# 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/Strongylocentrotus_purpuratus.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.4e-65 222.4 0.0 4e-54 184.7 0.0 3.1 3 tr|W4XQB7|W4XQB7_STRPU Uncharacterized protein OS=Strongyloc
5.4e-22 78.9 0.0 7.4e-07 29.0 0.0 4.0 4 tr|W4ZCS6|W4ZCS6_STRPU Uncharacterized protein OS=Strongyloc
4.2e-07 29.8 0.0 4.2e-07 29.8 0.0 1.0 1 tr|W4ZCL2|W4ZCL2_STRPU Uncharacterized protein OS=Strongyloc
------ inclusion threshold ------
0.017 14.6 0.0 0.018 14.5 0.0 1.1 1 tr|W4XUW1|W4XUW1_STRPU Uncharacterized protein OS=Strongyloc
0.027 14.0 0.2 0.04 13.4 0.2 1.2 1 tr|W4XM82|W4XM82_STRPU Uncharacterized protein OS=Strongyloc
0.24 10.8 0.0 23 4.3 0.0 2.2 2 tr|W4Y7B3|W4Y7B3_STRPU Uncharacterized protein OS=Strongyloc
Domain annotation for each sequence (and alignments):
>> tr|W4XQB7|W4XQB7_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.7 0.0 4.2e-07 0.002 2 31 .. 2 31 .. 1 43 [. 0.91
2 ! 184.7 0.0 8.3e-58 4e-54 45 388 .. 316 680 .. 290 699 .. 0.86
3 ! 16.3 0.0 1.1e-06 0.0053 387 416 .] 853 882 .. 829 882 .. 0.84
Alignments for each domain:
== domain 1 score: 17.7 bits; conditional E-value: 4.2e-07
TruD 2 lgielyvtdtegigGrlrespeDFiVeEie 31
+gie+yv+++eg+ G++++sp+DF V+Ei+
tr|W4XQB7|W4XQB7_STRPU 2 FGIECYVSQHEGFKGNVKTSPKDFQVTEIS 31
69**************************94 PP
== domain 2 score: 184.7 bits; conditional E-value: 8.3e-58
TruD 45 lvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikd.velevvgrarrklrlGdLaGN 128
+ ++++k+n +tl+++++lar +g++ +++++aG+KDk+AvTtQ +++++++ +l+++ e+++ +++ ++++ ++++ +G+L+GN
tr|W4XQB7|W4XQB7_STRPU 316 TGFTLQKTNTETLSAIQQLARLMGVQISDFTYAGIKDKKAVTTQEMAVKGITITRLQDVskELPGwLKVGSIHSRNKSMVTGELWGN 402
66899**************************************************9999777765489******************* PP
TruD 129 kFeirvrdv.aeee..............eaakraeeileelkekggvPNyfGvQRFGsr.....rpvthl....vGkaivkgdleeA 191
+F+i+++++ +++ e+++++e++++ ++++g + Ny+G QRFG+ + t + vG a+++g+++eA
tr|W4XQB7|W4XQB7_STRPU 403 HFDITLQNIeMKNGsnevragtvedkgrELQNCIEQCIRCVEDRG-FINYYGEQRFGASsvdpsKALTTIspadVGCAMLQGKYKEA 488
********9554447888888888888888888888888888877.***********86222223333324444************* PP
TruD 192 veayvg...kpfeeesedtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylF 272
++ +++ p+ + s+ t+ a++ +++tg +eal+++p + E +lk L + +++ kAl ++p+n+++++vhA+ S ++
tr|W4XQB7|W4XQB7_STRPU 489 IDLILSpddGPCADPSNATNVAKHCFQQTGSPREALKQMPTMKTRECLLLKGLNRhgtDDDGCIKALMNIPHNMRQMYVHAFCSLVW 575
*****8333478999999*************************************55444448999********************* PP
TruD 273 NrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegl 359
N++ s R+ r+ ++veGD+v+ ++ +++++vte+ + + k v++pl+G + + ++ +g+ ++ l+e+gl
tr|W4XQB7|W4XQB7_STRPU 576 NQMASWRMCRY--GCQVVEGDLVCIEDLG----TKVHAVTEDDITQGK----YSLTEVMLPLPGNNIQYPSHTAGAEYQRRLDEAGL 652
********999..459**********888....888889888888777....5556799**************************** PP
TruD 360 eledFklpklpelsskGtrRaillrvedl 388
+F++p+ +l++ G +R+++ ++++l
tr|W4XQB7|W4XQB7_STRPU 653 GECNFRIPA-LKLNVPGGYRKVIAQPRNL 680
********8.9***********9999854 PP
== domain 3 score: 16.3 bits; conditional E-value: 1.1e-06
TruD 387 dlelsaeedeltleFsLpkGsYATvvlrEi 416
+ +ls+++++l l+F Lp +YATv+lrE+
tr|W4XQB7|W4XQB7_STRPU 853 SSSLSCQRKTLNLSFDLPASCYATVFLREL 882
5678899999******************96 PP
>> tr|W4ZCS6|W4ZCS6_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.4 0.0 5.2e-07 0.0025 2 33 .. 159 190 .. 158 226 .. 0.86
2 ! 29.0 0.0 1.6e-10 7.4e-07 40 93 .. 291 344 .. 278 363 .. 0.88
3 ! 25.3 0.0 2e-09 9.5e-06 253 301 .. 369 415 .. 350 427 .. 0.83
4 ? 2.7 0.0 0.015 73 346 388 .. 417 458 .. 415 460 .] 0.85
Alignments for each domain:
== domain 1 score: 17.4 bits; conditional E-value: 5.2e-07
