# 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/Nematostella_vectensis.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.2e-72 243.7 0.0 6.4e-68 229.9 0.0 2.3 2 tr|A7T011|A7T011_NEMVE Predicted protein (Fragment) OS=Nemat
1.7e-18 67.1 0.0 2e-18 66.9 0.0 1.0 1 tr|A7SX02|A7SX02_NEMVE Predicted protein (Fragment) OS=Nemat
8.4e-06 25.3 0.1 0.00015 21.2 0.0 2.3 2 tr|A7SWX0|A7SWX0_NEMVE Predicted protein (Fragment) OS=Nemat
------ inclusion threshold ------
0.036 13.3 0.0 0.055 12.7 0.0 1.2 1 tr|A7SSD7|A7SSD7_NEMVE Predicted protein OS=Nematostella vec
Domain annotation for each sequence (and alignments):
>> tr|A7T011|A7T011_NEMVE Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g139787 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 11.7 0.0 1.9e-05 0.11 2 31 .. 4 33 .. 3 76 .. 0.89
2 ! 229.9 0.0 1e-71 6.4e-68 43 416 .] 143 531 .. 129 531 .. 0.91
Alignments for each domain:
== domain 1 score: 11.7 bits; conditional E-value: 1.9e-05
TruD 2 lgielyvtdtegigGrlrespeDFiVeEie 31
+gi +++++eg++G l++++ DFiV E +
tr|A7T011|A7T011_NEMVE 4 VGITEFIAKHEGFQGVLKQRYVDFIVYERN 33
8999***********************984 PP
== domain 2 score: 229.9 bits; conditional E-value: 1e-71
TruD 43 eylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlGdLaG 127
+++ + + k+n dt+++++ la+ l+++ +g+aGtKD+r+vT+Q +s +kv +e+l+ l ++++++l ++ ++klrlGdL G
tr|A7T011|A7T011_NEMVE 143 DHCKFVLFKENKDTMEAISLLAKLLHVKPGVFGYAGTKDRRGVTVQEVSGYKVLAERLQGLnnTLRGLRLGNFEYCKEKLRLGDLSG 229
56778899***************************************************998899********************** PP
TruD 128 NkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtreareav 214
N+F i++r+v+ +++ +e+ + +lk+ g + NyfG+QRFG+ th +G+a++ +++eAv+ ++ +p e +++d ++a e+
tr|A7T011|A7T011_NEMVE 230 NHFVITLRNVS---GNCEVIERAMTSLKDVG-FINYFGLQRFGTSCVPTHHIGRALILSQWSEAVD-LILNPREGKPKDFNKALEYW 311
*********83...45779**********98.*********************************8.5779**************** PP
TruD 215 aetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaee 300
+ tgd++ al++l ++ +E +l+ ++ ++d +Al+ +p+n + ++vhAyqSy++N+++s+R++++ pveGD+v+ +
tr|A7T011|A7T011_NEMVE 312 KSTGDAKGALSRLARKKCIESYLLQGFVNqGSQDLVGALQMIPRNTRLMYVHAYQSYIWNNMVSHRIREYG--LVPVEGDLVVSGHT 396
**************************99946789**********************************994..47*******99966 PP
TruD 301 rlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrve. 386
+ v++ + ++++ + v++p++G++++ + +v++ re+++ +g++ ++ + +++++ s +G++R+i+++++
tr|A7T011|A7T011_NEMVE 397 Q---------VRTLSHDDIS-SQKYSIHDVVMPVPGYDVTYPGKDVRDWYRELMAVDGVDIDKMR-HRVKDYSLSGAYRPIIIKPQh 472
5.........5555555555.2334455799*********************************9.4578***************** PP
TruD 387 ...........................dlelsaeede....ltleFsLpkGsYATvvlrEi 416
d + ae+d+ l++e +Lp+ +YAT+ lrE+
tr|A7T011|A7T011_NEMVE 473 tswkfihyndvtaplaltdldrlegrtD--IPAETDGqylaLQIELTLPSSCYATMALREV 531
***********************99653..444444445669999***************6 PP
>> tr|A7SX02|A7SX02_NEMVE Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g136095 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 66.9 0.0 3.2e-22 2e-18 213 382 .. 2 172 .. 1 178 [. 0.85
