# 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/Branchiostoma_floridae.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.4e-69 234.8 0.0 1e-63 216.3 0.0 3.1 3 tr|C3YAS5|C3YAS5_BRAFL Uncharacterized protein OS=Branchiost
1.7e-61 209.0 0.0 2.3e-53 182.2 0.0 3.3 3 tr|C3YUB6|C3YUB6_BRAFL Uncharacterized protein OS=Branchiost
2e-34 119.8 0.0 3.3e-34 119.1 0.0 1.4 1 tr|C3Z9T3|C3Z9T3_BRAFL Uncharacterized protein (Fragment) OS
9.3e-07 28.7 0.2 0.00082 19.0 0.0 2.4 2 tr|C3Z9T6|C3Z9T6_BRAFL Uncharacterized protein OS=Branchiost
------ inclusion threshold ------
0.011 15.2 0.9 4.1 6.8 0.0 3.1 3 tr|C3YGK9|C3YGK9_BRAFL Uncharacterized protein (Fragment) OS
0.14 11.6 0.7 0.2 11.1 0.7 1.1 1 tr|C3Y4L8|C3Y4L8_BRAFL Uncharacterized protein OS=Branchiost
Domain annotation for each sequence (and alignments):
>> tr|C3YAS5|C3YAS5_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_82453 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 5.2 0.0 0.0025 12 2 32 .. 25 55 .. 24 70 .. 0.87
2 ! 216.3 0.0 2.1e-67 1e-63 44 391 .. 420 770 .. 392 781 .. 0.88
3 ! 9.5 0.0 0.00013 0.6 391 416 .] 834 859 .. 806 859 .. 0.78
Alignments for each domain:
== domain 1 score: 5.2 bits; conditional E-value: 0.0025
TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32
gi ++++++ ++ G+++ peDF V Ei +
tr|C3YAS5|C3YAS5_BRAFL 25 CGITCHLSSHLPFRGNIKVFPEDFKVIEIDN 55
5899999999*******************54 PP
== domain 2 score: 216.3 bits; conditional E-value: 2.1e-67
TruD 44 ylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl....eikdvelevvgrarrklrlGdLa 126
y+ +++ krn +tld++++lar ++ + +++++aG+KDkrAvT Q ++ r+v+p++l+++ +++dv++e++ +++l+lG+La
tr|C3YAS5|C3YAS5_BRAFL 420 YTGFTLCKRNLETLDVIQRLARCVSAHPSDFSYAGVKDKRAVTWQAMAARGVTPDSLRSAsahpSLRDVQMEKFLLRQQPLHLGNLA 506
5778999**************************************************999999999********************* PP
TruD 127 GNkFeirvrdv..aeee......eaakraeeileelkekggvPNyfGvQRFGsr..rpvthlvGkaivkgdleeAveayvgkpfeee 203
GN F++ +rdv ++ ++++ + + ++++ke+g + NyfG+QRFGs ++ vG+a++kgd+++Av++++ +
tr|C3YAS5|C3YAS5_BRAFL 507 GNVFKVLLRDVrlCQ-GdtrdrrQLEAVVGAAMDSVKETG-FINYFGLQRFGSAdsKSFAPHVGRALLKGDMSAAVRCLLHPDPAD- 590
**********97433.247666666677888899999988.***********9722445557****************99765544. PP
TruD 204 sedtreareavaetgdleealeelpkslryEramlkrLaekpkd...ykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpld 287
+ +++a++++++tgd+ l+++p + + E +lk+L ++++d kA+ ++p+ ++ lFvh+y S ++Nr++s+R++ + +
tr|C3YAS5|C3YAS5_BRAFL 591 -DPVNAAKAYYMRTGDIPGTLSRMPAHKTRECLLLKALHRHGNDlegCTKAFLNVPHAMRALFVHSYCSLVWNRMVSHRIRTY--GR 674
.445699*********************************88885556789999***************************99..57 PP
TruD 288 epveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelss 374
++veGD+v++++ +++++++t++ v++ + i+ v++pl+G + + ++ +vge + l+e+g+e+++F++ + +l+
tr|C3YAS5|C3YAS5_BRAFL 675 RAVEGDLVLETDAG---NRKVKTLTQTDVDQGNYSIH----DVVLPLLGNSIQYPSNRVGEEYARALQEDGMERSSFRMRA-LKLNI 753
***********888...88999999999999997775....599**********************************997.9**** PP
TruD 375 kGtrRaillrvedlels 391
G++R++ r++dl+ +
tr|C3YAS5|C3YAS5_BRAFL 754 PGDYRHVTARPKDLAWE 770
**********9987655 PP
== domain 3 score: 9.5 bits; conditional E-value: 0.00013
TruD 391 saeedeltleFsLpkGsYATvvlrEi 416
+ ++ ++ +F+L++ +YAT++lrE+
tr|C3YAS5|C3YAS5_BRAFL 834 HGDSFHVRTRFALDPSCYATMFLREV 859
344445899****************6 PP
