# 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/Danio_rerio.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.5e-72 245.3 0.0 3.4e-67 227.6 0.0 2.5 2 tr|B1H1H9|B1H1H9_DANRE Pseudouridine synthase 7 OS=Danio rer
6e-67 226.8 0.0 2.8e-61 208.1 0.0 2.1 2 sp|Q1L8I0|PUS7L_DANRE Pseudouridylate synthase 7 homolog-li
------ inclusion threshold ------
0.56 9.5 3.1 1.3 8.3 3.1 1.5 1 tr|E7F3M3|E7F3M3_DANRE Rho guanine nucleotide exchange facto
Domain annotation for each sequence (and alignments):
>> tr|B1H1H9|B1H1H9_DANRE Pseudouridine synthase 7 OS=Danio rerio OX=7955 GN=pus7 PE=1 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 14.9 0.0 1.5e-06 0.013 2 32 .. 68 98 .. 67 114 .. 0.89
2 ! 227.6 0.0 4e-71 3.4e-67 39 416 .] 218 608 .. 204 608 .. 0.90
Alignments for each domain:
== domain 1 score: 14.9 bits; conditional E-value: 1.5e-06
TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32
+gi+ +++++ g+ G l+e++ DF+V+Ei++
tr|B1H1H9|B1H1H9_DANRE 68 VGIHRFISEHTGFSGILKERYSDFVVHEINK 98
899**************************55 PP
== domain 2 score: 227.6 bits; conditional E-value: 4e-71
TruD 39 akegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlG 123
+++g+++ + + k+n dt+++++ l+r l++ + ++++GtKDkrA+++Q i++ k+++e+l++l + +++l ++ ++++l+lG
tr|B1H1H9|B1H1H9_DANRE 218 KNRGSFCHFVLYKENKDTMEAINILSRFLRVRPNMFSYMGTKDKRAISVQEIAVLKISAERLSHLnkCLMNLKLGNFCYKKHPLKLG 304
6789***********************************************************996668****************** PP
TruD 124 dLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtrea 210
+L+GN+F++++r+++ ++++++ +++l+++g + Ny+G+QRFG++ th vG+ai++++++e v+ ++ +e+ +
tr|B1H1H9|B1H1H9_DANRE 305 ELQGNHFTVVLRNIS---GSQQQVDQAMNSLQNTG-FINYYGMQRFGTTAVPTHRVGRAILQNNWKEVVDLILKPRPGAEKGYLVKC 387
*************94...34579**********99.***********************************99999999******** PP
TruD 211 reavaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296
re a+t+d ++al++lp + +E ++l+ La+ ++++ A++ +p+n + +++h+yqSy++N ++s+R++++ ++veGD+++
tr|B1H1H9|B1H1H9_DANRE 388 REEWARTQDPAAALRKLPVKRCVEGQLLRGLAKhGKHNIITAFALIPRNNRLMYIHSYQSYVWNSMVSRRVDAY-G-LRAVEGDLIL 472
*********************************4456799********************************99.3.59*******9 PP
TruD 297 faeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaill 383
++ ++ ++e++ + v++pl+G+++ + vg+ re+l+ ++l+ ++ + +k+ + s +G++R++l+
tr|B1H1H9|B1H1H9_DANRE 473 RGGSA-----HVLSADEAQK--------HSIHDVVMPLPGFDVIYPTHSVGQGYREMLSADDLDIDNMR-HKVRDYSLAGAYRRVLI 545
99666.....3444444333........3445899*********************************9.5579************* PP
TruD 384 rve.............................dlelsaeede.........ltleFsLpkGsYATvvlrEi 416
r++ l++eFsLp+ +YAT+ +rE+
tr|B1H1H9|B1H1H9_DANRE 546 RPSdvswelvqyddprvplvhtdleklenkpaP--------VyltegkycaLKMEFSLPSSTYATMAVREV 608
********************8888877776542........022222345699****************96 PP
>> sp|Q1L8I0|PUS7L_DANRE Pseudouridylate synthase 7 homolog-like protein OS=Danio rerio OX=7955 GN=pus7l PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 16.7 0.0 4.3e-07 0.0037 5 33 .. 7 35 .. 4 59 .. 0.78
2 ! 208.1 0.0 3.3e-65 2.8e-61 38 416 .] 241 637 .. 220 637 .. 0.87
Alignments for each domain:
== domain 1 score: 16.7 bits; conditional E-value: 4.3e-07