Alignments for each domain:
== domain 1 score: 66.9 bits; conditional E-value: 3.2e-22
TruD 213 avaetgdleealeelpkslryEramlkrLaekpkd...ykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296
+++etgd+ l ++p + Er +lk+L ++++d +Al +lp + l+ h+y S ++N++ s+R++ + +++ +GD+v+
tr|A7SX02|A7SX02_NEMVE 2 YYEETGDIPGTLARMPPGQTRERLILKALHRHGRDkygCTQALLSLPYSARLLYAHSYTSLAWNHAASARVRLYG-STRVAAGDLVY 87
6899***************************7777555899*******************************995.59********* PP
TruD 297 faeer...lp.dtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrR 379
+++++ +p d+ ++ +v+e+ + + a v++pl+G+++ +e + + + l+++ l++edF+l k +ls G++R
tr|A7SX02|A7SX02_NEMVE 88 DSQSAssqTPiDKCAVRVVSEDDAG----SGKYSMADVVLPLPGYSVIYPENKIADSYQGTLNSDRLRAEDFRLRK-LGLSLPGAYR 169
**88865322022222223332222....34677899*************************************99.9********* PP
TruD 380 ail 382
+++
tr|A7SX02|A7SX02_NEMVE 170 KLV 172
986 PP
>> tr|A7SWX0|A7SWX0_NEMVE Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g218766 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.5 0.0 0.023 1.4e+02 21 36 .. 22 36 .. 20 68 .. 0.73
2 ! 21.2 0.0 2.4e-08 0.00015 132 188 .. 399 460 .] 397 460 .] 0.63
Alignments for each domain:
== domain 1 score: 1.5 bits; conditional E-value: 0.023
TruD 21 speDFiVeEieefsge 36
speDFiV+E+ e ge
tr|A7SWX0|A7SWX0_NEMVE 22 SPEDFIVTELDEN-GE 36
89********554.33 PP
== domain 2 score: 21.2 bits; conditional E-value: 2.4e-08
TruD 132 irvrdv.aeee...eaakraeeileelkekggvPNyfGvQRFGsr..rpvthlvGkaivkgdl 188
i+vr+v + ++ ++ ++ +++++++ g+ NyfG QRFG++ + vG a+++gd+
tr|A7SWX0|A7SWX0_NEMVE 399 IKVRGVqPLASssqGITELVKTAVSNVSRH-GFVNYFGPQRFGQEdnSVNASDVGLAMLQGDV 460
788887332221112333344444455554.6***********8622568889*******995 PP
>> tr|A7SSD7|A7SSD7_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g247105 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.7 0.0 8.9e-06 0.055 288 376 .. 6 93 .. 2 109 .. 0.88
Alignments for each domain:
== domain 1 score: 12.7 bits; conditional E-value: 8.9e-06
TruD 288 epveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelss 374
++v+ D+v++++ ++ ++dr +v++ +ev++li+ ++ +++ v + ++g+ ++ e+e+ e+ g++l+d k k++ l+s
tr|A7SSD7|A7SSD7_NEMVE 6 QTVDYDFVLDSNIHVIQPDRGVRVRRWLSHEVEQLIDLFEERPCLWDVSNKEYYQKGNRQRAEEEIAEQMGITLNDVKS-KIKSLRS 91
6788899****9999*************************************************************994.4677777 PP
TruD 375 kG 376
+
tr|A7SSD7|A7SSD7_NEMVE 92 QL 93
64 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 24428 (8257945 residues searched)
Passed MSV filter: 759 (0.0310709); expected 488.6 (0.02)
Passed bias filter: 411 (0.016825); expected 488.6 (0.02)
Passed Vit filter: 31 (0.00126904); expected 24.4 (0.001)
Passed Fwd filter: 4 (0.000163747); expected 0.2 (1e-05)
Initial search space (Z): 24428 [actual number of targets]
Domain search space (domZ): 4 [number of targets reported over threshold]
# CPU time: 0.23u 0.01s 00:00:00.24 Elapsed: 00:00:00.10
# Mc/sec: 34353.05
//
[ok]