# 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/Trypanosoma_brucei.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-62 211.2 0.0 4.2e-56 189.5 0.0 2.7 3 tr|Q38A69|Q38A69_TRYB2 Uncharacterized protein OS=Trypanosom 3.2e-40 137.2 0.0 1.5e-26 92.1 0.0 3.2 3 tr|Q381B8|Q381B8_TRYB2 Uncharacterized protein OS=Trypanosom 1.5e-33 115.2 0.0 1.6e-30 105.2 0.0 2.7 2 tr|Q383Z8|Q383Z8_TRYB2 tRNA pseudouridine synthase, putative 3.6e-18 64.5 0.0 1.7e-08 32.7 0.0 4.2 4 tr|Q4GZ59|Q4GZ59_TRYB2 Uncharacterized protein OS=Trypanosom 8.9e-06 23.7 0.0 1.5e-05 22.9 0.0 1.2 1 tr|Q38BP8|Q38BP8_TRYB2 Uncharacterized protein OS=Trypanosom Domain annotation for each sequence (and alignments): >> tr|Q38A69|Q38A69_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.9 0.0 0.3 5.2e+02 18 34 .. 63 79 .. 57 97 .. 0.75 2 ! 189.5 0.0 2.5e-59 4.2e-56 40 301 .. 213 475 .. 187 511 .. 0.88 3 ! 18.5 0.0 2e-07 0.00034 395 416 .] 640 661 .. 611 661 .. 0.85 Alignments for each domain: == domain 1 score: -1.9 bits; conditional E-value: 0.3 TruD 18 lrespeDFiVeEieefs 34 +++ + DF+V+E++ tr|Q38A69|Q38A69_TRYB2 63 MKTLYSDFVVRELSLLY 79 788899******96653 PP == domain 2 score: 189.5 bits; conditional E-value: 2.5e-59 TruD 40 kegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl......eikdvelevvgrarrkl 120 ++ ++l +++ k+n+d+++++re+a+ l++ + + f+GtKDkrAvT Q +++r+v+pe+l + + ++v++ ++ ++++ l tr|Q38A69|Q38A69_TRYB2 213 RSQKFLHFTLYKENIDSNHALREVASYLHVPTRSLLFSGTKDKRAVTLQRVAVRGVSPEKLIGInsrsfgQDRKVKVCSFRTMDHGL 299 457899******************************************************99996665555599************* PP TruD 121 rlGdLaGNkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesed 206 rlGd +GN+F i +r + ++++ ++++++ + ++++++g v NyfG+QRFG++ t vG +++ g +e+A++ + ++ e+ tr|Q38A69|Q38A69_TRYB2 300 RLGDAVGNHFLIALRLLpESRDIDSDTLNTVESTINREG-VVNYFGTQRFGTTDVLTGDVGIQLLSGHFENALRLVFRSKSMVEPSM 385 *****************7666666778888888888876.*********************************98888877777766 PP TruD 207 treareavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGD 293 +a +a+ e+g +eea++++p+ ++ Er ml++L+++p+d+ ++++++p+++++++ hA+qS ++N + s+Rle g+ p GD tr|Q38A69|Q38A69_TRYB2 386 -LAAVDAL-EKGSFEEAVKLVPHYCHQERDMLNHLVDSPNDFLGSFSKIPRTMSMMYFHAVQSLIWNIMASKRLEVGV---VPQVGD 467 .5677777.8*******************************************************************5...599*** PP TruD 294 vvifaeer 301 +v++++ + tr|Q38A69|Q38A69_TRYB2 468 LVLKSRYT 475 **998766 PP == domain 3 score: 18.5 bits; conditional E-value: 2e-07 TruD 395 deltleFsLpkGsYATvvlrEi 416 + +++eFsLp+G YAT+vlrE+ tr|Q38A69|Q38A69_TRYB2 640 KAIVVEFSLPPGAYATCVLREF 661 5689*****************7 PP >> tr|Q381B8|Q381B8_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.8 0.0 0.0015 2.5 16 35 .. 20 38 .. 6 57 .. 0.77 2 ! 92.1 0.0 9e-30 1.5e-26 44 278 .. 300 559 .. 284 567 .. 0.73 3 ! 36.0 0.0 9.5e-13 1.6e-09 327 416 .] 564 662 .. 558 662 .. 0.81 Alignments for each domain: == domain 1 score: 5.8 bits; conditional E-value: 0.0015 TruD 16 GrlrespeDFiVeEieefsg 35 rl++ peDFiV E+ + g tr|Q381B8|Q381B8_TRYB2 20 ARLKDCPEDFIVAEVDPA-G 38 69*************433.2 PP == domain 2 score: 92.1 bits; conditional E-value: 9e-30 TruD 44 ylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.................ei.kdvel.e 111 ++ l ++krn d ++l la+++ + ++v aG+KDk AvT+Q s+ ++ + ++ ++ + ve+ + tr|Q381B8|Q381B8_TRYB2 300 FTHLLIRKRNLDIMELRMLLAEHFCVPIDAVCTAGMKDKCAVTYQRCSVPCTRQLRHPREeesgidgdvplrltwtdDLsSYVEIlQ 386 58899*******************************************744332222222233456778887888773336677615 PP TruD 112 vvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGsrr.pvthlvGkaivkgdleeAveayv 196 g ++ ++ +G+L+GN F+ir+rdv + +++ + + +l+++g + NyfG+QRF + +G +i+ g + eAv++++ tr|Q381B8|Q381B8_TRYB2 387 TSGPHSAPVGIGELKGNMFHIRLRDVrGI---TPSELMQRSCRLEKEG-FLNYFGQQRFSEHAeCFMDHIGVHILGGRWPEAVRCLL 469 6799*********************9443...4468999999999988.**********9864134556****************99 PP TruD 197 gkpfeee.....sedtreareavaetgdleealeelpkslry...EramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNr 274 + e + + r + + + + + + +al++l+++ ry ra +++ ++ + + Al+a+p + l++ +qS +FNr tr|Q381B8|Q381B8_TRYB2 470 RGAPELYdlfptHMEPRYVPARLRDARCIVQALNRLHRT-RYttlTRADVTECTQlWRDVCRDALQAVPYAFRVLWLCGAQSLIFNR 555 654443201000222334444445555555666655544.3312244444444445556699************************* PP TruD 275 vlse 278 +ls+ tr|Q381B8|Q381B8_TRYB2 556 LLSM 559 **97 PP == domain 3 score: 36.0 bits; conditional E-value: 9.5e-13 TruD 327 rafvtaplvGtetelaegevgeierevleeegl.eledFk.lpklpelsskGtrRaillrve.........dlelsaeede...... 396 + vt+pl+G+++ + eg v+ ++vl e +l + ++F+ +k+ ++++ G+ Ra ++r+ + + tr|Q381B8|Q381B8_TRYB2 564 QLPVTLPLLGYNVSV-EGGVRSAVDKVLMELNLgTVDEFAqRKKVLGVGMPGALRATVVRPVgcsvsfttvE-----G--Gssdvfd 642 5679**********9.5668888999999999956789*9888999**************997766433221.....2..1334666 PP TruD 397 ltleFsLpkGsYATvvlrEi 416 +tl+F+Lp+ sYAT++lrE+ tr|Q381B8|Q381B8_TRYB2 643 ATLSFFLPSSSYATIFLREV 662 9******************6 PP >> tr|Q383Z8|Q383Z8_TRYB2 tRNA pseudouridine synthase, putative OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) O # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 6.7 0.0 0.00073 1.3 6 36 .. 185 215 .. 180 227 .. 0.72 2 ! 105.2 0.0 9.3e-34 1.6e-30 37 415 .. 318 731 .. 308 732 .. 0.80 Alignments for each domain: == domain 1 score: 6.7 bits; conditional E-value: 0.00073 TruD 6 lyvt.dtegigGrlrespeDFiVeEieefsge 36 +v+ +++g+ G +r++++DF+V+E+ e tr|Q383Z8|Q383Z8_TRYB2 185 AFVSpNAPGFSGIFRQHWKDFLVTEMVYD-SE 215 55553679*****************9333.22 PP == domain 2 score: 105.2 bits; conditional E-value: 9.3e-34 TruD 37 eeakegey.lvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl......eikdvelevvgra 116 +e ++g++ l + ++k+ + + +++++a++l+++ + ++ aG+KD + T Q + +++v+p++ ++ + ++l+++ + tr|Q383Z8|Q383Z8_TRYB2 318 SEFRTGKFyLQCYLRKQHIAHSVALSNIAQTLRMHPSCISVAGIKDYIGDTLQRVRLQNVTPASALEAnrvfrkKKWAMTLSDFSYH 404 46677887799************************************************999985555555554447899******* PP TruD 117 rrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeee 203 ++l G+L GN+F+i++rdv+ + ++++++ + el+++g +PNy+G QRF t + ai+++++ +++ +++g ++ e tr|Q383Z8|Q383Z8_TRYB2 405 TEPLFPGRLFGNHFKIVLRDVT-VP--KTCIQQAVYELQTHG-FPNYYGCQRFSWF-GGTNDAAFAILNQNWLAFAFRFLGYTSRE- 485 ********************83.33..479**********98.