>> tr|C3YUB6|C3YUB6_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_79734 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.5 0.0 4.9e-07 0.0023 2 31 .. 96 125 .. 95 139 .. 0.87
2 ! 5.3 0.0 0.0024 12 43 73 .. 237 267 .. 222 269 .. 0.88
3 ! 182.2 0.0 4.9e-57 2.3e-53 112 416 .] 282 587 .. 270 587 .. 0.85
Alignments for each domain:
== domain 1 score: 17.5 bits; conditional E-value: 4.9e-07
TruD 2 lgielyvtdtegigGrlrespeDFiVeEie 31
+gi y++++eg+ G +++++ DF+V+E+
tr|C3YUB6|C3YUB6_BRAFL 96 VGITEYISKHEGFSGIIKQRYSDFLVREVD 125
89**************************93 PP
== domain 2 score: 5.3 bits; conditional E-value: 0.0024
TruD 43 eylvlrvekrnwdtldlvrelaralgisrkr 73
+y+ + + k+n dt+d+++ la +l+i +r
tr|C3YUB6|C3YUB6_BRAFL 237 DYCHFVLYKENLDTMDAINMLAMNLRIAAER 267
78999**********************9988 PP
== domain 3 score: 182.2 bits; conditional E-value: 4.9e-57
TruD 112 vvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgk 198
++ ++++l+lG L GN+F+i++r+++ ++ +++e+ + +l+++g + NyfG+QRFG++ +h vG+a+++ ++eeA+e ++
tr|C3YUB6|C3YUB6_BRAFL 282 NFRYTEQPLKLGLLSGNHFTIVLRNCTGSP---EQIEAGMTSLRDNG-FINYFGMQRFGTTSVPSHHVGRALLHSKWEEAIELILKP 364
5677899******************85455...59**********98.*********************************977654 PP
TruD 199 pf.eeesedtreareavaetgdleealeelpksl...ryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRle 281
e+++ + + r++ ++t+d++ ale +p++ ++E +l+ L++++kd +Al+++p+n + ++vh+yqS+++N+++s+Rl+
tr|C3YUB6|C3YUB6_BRAFL 365 REgEHQEGAVSACRDFWWKTRDAKGALEMMPRRNmskDIEGRLLEGLVKNGKDLVGALSNIPRNTRLMYVHSYQSFIWNNIVSRRLQ 451
3313344467888******************9752224699********************************************** PP
TruD 282 rglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpk 368
++ +p+ GD+v++++e+ +++++ +++te+ + +++ v+ pl+G+++ ++ +++e re+l+ ++l++++ + +
tr|C3YUB6|C3YUB6_BRAFL 452 EY--GYQPIVGDLVLEEKEDGAQRSEAKVLTEEDMGNYT------IHDVVFPLFGYDVIYPKHKAEEWYREMLSVDQLDMDNIRHK- 529
99..469**********9998899999999988887777......45799********************************9943. PP
TruD 369 lpelsskGtrRaillrve..........dlelsaeedeltleFsLpkGsYATvvlrEi 416
++ + +++ l+ ++ ++ + + + l++eF+Lp+ +YAT+ lrEi
tr|C3YUB6|C3YUB6_BRAFL 530 VKSVMCYDDVKIPLMLTDkdvldgkeapLASSEGKMKALKVEFTLPPSTYATMALREI 587
45555555555444444478999998763344555566*******************7 PP
>> tr|C3Z9T3|C3Z9T3_BRAFL Uncharacterized protein (Fragment) OS=Branchiostoma floridae OX=7739 GN=Hsd11b1H PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 119.1 0.0 7e-38 3.3e-34 177 416 .] 1 258 [. 1 258 [. 0.91
Alignments for each domain:
== domain 1 score: 119.1 bits; conditional E-value: 7e-38
TruD 177 hlvGkaivkgdleeAveayvgkpfeeesedtreareavaetgdleealeelpksl...ryEramlkrLaekpkdykkAlealpknLq 260
h + +a+++ ++eeA+e ++ ++ + + r++ ++t+d++ ale +p++ ++E +l+ L++++kd +Al+++p+n +
tr|C3Z9T3|C3Z9T3_BRAFL 1 HFLHRALLHSKWEEAIELILKPREGGTEGAVSACRDYWWKTRDAKGALEMMPRRNmskDIEGRLLEGLVKNGKDLVGALSNIPRNTR 87
667799***********99999999999999*********************9752224699************************* PP
TruD 261 rlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevg 347
++vh+yqS+++N+++s+Rl+++ + +p++GD+v++++e+ +++te+ + +++ v+ pl+G+++ ++ +++
tr|C3Z9T3|C3Z9T3_BRAFL 88 LMYVHSYQSFIWNNIVSRRLQEY-GF-QPIAGDLVLEEREA-------KVLTEEDLGNYT------IHDVVFPLFGYDVIYPKHKAE 159
*********************99.44.8*******999776.......888888888777......45799**************** PP
TruD 348 eierevleeegleledFklpklpelsskGtrRaillrve...............................dlelsaeedeltleFsL 403
e re+l+ ++l++++ + +k+++ s +G++R+i+++++ ++ + + + l++eF+L
