# 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/Caenorhabditis_elegans.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.4e-58 198.1 0.0 8.6e-55 186.4 0.0 3.2 2 sp|Q17426|YQ4B_CAEEL Putative pseudouridine synthase B0024.1
Domain annotation for each sequence (and alignments):
>> sp|Q17426|YQ4B_CAEEL Putative pseudouridine synthase B0024.11 OS=Caenorhabditis elegans OX=6239 GN=B0024.11 PE=3 SV=
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 3.9 0.0 0.0011 21 12 33 .. 17 38 .. 4 80 .. 0.76
2 ! 186.4 0.0 4.3e-59 8.6e-55 41 416 .] 148 530 .. 101 530 .. 0.85
Alignments for each domain:
== domain 1 score: 3.9 bits; conditional E-value: 0.0011
TruD 12 egigGrlrespeDFiVeEieef 33
++ + l+e + DFiV+Ei +
sp|Q17426|YQ4B_CAEEL 17 TPVPCLLKEMYSDFIVQEILAD 38
467789*************655 PP
== domain 2 score: 186.4 bits; conditional E-value: 4.3e-59
TruD 41 egeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlGdLaG 127
+ + +++ k+n +t + + +a+ l++ ++++ G+KDkrAvT+Q +s++kv+++++ +l +++++++ ++ ++++G ++G
sp|Q17426|YQ4B_CAEEL 148 VPKECHFTICKENKETSFACQLIAKFLNVGPNNIRTHGIKDKRAVTSQRVSVTKVHERTILDLnsKLRGIRVFGCEYKDDPVQMGAHWG 236
3556999*****************************************************9998889********************** PP
TruD 128 NkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeee..sedtreareav 214
N+F i++r ++++ ++ +++ le+ +++g + NyfG+QRFGsr ++t ++G aivk+d+e+Av+ +++++++++ ++ a + +
sp|Q17426|YQ4B_CAEEL 237 NRFSIVLRSLPDD--SEQLLHQRLETFQNTG-FINYFGTQRFGSRSSTTAEIGLAIVKRDWEKAVKMIMTNAMPDHlgYGSVGYAAKCF 322
*********8644..45899*********99.***************************************9999822467889999** PP
TruD 215 aetgdleealeelpkslry...EramlkrLaekpkdykkAl.ealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifae 299
++tgd+++a ++l+ + E ++lk L + ++++++ + ea+p + ++l+vhAyqS ++N+v s+R++++ +++ e Dv +
sp|Q17426|YQ4B_CAEEL 323 SQTGDARKAFSKLKGAQAFatvEGNILKCLSK-GGTWQNCItEAIPIQSRSLYVHAYQSLIWNKVASRRVKEYG--TRVHESDVGANG- 407
*********9999876543334**********.999**9984579**************************993..355555554332. PP
TruD 300 erlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFk.lpklpelsskGtrRaillrve. 386
++ +++ + + +pl+G + +++ + ++e+lee+gl++++F l++ ++s + R ++++ +
sp|Q17426|YQ4B_CAEEL 408 -----------------FSLGEHA--THYDIHIPLPGENLPFEGSYGAKWISELLEEDGLTQSSFTaLKD--RFSLGESSRCLFVEAKe 475
.................2233333..4456779*********************************6665..78777778999999999 PP
TruD 387 .........................dlelsaeede.....ltleFsLpkGsYATvvlrEi 416
+ e++ l+++FsL +GsYATv lrE+
sp|Q17426|YQ4B_CAEEL 476 lkwkfirygnardllqdglqtraipE-----AEQKgpllaLQIQFSLISGSYATVALREV 530
99***************998643222.....22223567799*****************6 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 20008 (8229220 residues searched)
Passed MSV filter: 718 (0.0358856); expected 400.2 (0.02)
Passed bias filter: 354 (0.0176929); expected 400.2 (0.02)
Passed Vit filter: 25 (0.0012495); expected 20.0 (0.001)
Passed Fwd filter: 1 (4.998e-05); expected 0.2 (1e-05)
Initial search space (Z): 20008 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.23u 0.01s 00:00:00.24 Elapsed: 00:00:00.09
# Mc/sec: 38037.28
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