# 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/Trypanosoma_brucei.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.1e-62 211.2 0.0 4.2e-56 189.5 0.0 2.7 3 tr|Q38A69|Q38A69_TRYB2 Uncharacterized protein OS=Trypanosom
3.2e-40 137.2 0.0 1.5e-26 92.1 0.0 3.2 3 tr|Q381B8|Q381B8_TRYB2 Uncharacterized protein OS=Trypanosom
1.5e-33 115.2 0.0 1.6e-30 105.2 0.0 2.7 2 tr|Q383Z8|Q383Z8_TRYB2 tRNA pseudouridine synthase, putative
3.6e-18 64.5 0.0 1.7e-08 32.7 0.0 4.2 4 tr|Q4GZ59|Q4GZ59_TRYB2 Uncharacterized protein OS=Trypanosom
8.9e-06 23.7 0.0 1.5e-05 22.9 0.0 1.2 1 tr|Q38BP8|Q38BP8_TRYB2 Uncharacterized protein OS=Trypanosom
Domain annotation for each sequence (and alignments):
>> tr|Q38A69|Q38A69_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.9 0.0 0.3 5.2e+02 18 34 .. 63 79 .. 57 97 .. 0.75
2 ! 189.5 0.0 2.5e-59 4.2e-56 40 301 .. 213 475 .. 187 511 .. 0.88
3 ! 18.5 0.0 2e-07 0.00034 395 416 .] 640 661 .. 611 661 .. 0.85
Alignments for each domain:
== domain 1 score: -1.9 bits; conditional E-value: 0.3
TruD 18 lrespeDFiVeEieefs 34
+++ + DF+V+E++
tr|Q38A69|Q38A69_TRYB2 63 MKTLYSDFVVRELSLLY 79
788899******96653 PP
== domain 2 score: 189.5 bits; conditional E-value: 2.5e-59
TruD 40 kegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl......eikdvelevvgrarrkl 120
++ ++l +++ k+n+d+++++re+a+ l++ + + f+GtKDkrAvT Q +++r+v+pe+l + + ++v++ ++ ++++ l
tr|Q38A69|Q38A69_TRYB2 213 RSQKFLHFTLYKENIDSNHALREVASYLHVPTRSLLFSGTKDKRAVTLQRVAVRGVSPEKLIGInsrsfgQDRKVKVCSFRTMDHGL 299
457899******************************************************99996665555599************* PP
TruD 121 rlGdLaGNkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesed 206
rlGd +GN+F i +r + ++++ ++++++ + ++++++g v NyfG+QRFG++ t vG +++ g +e+A++ + ++ e+
tr|Q38A69|Q38A69_TRYB2 300 RLGDAVGNHFLIALRLLpESRDIDSDTLNTVESTINREG-VVNYFGTQRFGTTDVLTGDVGIQLLSGHFENALRLVFRSKSMVEPSM 385
*****************7666666778888888888876.*********************************98888877777766 PP
TruD 207 treareavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGD 293
+a +a+ e+g +eea++++p+ ++ Er ml++L+++p+d+ ++++++p+++++++ hA+qS ++N + s+Rle g+ p GD
tr|Q38A69|Q38A69_TRYB2 386 -LAAVDAL-EKGSFEEAVKLVPHYCHQERDMLNHLVDSPNDFLGSFSKIPRTMSMMYFHAVQSLIWNIMASKRLEVGV---VPQVGD 467
.5677777.8*******************************************************************5...599*** PP
TruD 294 vvifaeer 301
+v++++ +
tr|Q38A69|Q38A69_TRYB2 468 LVLKSRYT 475
**998766 PP
== domain 3 score: 18.5 bits; conditional E-value: 2e-07
TruD 395 deltleFsLpkGsYATvvlrEi 416
+ +++eFsLp+G YAT+vlrE+
tr|Q38A69|Q38A69_TRYB2 640 KAIVVEFSLPPGAYATCVLREF 661
5689*****************7 PP
