..********************99...7899********9888.********************* PP EEEETTEEEEES----TT-EEEEEEE--HHHH CS TrmO 88 ekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119 + +gnvl v++vD+ldgtp+lDiKPYvp++D tr|Q5JG53|Q5JG53_THEKO 110 VERRGNVLIVEDVDVLDGTPLLDIKPYVPEFD 141 ******************************99 PP >> tr|Q5JED3|Q5JED3_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 ! 87.6 0.0 7.8e-29 9e-26 13 119 .] 22 128 .. 15 128 .. 0.87 Alignments for each domain: == domain 1 score: 87.6 bits; conditional E-value: 7.8e-29 EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.S..S--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEEEEEETTEEEE CS TrmO 13 eaeielepeynseealegleefshlwllfvfhenaekklk..akvrpprlggnervGvfatRsphRpnpiglsvvklekvegnvlev 97 e+ ie+ pe+ + a++gl e + + l+ +fhe+++ + + kv+p +n +GvfatRsp+Rpnpi+l +v+++++++n+l++ tr|Q5JED3|Q5JED3_THEKO 22 ETFIEILPEF--RGAIDGLREGDWIKLVLWFHESDTPARRrvLKVHPYGNPKNPLTGVFATRSPYRPNPIALYTVRVHRIDENRLYI 106 67799*****..99******************995544330144455555677889******************************* PP ES----TT-EEEEEEE--HHHH CS TrmO 98 sgvDlldgtpvlDiKPYvpyaD 119 +D+ dgtpv+DiK +v+++D tr|Q5JED3|Q5JED3_THEKO 107 DWIDAHDGTPVVDIKIFVERYD 128 *******************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (119 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 30 (0.0130378); expected 46.0 (0.02) Passed bias filter: 28 (0.0121686); expected 46.0 (0.02) Passed Vit filter: 3 (0.00130378); expected 2.3 (0.001) Passed Fwd filter: 2 (0.000869187); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok]