# 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]