>> tr|Q381B8|Q381B8_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 5.8 0.0 0.0015 2.5 16 35 .. 20 38 .. 6 57 .. 0.77
2 ! 92.1 0.0 9e-30 1.5e-26 44 278 .. 300 559 .. 284 567 .. 0.73
3 ! 36.0 0.0 9.5e-13 1.6e-09 327 416 .] 564 662 .. 558 662 .. 0.81
Alignments for each domain:
== domain 1 score: 5.8 bits; conditional E-value: 0.0015
TruD 16 GrlrespeDFiVeEieefsg 35
rl++ peDFiV E+ + g
tr|Q381B8|Q381B8_TRYB2 20 ARLKDCPEDFIVAEVDPA-G 38
69*************433.2 PP
== domain 2 score: 92.1 bits; conditional E-value: 9e-30
TruD 44 ylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.................ei.kdvel.e 111
++ l ++krn d ++l la+++ + ++v aG+KDk AvT+Q s+ ++ + ++ ++ + ve+ +
tr|Q381B8|Q381B8_TRYB2 300 FTHLLIRKRNLDIMELRMLLAEHFCVPIDAVCTAGMKDKCAVTYQRCSVPCTRQLRHPREeesgidgdvplrltwtdDLsSYVEIlQ 386
58899*******************************************744332222222233456778887888773336677615 PP
TruD 112 vvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGsrr.pvthlvGkaivkgdleeAveayv 196
g ++ ++ +G+L+GN F+ir+rdv + +++ + + +l+++g + NyfG+QRF + +G +i+ g + eAv++++
tr|Q381B8|Q381B8_TRYB2 387 TSGPHSAPVGIGELKGNMFHIRLRDVrGI---TPSELMQRSCRLEKEG-FLNYFGQQRFSEHAeCFMDHIGVHILGGRWPEAVRCLL 469
6799*********************9443...4468999999999988.**********9864134556****************99 PP
TruD 197 gkpfeee.....sedtreareavaetgdleealeelpkslry...EramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNr 274
+ e + + r + + + + + + +al++l+++ ry ra +++ ++ + + Al+a+p + l++ +qS +FNr
tr|Q381B8|Q381B8_TRYB2 470 RGAPELYdlfptHMEPRYVPARLRDARCIVQALNRLHRT-RYttlTRADVTECTQlWRDVCRDALQAVPYAFRVLWLCGAQSLIFNR 555
654443201000222334444445555555666655544.3312244444444445556699************************* PP
TruD 275 vlse 278
+ls+
tr|Q381B8|Q381B8_TRYB2 556 LLSM 559
**97 PP
== domain 3 score: 36.0 bits; conditional E-value: 9.5e-13
TruD 327 rafvtaplvGtetelaegevgeierevleeegl.eledFk.lpklpelsskGtrRaillrve.........dlelsaeede...... 396
+ vt+pl+G+++ + eg v+ ++vl e +l + ++F+ +k+ ++++ G+ Ra ++r+ + +
tr|Q381B8|Q381B8_TRYB2 564 QLPVTLPLLGYNVSV-EGGVRSAVDKVLMELNLgTVDEFAqRKKVLGVGMPGALRATVVRPVgcsvsfttvE-----G--Gssdvfd 642
5679**********9.5668888999999999956789*9888999**************997766433221.....2..1334666 PP
TruD 397 ltleFsLpkGsYATvvlrEi 416
+tl+F+Lp+ sYAT++lrE+
tr|Q381B8|Q381B8_TRYB2 643 ATLSFFLPSSSYATIFLREV 662
9******************6 PP
>> tr|Q383Z8|Q383Z8_TRYB2 tRNA pseudouridine synthase, putative OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) O
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 6.7 0.0 0.00073 1.3 6 36 .. 185 215 .. 180 227 .. 0.72
2 ! 105.2 0.0 9.3e-34 1.6e-30 37 415 .. 318 731 .. 308 732 .. 0.80
Alignments for each domain:
== domain 1 score: 6.7 bits; conditional E-value: 0.00073
