# 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/Ciona_intestinalis.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
6.3e-65 219.5 0.1 1.4e-59 201.9 0.0 2.4 2 tr|F6PJM3|F6PJM3_CIOIN Uncharacterized protein OS=Ciona inte
8e-49 166.5 0.0 1.1e-48 166.0 0.0 1.2 1 tr|F6SVP7|F6SVP7_CIOIN Uncharacterized protein OS=Ciona inte
------ inclusion threshold ------
0.082 11.6 0.0 4.5 5.9 0.0 2.0 2 tr|F6WVN8|F6WVN8_CIOIN Uncharacterized protein OS=Ciona inte
Domain annotation for each sequence (and alignments):
>> tr|F6PJM3|F6PJM3_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 GN=LOC100181071 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 15.1 0.1 1.2e-06 0.0069 2 32 .. 9 39 .. 8 56 .. 0.86
2 ! 201.9 0.0 2.6e-63 1.4e-59 39 416 .] 153 545 .. 133 545 .. 0.90
Alignments for each domain:
== domain 1 score: 15.1 bits; conditional E-value: 1.2e-06
TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32
+g+ y+ +++g+ G l+ +++DF+V+Ei
tr|F6PJM3|F6PJM3_CIOIN 9 VGMTEYIGKHKGFTGILKMRYQDFMVNEIDL 39
89***************************43 PP
== domain 2 score: 201.9 bits; conditional E-value: 2.6e-63
TruD 39 akegeylvlrvekrnwdtldlvrelaralgisrkr.vgfaGtKDkrAvTtQlisirkvepeelekl.ei.kdvelevvgrarrklrl 122
+ +y+ + + k+n+ t+d+v+ + ++l++ + r +++aG KDkr+vT+Q ++ ++pe+l + +i +++++ ++++ + + rl
tr|F6PJM3|F6PJM3_CIOIN 153 DRGFPYCKFVLYKENIATMDAVNLILKKLNLRHARcFQYAGNKDKRGVTVQEVTT-SISPERLVPVnQIlSNIRVGNLVSCKTAKRL 238
3334789999*********************9988579**************995.46666654443444***************** PP
TruD 123 GdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtre 209
GdL GN+F i++r++ + e ++++++ +++ +++g + NyfG+QRFG++ t+++Gk i+ +ee v+ +++ f++ se+t +
tr|F6PJM3|F6PJM3_CIOIN 239 GDLNGNQFSIVIRNTLDIE--ESDLKAAIKSFSQTG-FINYFGMQRFGTNNVPTYEIGKSIISSRWEETVDLILSSCFKDCSEETIN 322
**************85555..489**********99.************************************************** PP
TruD 210 areavaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvv 295
++ e++++++a ++l+++ ++E +l + + pk+ ++l+++p+n ++l++h+yqS+++Nr++s+R+ d+pv GD+v
tr|F6PJM3|F6PJM3_CIOIN 323 LIRNWREENNAKKAFDKLNRRSSFEGYLLLGISHfGPKQLVQSLARIPRNTRMLYLHSYQSFVWNRIVSRRFLTF--GDSPVVGDLV 407
********************************9999************************************988..589******* PP
TruD 296 ifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRail 382
+ +e+ ++e+n+++++ v++pl+G +++ + + + ++ ++ +g+e ++F+ k++e G++R+i+
tr|F6PJM3|F6PJM3_CIOIN 408 LAGNEK------EVYMHEENIDNYS------IHDVIMPLPGHKVTYPTNSALQWYKDEFKAAGIEESMFDH-KVKEYYLPGAYRKII 481
*99887......8888999999988......44799**********************************5.579************ PP
TruD 383 lrve..............................dlelsaeedeltleFsLpkGsYATvvlrEi 416
+++ + e + + + l ++FsL + +YATv +rE+
tr|F6PJM3|F6PJM3_CIOIN 482 NKPNdvewdivkyndyqkpllasdkdilqggerpSGEKDGKFTALRISFSLSSSCYATVAMREV 545
***99**********************999865522333333459******************6 PP
>> tr|F6SVP7|F6SVP7_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 GN=LOC100184413 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 166.0 0.0 2e-52 1.1e-48 56 416 .] 1 416 [. 1 416 [. 0.81
Alignments for each domain:
== domain 1 score: 166.0 bits; conditional E-value: 2e-52
TruD 56 tldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.......ei..kdvelevvgrarrklrlGdLaGNkFeir 133
