# 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/TruD.hmm.txt
# target sequence database: proteomes/Thermococcus_kodakarensis.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TruD [M=416]
Accession: PF01142.17
Description: tRNA pseudouridine synthase D (TruD)
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.6e-137 455.1 0.0 3.1e-137 454.9 0.0 1.0 1 sp|Q5JDB6|TRUD_THEKO Probable tRNA pseudouridine synthase D
Domain annotation for each sequence (and alignments):
>> sp|Q5JDB6|TRUD_THEKO Probable tRNA pseudouridine synthase D OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 454.9 0.0 1.3e-140 3.1e-137 7 416 .] 12 412 .. 7 412 .. 0.96
Alignments for each domain:
== domain 1 score: 454.9 bits; conditional E-value: 1.3e-140
TruD 7 yvtdtegigGrlrespeDFiVeEieefsgeeeakegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkv 95
++++++gigG+++ peDFiV E + s + +y ++ ++krnw+t+ +v+e+a+++gi+ +++gfaGtKD++AvT+Q+is+
sp|Q5JDB6|TRUD_THEKO 12 HLSEKPGIGGKIKIYPEDFIVIEEPIPS---IFEGRKYAIFLLKKRNWETMAAVKEIAKRAGINYREIGFAGTKDRHAVTYQYISVPAE 97
6789*****************8874443...3567899************************************************999 PP
TruD 96 epeelekleikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaiv 184
e++e+++i+d+el+ v +r ++lG+L GN+F+i+vrdv +e+a +r++ei++el+ekgg+PNyfG+QRFG+rr v+h++Gk ++
sp|Q5JDB6|TRUD_THEKO 98 ARERVEQVSIRDIELRFVS-YGRFIKLGHLLGNRFRIIVRDV--SEDAFDRTKEIVRELREKGGFPNYFGYQRFGERRVVNHIIGKLLL 183
99*************9987.78*******************8..456899*************************************** PP
TruD 185 kgdleeAveayvgkpfeeesedtreareavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFN 273
+gd+e+A++ ++g + +++ d ear++++etgd+e+alee+p lryEr++l+r+++ ++++k+A+ +lp ++ r+F+hAyqSylFN
sp|Q5JDB6|TRUD_THEKO 184 QGDFEGAARLFLGAHDGSMEGD--EARKNFWETGDVERALEEFPGFLRYERTLLHRYKD-TGNWKRAFLSLPLPIMRIFIHAYQSYLFN 269
**************99999888..9*********************************9.***************************** PP
TruD 274 rvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeeglele 362
+ls+R+e+glpl+ep+ GD+v++ + +p +dr+ +vte+n+e v++++++++a+v++pl+G+ ++ a+g +ge+e+e+leeegl+le
sp|Q5JDB6|TRUD_THEKO 270 LYLSRRIEEGLPLNEPLVGDIVVQVKGGIPYRDRTYRVTETNLEFVREKVRKNQAMVSGPLFGFAMRRAKGLPGELEKEILEEEGLSLE 358
***************************************************************************************** PP
TruD 363 dFk.lpklpelsskGtrRaillrvedlelsaeede.ltleFsLpkGsYATvvlrEi 416
F+ lpk +++ G rR++llr++ +++ ++e ++++F+LpkG+YAT+vlrEi
sp|Q5JDB6|TRUD_THEKO 359 TFRrLPK--PMAEPGGRRELLLRPMGMAYGYIQEEgMCFRFFLPKGTYATSVLREI 412
***9999..****************99998765555*******************7 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 2301 (637680 residues searched)
Passed MSV filter: 84 (0.0365059); expected 46.0 (0.02)
Passed bias filter: 62 (0.0269448); expected 46.0 (0.02)
Passed Vit filter: 5 (0.00217297); expected 2.3 (0.001)
Passed Fwd filter: 1 (0.000434594); expected 0.0 (1e-05)
Initial search space (Z): 2301 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 26527.49
//
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