TruD 6 lyvt.dtegigGrlrespeDFiVeEieefsge 36
+v+ +++g+ G +r++++DF+V+E+ e
tr|Q383Z8|Q383Z8_TRYB2 185 AFVSpNAPGFSGIFRQHWKDFLVTEMVYD-SE 215
55553679*****************9333.22 PP
== domain 2 score: 105.2 bits; conditional E-value: 9.3e-34
TruD 37 eeakegey.lvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl......eikdvelevvgra 116
+e ++g++ l + ++k+ + + +++++a++l+++ + ++ aG+KD + T Q + +++v+p++ ++ + ++l+++ +
tr|Q383Z8|Q383Z8_TRYB2 318 SEFRTGKFyLQCYLRKQHIAHSVALSNIAQTLRMHPSCISVAGIKDYIGDTLQRVRLQNVTPASALEAnrvfrkKKWAMTLSDFSYH 404
46677887799************************************************999985555555554447899******* PP
TruD 117 rrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeee 203
++l G+L GN+F+i++rdv+ + ++++++ + el+++g +PNy+G QRF t + ai+++++ +++ +++g ++ e
tr|Q383Z8|Q383Z8_TRYB2 405 TEPLFPGRLFGNHFKIVLRDVT-VP--KTCIQQAVYELQTHG-FPNYYGCQRFSWF-GGTNDAAFAILNQNWLAFAFRFLGYTSRE- 485
********************83.33..479**********98.**********885.778889******************98843. PP
TruD 204 sedtreareavaetgdleealeelpkslryEramlkrLae..................................kpkd.....ykkA 251
+ re++++++ + p + +y r++++rL++ + + ++A
tr|Q383Z8|Q383Z8_TRYB2 486 ----LTLRELLQREKKY-----PNPVQDEYRRNIVRRLRSiaiepseldtapflacpslgapltatdggpvskkQ--ElillqLQGA 561
....3567777444333.....3355667889999999999999999999999***************9997541..24555599** PP
TruD 252 lealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer..lpdtdrlqlvteknveevkrliergrafvtapl.v 335
+l+ +rl + Syl+N+vl Rl++ +e++eGD+v+ + r ++++++ ++ ++ v+ er+r +++ ++ +
tr|Q383Z8|Q383Z8_TRYB2 562 YLDLSVMSRRLTAQRLCSYLWNQVLTLRLHHF-GGKEVLEGDMVLPEVLRrvQTSPEERTDWYRQGIHLVETEEERERTSIMNVIhP 647
******************************98.67**********998886644444444445566677777777777665543325 PP
TruD 336 Gt...etelaegevgeierevleeegleledFklpklpelsskGtr...Raillrve..dlelsaeedeltleFsLpkGsYATvvlr 414
G+ +++l++ vge+ +v +++ le ++ + +l+ + + R+i+ +++ + ++++e+ +ltleFsL++GsYA vvl
tr|Q383Z8|Q383Z8_TRYB2 648 GFsfnSMRLPQNAVGEYFLQVCQKYHLEWHSRHS----RLGIHDFFeppRPIIRKPMnlRYDYDTESCKLTLEFSLERGSYANVVLT 730
541124789999************9999877652....3444444444599999999454445555666*****************9 PP
TruD 415 E 415
E
tr|Q383Z8|Q383Z8_TRYB2 731 E 731
8 PP
>> tr|Q4GZ59|Q4GZ59_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=TB
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.4 0.0 0.03 51 11 30 .. 74 93 .. 68 114 .. 0.85
2 ! 32.7 0.0 9.8e-12 1.7e-08 113 207 .. 913 1004 .. 894 1025 .. 0.82
3 ! 17.6 0.0 3.8e-07 0.00065 253 359 .. 1100 1204 .. 1091 1227 .. 0.88
4 ! 6.8 0.0 0.00068 1.2 375 416 .] 1395 1437 .. 1386 1437 .. 0.78
Alignments for each domain:
== domain 1 score: 1.4 bits; conditional E-value: 0.03