TruD 5 elyvtdtegigGrlrespeDFiVeEieef 33
+++++d+eg++G++++sp+DF+V Ei +
sp|Q1L8I0|PUS7L_DANRE 7 SCFISDHEGFNGTIKNSPQDFVVIEIDTN 35
689***********************554 PP
== domain 2 score: 208.1 bits; conditional E-value: 3.3e-65
TruD 38 eakegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl....eikdvelevvgrarrklr 121
++e y+ ++++k+n +tl++++ +a lg+ +++++aG+KDkrA+T+Q + ++k++pe+l + e +++e++ v a ++l+
sp|Q1L8I0|PUS7L_DANRE 241 MQEESLYTAFTLRKENLETLEAISYMAAVLGVLPSDFTYAGIKDKRAITYQAMVVKKISPERLLEKgsefERRGMEISRVRPAFEALK 328
45567789******************************************************8776676677**************** PP
TruD 122 lGdLaGNkFeirvrdv.aeee.....eaakraeeileelkekggvPNyfGvQRFGsrrpv.thlvGkaivkgdleeAveayvgkpfee 202
lG+L+GN+Fe+++rd+ ++ e+ k +ee +e++k+kg + Ny+G QRFGs v vG a++k+++e+ v+ +++ ++
sp|Q1L8I0|PUS7L_DANRE 329 LGRLQGNHFELVIRDLkHH-GkhglaELPKVIEEAVENVKNKG-FVNYYGPQRFGSGSCVqADQVGLALLKENMEASVKLFFTPEDDD 414
***************8444.35888888899999999999988.************88762579**************9998765544 PP
TruD 203 esedtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpld 287
+ ++a++++ +tg+++e+l ++p Er ml++L + ++ + +lp+ ++ +++h+y S ++N++ + Rl++ +
sp|Q1L8I0|PUS7L_DANRE 415 --DLQNKAKRHFLHTGNAKESLVLMPAYKARERLMLRALHRygsGQEGCTRGWLSLPHSMRVFYLHSYCSRVWNQAAKYRLQKL-GF- 498
..34446777777****************************77666678889999***************************77.55. PP
TruD 288 epveGDvvifaeerlpdtdrlqlvteknveevkrliergraf....vtaplvGtetelaegevgeierevleeegleledFklpklpe 371
+pv+GD+v+ + + +d+++ +++ +++ v++ e++++f v++p++G +++ +e g+ ++ l+++gle F+++ +
sp|Q1L8I0|PUS7L_DANRE 499 KPVQGDLVWAEPVK-GLKDATEELSAPQIHVVTSDEEKNEVFsldqVILPMPGNSVKYPENLLGQWYQDRLAQDGLESCRFRVTP-LK 584
8********99766.888999999999999999999998886444489**********************************876.7* PP
TruD 372 lsskGtrRaillrve......dlelsaeede..ltleFsLpkGsYATvvlrEi 416
l++ G +R++l +++ +++ s+e+++ l l+F L+ +YATv l Ei
sp|Q1L8I0|PUS7L_DANRE 585 LNVPGCYRPLLAKPQnityslQTSSSDESNThcLSLNFDLEASCYATVCLGEI 637
***************88887733333333335699*************99885 PP
>> tr|E7F3M3|E7F3M3_DANRE Rho guanine nucleotide exchange factor (GEF) 37 OS=Danio rerio OX=7955 GN=arhgef37 PE=1 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 8.3 3.1 0.00015 1.3 186 264 .. 21 103 .. 20 105 .. 0.82
Alignments for each domain:
== domain 1 score: 8.3 bits; conditional E-value: 0.00015
TruD 186 gdleeAveayvgkpfeeesedtrea.reavaetgdleealeelpkslryEramlkrLaekpkdykkAleal...pknLqrlFv 264
+++e+A+e++ + ++e+ + r a ea+a+++ +++ l ++ + +++E+++lk+L+ + ++++ l++l p+nL+++F
tr|E7F3M3|E7F3M3_DANRE 21 KEMENALEELAEEEEDKEERKARVAaEEAAARERAAQRQLMAIEEMVHTEKNYLKHLQICTVTINSNLQKLqppPPNLENMFQ 103
588999999999998888888775516667889999**********************9788888877776444789999995 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 25687 (13798380 residues searched)
Passed MSV filter: 1137 (0.0442636); expected 513.7 (0.02)
Passed bias filter: 500 (0.0194651); expected 513.7 (0.02)
Passed Vit filter: 49 (0.00190758); expected 25.7 (0.001)
Passed Fwd filter: 3 (0.000116791); expected 0.3 (1e-05)
Initial search space (Z): 25687 [actual number of targets]
Domain search space (domZ): 3 [number of targets reported over threshold]
# CPU time: 0.39u 0.02s 00:00:00.41 Elapsed: 00:00:00.12
# Mc/sec: 47834.38
//
[ok]