t++++++l+ l ++++++++aG+KDkrA+T Q +++++v++++ +++ ++ ++++++ v+ ++ +l +G+L+GN+F+i+
tr|F6SVP7|F6SVP7_CIOIN 1 TIQAIHQLSLLLDVKSSEFSYAGMKDKRAITLQRVAVSGVSKDNFKNVykllevsHVlpDHLRISHVIVTSLRLITGNLVGNRFDIK 87
67899***************************************999998887663367899************************* PP
TruD 134 vrdv.aeeeeaakraeeileelkekg.....gvPNyfGvQRFGsrrpvthl...........vGkaivkgdleeAveayvgkpfeee 203
+r+v + + + +++ i+ + + g+ NyfG QRFG+ r t++ vG a++k+++++Ave+++ + e+
tr|F6SVP7|F6SVP7_CIOIN 88 LRNVhGGKTTINIHLTLITTIIYAILffktkGFINYFGPQRFGR-RIDTKEpgsipqweapsVGLAMLKQNMKRAVEILLLPAVEAG 173
***95544444444444444333322555568***********9.67776444444444444*****************98887766 PP
TruD 204 s..edtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglp 285
+ +d ++ + ++++t ++eeal+++p++ E +l++L++ +++ +kAl ++p + + ++ h+y Syl+Nrv seRl++
tr|F6SVP7|F6SVP7_CIOIN 174 KpiDDEQKGKLLFQQTWNVEEALKLMPRHRFREIGILQSLQQtssSEQFCSKALLTIPFKERTFYAHSYSSYLWNRVASERLRQL-G 259
5236888999999****************999**********776666699********************************87.3 PP
TruD 286 ldepveGDvvifaeer.lpdtdrlqlvteknveevkrliergraf.vtaplvGtetelaegevgeierevleeegl.......eled 363
+++eGD+vi+++ + +++ + v+ ++vk ++r+ + v++pl+G +++ + +++ +++++e++l +
tr|F6SVP7|F6SVP7_CIOIN 260 -CDVIEGDLVIQRTGDsENIERHDSEVHVVVSDDVK--CNRFSIYdVVLPLPGNRVQYPPN-LDAVYDRIFKEDQLfigtepkASNY 342
.58*********977732233333445555555555..7888764489**********765.6889999**9999855554433456 PP
TruD 364 FklpklpelsskGtrRaillrve......................dlelsaeedeltleFsLpkGsYATvvlrEi 416
F+++k +l+ Gt+R+++ +++ ++l +++ +l l+F Lp+ +YAT++lrE+
tr|F6SVP7|F6SVP7_CIOIN 343 FRVNK-LKLNLCGTYRRLIEKPKnftinwesdvssqavtgdegmrCTTLADDGATLGLKFDLPSSCYATSILREL 416
88998.89**************9*****************99665334445555699****************96 PP
>> tr|F6WVN8|F6WVN8_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 3.9 0.1 0.0033 18 351 392 .. 9 45 .. 2 53 .. 0.72
2 ? 5.9 0.0 0.00082 4.5 288 368 .. 59 135 .. 51 141 .. 0.82
Alignments for each domain:
== domain 1 score: 3.9 bits; conditional E-value: 0.0033
TruD 351 revleeegleledFklpklpelsskGtrRaillrvedlelsa 392
+ e l+++d k + ++ ++s+G +R++ ++++++ +++
tr|F6WVN8|F6WVN8_CIOIN 9 N-----EALTADDLKSQMFQSMKSAGVVRQLKVQLRQTMINE 45
3.....44555566655555899**********999766554 PP
== domain 2 score: 5.9 bits; conditional E-value: 0.00082
TruD 288 epveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpk 368
+ + D++ + + +++ + v+++ ++ v ++i++ + t+ l+ e+ ++ + +++++l++ gl+ +d ++ +
tr|F6WVN8|F6WVN8_CIOIN 59 NLENSDLIAATMH---RRKSYSWVQTALDNIVLHHIKQSKYYYTLSLFEQESSVS-CYSKSLTEQLLSRLGLHDSDIEIDS 135
5555666666644...48889999999999*********************9995.66899999*********99988765 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 16678 (5370518 residues searched)
Passed MSV filter: 570 (0.0341768); expected 333.6 (0.02)
Passed bias filter: 267 (0.0160091); expected 333.6 (0.02)
Passed Vit filter: 22 (0.0013191); expected 16.7 (0.001)
Passed Fwd filter: 3 (0.000179878); expected 0.2 (1e-05)
Initial search space (Z): 16678 [actual number of targets]
Domain search space (domZ): 3 [number of targets reported over threshold]
# CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.06
# Mc/sec: 37235.59
//
[ok]