TruD 2 lgielyvtdtegigGrlrespeDFiVeEieef 33
+gi y++d+eg+ G +++++ DF+V+Ei e
tr|W4ZCS6|W4ZCS6_STRPU 159 VGIIEYMSDHEGVPGIIKQRYRDFLVHEIDEQ 190
79999************************655 PP
== domain 2 score: 29.0 bits; conditional E-value: 1.6e-10
TruD 40 kegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisir 93
++ +y+ + + k+n+d +++++ +a+ l+i + +++aG KDkr+vT+Q ++
tr|W4ZCS6|W4ZCS6_STRPU 291 ETPKYCRFVLFKENMDLNEALNIVAKYLHIGPHHFQYAGSKDKRGVTVQEVTAH 344
566899999****************************************98754 PP
== domain 3 score: 25.3 bits; conditional E-value: 2e-09
TruD 253 ealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer 301
+++p+n + +++h+yqSy++N + +Rl+r +pv GD+v ++ +
tr|W4ZCS6|W4ZCS6_STRPU 369 HSIPRNTRLIYLHSYQSYIWNVITTQRLQRD-G-FTPVVGDLVSAKNIQ 415
579**************************99.4.48*******988655 PP
== domain 4 score: 2.7 bits; conditional E-value: 0.015
TruD 346 vgeierevleeegleledFklpklpelsskGtrRaillrvedl 388
+ge e l++++l+ e+ k ++ +ls +G++R+ +++++d+
tr|W4ZCS6|W4ZCS6_STRPU 417 AGEWYTEELAKDDLTVEMLKNTN-RDLSLSGAYRKCVVKPTDV 458
5777788899**********554.6*************99876 PP
>> tr|W4ZCL2|W4ZCL2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 29.8 0.0 8.8e-11 4.2e-07 142 186 .. 11 54 .. 2 64 .] 0.82
Alignments for each domain:
== domain 1 score: 29.8 bits; conditional E-value: 8.8e-11
TruD 142 eaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkg 186
++++++ +++l++ g + NyfG+QRFG+ t+ vG ++ +
tr|W4ZCL2|W4ZCL2_STRPU 11 GSKEQINHAMSSLRDAG-FINYFGMQRFGNSLIATYHVGSYVTVN 54
346799999*****988.*********************998655 PP
>> tr|W4XUW1|W4XUW1_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 14.5 0.0 3.9e-06 0.018 395 416 .] 63 84 .. 43 84 .. 0.88
Alignments for each domain:
== domain 1 score: 14.5 bits; conditional E-value: 3.9e-06
TruD 395 deltleFsLpkGsYATvvlrEi 416
+ l+ eFsLp+ +YAT+ lrE+
tr|W4XUW1|W4XUW1_STRPU 63 SALKAEFSLPSSCYATMALREV 84
56899****************6 PP
>> tr|W4XM82|W4XM82_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.4 0.2 8.4e-06 0.04 182 284 .. 224 331 .. 213 361 .. 0.84
Alignments for each domain:
== domain 1 score: 13.4 bits; conditional E-value: 8.4e-06
TruD 182 aivkg.dleeAveayvgkpfeeesedtreareavaetgdleealeelpkslryEr..amlkrLae..kpkdykkAlealpknLqrlF 263
+++++ +e ++y++ p+++e+++t+ + + e ++ ++ p + + Er a +++L++ + + ++ l++l+k+L ++
tr|W4XM82|W4XM82_STRPU 224 HLLQRaAIETEHRIYISLPSDDEHQNTHPLGQSLVECFPPKKQQRLTPIQQTAERcrAKIDSLVQllDVCNNQRILRELEKQLDDML 310
55544146677899****************99999988888888888877777752267888888777889999************* PP
TruD 264 vhAyqSylFNrvlseRlergl 284
v qS+ F++ +eRl++g
tr|W4XM82|W4XM82_STRPU 311 VMMKQSMEFEKNTKERLNKGR 331
******************984 PP
>> tr|W4Y7B3|W4Y7B3_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 4.3 0.0 0.0048 23 158 172 .. 102 114 .. 86 134 .. 0.81
2 ? 3.9 0.0 0.0062 30 158 172 .. 178 190 .. 163 197 .. 0.81
Alignments for each domain:
== domain 1 score: 4.3 bits; conditional E-value: 0.0048
TruD 158 ggvPNyfGvQRFGsr 172
g PN+fG+QR G +
tr|W4Y7B3|W4Y7B3_STRPU 102 G--PNFFGIQRLGMQ 114
3..**********85 PP
== domain 2 score: 3.9 bits; conditional E-value: 0.0062
TruD 158 ggvPNyfGvQRFGsr 172
g PN+fG+QR G +
tr|W4Y7B3|W4Y7B3_STRPU 178 G--PNFFGIQRLGMQ 190
3..*********975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 28594 (14266044 residues searched)
Passed MSV filter: 1052 (0.0367909); expected 571.9 (0.02)
Passed bias filter: 522 (0.0182556); expected 571.9 (0.02)
Passed Vit filter: 49 (0.00171365); expected 28.6 (0.001)
Passed Fwd filter: 6 (0.000209834); expected 0.3 (1e-05)
Initial search space (Z): 28594 [actual number of targets]
Domain search space (domZ): 6 [number of targets reported over threshold]
# CPU time: 0.42u 0.01s 00:00:00.43 Elapsed: 00:00:00.14
# Mc/sec: 42390.53
//
[ok]