TruD 11 tegigGrlrespeDFiVeEi 30
+g++ +++sp+D++V+E+
tr|Q4GZ59|Q4GZ59_TRYB2 74 VKGFQAYIKSSPDDYVVKEL 93
689999*************9 PP
== domain 2 score: 32.7 bits; conditional E-value: 9.8e-12
TruD 113 vgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsr.rpvthlvGkaivkgdleeAveayv 196
v +a+ +lr+Gd G ++++++r ++ ++ ++ + +l+++g + NyfG QRF s r + h G +++kg++++A+ ++v
tr|Q4GZ59|Q4GZ59_TRYB2 913 VTSASYDLRMGDNDGYDYRVKLRRIP--QSHFPLVKPAMVSLQKHG-FINYFGPQRFSSYtRYNMH-PGLHLLKGEFHAAASIIV 993
4566789*****************94..456899**********98.**********996266666.8*************9999 PP
TruD 197 gkpfeeesedt 207
+ + + +
tr|Q4GZ59|Q4GZ59_TRYB2 994 QQFYMDSDLAA 1004
88776655444 PP
== domain 3 score: 17.6 bits; conditional E-value: 3.8e-07
TruD 253 ealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGt 337
+++ ++ ++ vh + ++l+N+++++Rl+r+ ++ +++GD+v + + p+++++ +v ++ ++++ + + v++p++G
tr|Q4GZ59|Q4GZ59_TRYB2 1100 RVVGPKACSMLVHEFLAFLWNDIVNQRLQRYGTF-AILPGDLVRLNPLASPHSNEFGRVVYASKNSIE-KGKYTCYDVVLPVPGA 1182
567778889**********************776.7**********9999999999999999888888.667778899******* PP
TruD 338 etelaegevgeierevleeegl 359
+el++ ++ ++ l++ g+
tr|Q4GZ59|Q4GZ59_TRYB2 1183 GVELPDNHTADLYVVTLKRMGI 1204
******9999988888887776 PP
== domain 4 score: 6.8 bits; conditional E-value: 0.00068
TruD 375 kGtrRaillrvedlelsaeede.ltleFsLpkGsYATvvlrEi 416
G+rRa l+ + l +++++ l+l+F+Lp+ Y ++lrE+
tr|Q4GZ59|Q4GZ59_TRYB2 1395 GGKRRARTLPAAPYWLPEKNNGcLELSFQLPSSVYPSMLLREV 1437
577777777777666666666669******************6 PP
>> tr|Q38BP8|Q38BP8_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 22.9 0.0 8.8e-09 1.5e-05 210 316 .. 572 679 .. 558 696 .. 0.74
Alignments for each domain:
== domain 1 score: 22.9 bits; conditional E-value: 8.8e-09
TruD 210 areavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296
r+++++ + +++a + ++ + r+ lk++ +++++++ ++++p +r +++A +S ++N + s+Rl +++++GD+v+
tr|Q38BP8|Q38BP8_TRYB2 572 LRQFIKRPNVITAARARRASTDPTIRQALKNYELTQGNWEQTVARIPYVWRRRWLNALRSSVWNVMASRRLSLDGASRRVIPGDIVF 658
5666643333444444444444567999999999***************************************99***********9 PP
TruD 297 faeer.lpdtdrlqlvteknv 316
e r +++ + +v++++v
tr|Q38BP8|Q38BP8_TRYB2 659 RPEYRaDVHHRMIPTVKAEHV 679
998883222222233333333 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 8561 (4332363 residues searched)
Passed MSV filter: 327 (0.0381965); expected 171.2 (0.02)
Passed bias filter: 147 (0.0171709); expected 171.2 (0.02)
Passed Vit filter: 21 (0.00245298); expected 8.6 (0.001)
Passed Fwd filter: 5 (0.000584044); expected 0.1 (1e-05)
Initial search space (Z): 8561 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.05
# Mc/sec: 36045.26
//
[ok]