tr|C3Z9T3|C3Z9T3_BRAFL 160 EWYREMLSVDQLDMDNIR-HKVKDYSLSGAYRKIIVKPTnckwqvcykvqscriplmltdkdvldgkeapLASSEGKMKALKVEFTL 245
*****************9.5579***************9*************************9998763344555566******* PP
TruD 404 pkGsYATvvlrEi 416
p+ +YAT+ lrEi
tr|C3Z9T3|C3Z9T3_BRAFL 246 PPSTYATMALREI 258
************7 PP
>> tr|C3Z9T6|C3Z9T6_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_81246 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 19.0 0.0 1.7e-07 0.00082 2 33 .. 93 123 .. 92 138 .. 0.86
2 ! 7.5 0.0 0.00052 2.5 41 73 .. 232 264 .. 205 266 .. 0.85
Alignments for each domain:
== domain 1 score: 19.0 bits; conditional E-value: 1.7e-07
TruD 2 lgielyvtdtegigGrlrespeDFiVeEieef 33
+gi y++++eg+ G +++++ DF+V+E+ +
tr|C3Z9T6|C3Z9T6_BRAFL 93 VGITEYISKHEGFSGIIKQRYSDFLVREVD-V 123
89**************************93.3 PP
== domain 2 score: 7.5 bits; conditional E-value: 0.00052
TruD 41 egeylvlrvekrnwdtldlvrelaralgisrkr 73
+ +y+ + + k+n dt+d+++ la +l+i +r
tr|C3Z9T6|C3Z9T6_BRAFL 232 RPDYCHFVLYKENLDTMDAINMLAMNLRIAAER 264
467999***********************9988 PP
>> tr|C3YGK9|C3YGK9_BRAFL Uncharacterized protein (Fragment) OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_79351 PE=4
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 6.8 0.0 0.00086 4.1 154 178 .. 104 127 .. 86 133 .. 0.82
2 ? 2.4 0.0 0.018 85 154 175 .. 331 351 .. 311 359 .. 0.78
3 ? 2.4 0.0 0.018 85 154 175 .. 629 649 .. 609 657 .. 0.78
Alignments for each domain:
== domain 1 score: 6.8 bits; conditional E-value: 0.00086
TruD 154 lkekggvPNyfGvQRFGsrrpvthl 178
l + g +P f +QR+G +r +t+
tr|C3YGK9|C3YGK9_BRAFL 104 LPADG-LPDSFEWQRYGYVRYITKA 127
45545.****************984 PP
== domain 2 score: 2.4 bits; conditional E-value: 0.018
TruD 154 lkekggvPNyfGvQRFGsrrpv 175
l + g +P f +QR+G +r +
tr|C3YGK9|C3YGK9_BRAFL 331 LPADG-LPCSFEWQRYGYVRYT 351
45545.9***********9964 PP
== domain 3 score: 2.4 bits; conditional E-value: 0.018
TruD 154 lkekggvPNyfGvQRFGsrrpv 175
l + g +P f +QR+G +r +
tr|C3YGK9|C3YGK9_BRAFL 629 LPADG-LPCSFEWQRYGYVRYT 649
45545.9***********9964 PP
>> tr|C3Y4L8|C3Y4L8_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_73889 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.1 0.7 4.2e-05 0.2 195 310 .. 435 553 .. 432 581 .. 0.79
Alignments for each domain:
== domain 1 score: 11.1 bits; conditional E-value: 4.2e-05
TruD 195 yvgkpfeeesedtreareavae..tgdleea.leelpkslryEramlkrLae....kpkdykkAlealpknLqrlFvhAyqSylFNr 274
y+ p+++ e+ r+ rea ++ ++d++ a l+++ k +r +++++ + + +++++ +A e+++++ +F + +qS++F r
tr|C3Y4L8|C3Y4L8_BRAFL 435 YLHSPTPTSVEEARKHREAWQQelSRDIQVAfLQTMVKLFRDVKEYVSTVNHrrylNKDKFLAAQEDVDQP---FFREVCQSHMFKR 518
88889999999999999998665678988654788889999999999999887777777777777777765...789********** PP
TruD 275 vlseRlerglpldepveGDvvifaeerlpdtdrlql 310
+l++R++++ ++ +++e+ + ++ ee+ ++ + ++
tr|C3Y4L8|C3Y4L8_BRAFL 519 FLQDRMDQKRDYYSIMEETMQWQGEEK-AEIPDNKI 553
************999999999998877.33333333 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (416 nodes)
Target sequences: 28542 (13248087 residues searched)
Passed MSV filter: 958 (0.0335646); expected 570.8 (0.02)
Passed bias filter: 466 (0.0163268); expected 570.8 (0.02)
Passed Vit filter: 37 (0.00129634); expected 28.5 (0.001)
Passed Fwd filter: 6 (0.000210217); expected 0.3 (1e-05)
Initial search space (Z): 28542 [actual number of targets]
Domain search space (domZ): 6 [number of targets reported over threshold]
# CPU time: 0.39u 0.01s 00:00:00.40 Elapsed: 00:00:00.12
# Mc/sec: 45926.70
//
[ok]