**********885.778889******************98843. PP TruD 204 sedtreareavaetgdleealeelpkslryEramlkrLae..................................kpkd.....ykkA 251 + re++++++ + p + +y r++++rL++ + + ++A tr|Q383Z8|Q383Z8_TRYB2 486 ----LTLRELLQREKKY-----PNPVQDEYRRNIVRRLRSiaiepseldtapflacpslgapltatdggpvskkQ--ElillqLQGA 561 ....3567777444333.....3355667889999999999999999999999***************9997541..24555599** PP TruD 252 lealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer..lpdtdrlqlvteknveevkrliergrafvtapl.v 335 +l+ +rl + Syl+N+vl Rl++ +e++eGD+v+ + r ++++++ ++ ++ v+ er+r +++ ++ + tr|Q383Z8|Q383Z8_TRYB2 562 YLDLSVMSRRLTAQRLCSYLWNQVLTLRLHHF-GGKEVLEGDMVLPEVLRrvQTSPEERTDWYRQGIHLVETEEERERTSIMNVIhP 647 ******************************98.67**********998886644444444445566677777777777665543325 PP TruD 336 Gt...etelaegevgeierevleeegleledFklpklpelsskGtr...Raillrve..dlelsaeedeltleFsLpkGsYATvvlr 414 G+ +++l++ vge+ +v +++ le ++ + +l+ + + R+i+ +++ + ++++e+ +ltleFsL++GsYA vvl tr|Q383Z8|Q383Z8_TRYB2 648 GFsfnSMRLPQNAVGEYFLQVCQKYHLEWHSRHS----RLGIHDFFeppRPIIRKPMnlRYDYDTESCKLTLEFSLERGSYANVVLT 730 541124789999************9999877652....3444444444599999999454445555666*****************9 PP TruD 415 E 415 E tr|Q383Z8|Q383Z8_TRYB2 731 E 731 8 PP >> tr|Q4GZ59|Q4GZ59_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=TB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.4 0.0 0.03 51 11 30 .. 74 93 .. 68 114 .. 0.85 2 ! 32.7 0.0 9.8e-12 1.7e-08 113 207 .. 913 1004 .. 894 1025 .. 0.82 3 ! 17.6 0.0 3.8e-07 0.00065 253 359 .. 1100 1204 .. 1091 1227 .. 0.88 4 ! 6.8 0.0 0.00068 1.2 375 416 .] 1395 1437 .. 1386 1437 .. 0.78 Alignments for each domain: == domain 1 score: 1.4 bits; conditional E-value: 0.03 TruD 11 tegigGrlrespeDFiVeEi 30 +g++ +++sp+D++V+E+ tr|Q4GZ59|Q4GZ59_TRYB2 74 VKGFQAYIKSSPDDYVVKEL 93 689999*************9 PP == domain 2 score: 32.7 bits; conditional E-value: 9.8e-12 TruD 113 vgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsr.rpvthlvGkaivkgdleeAveayv 196 v +a+ +lr+Gd G ++++++r ++ ++ ++ + +l+++g + NyfG QRF s r + h G +++kg++++A+ ++v tr|Q4GZ59|Q4GZ59_TRYB2 913 VTSASYDLRMGDNDGYDYRVKLRRIP--QSHFPLVKPAMVSLQKHG-FINYFGPQRFSSYtRYNMH-PGLHLLKGEFHAAASIIV 993 4566789*****************94..456899**********98.**********996266666.8*************9999 PP TruD 197 gkpfeeesedt 207 + + + + tr|Q4GZ59|Q4GZ59_TRYB2 994 QQFYMDSDLAA 1004 88776655444 PP == domain 3 score: 17.6 bits; conditional E-value: 3.8e-07 TruD 253 ealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGt 337 +++ ++ ++ vh + ++l+N+++++Rl+r+ ++ +++GD+v + + p+++++ +v ++ ++++ + + v++p++G tr|Q4GZ59|Q4GZ59_TRYB2 1100 RVVGPKACSMLVHEFLAFLWNDIVNQRLQRYGTF-AILPGDLVRLNPLASPHSNEFGRVVYASKNSIE-KGKYTCYDVVLPVPGA 1182 567778889**********************776.7**********9999999999999999888888.667778899******* PP TruD 338 etelaegevgeierevleeegl 359 +el++ ++ ++ l++ g+ tr|Q4GZ59|Q4GZ59_TRYB2 1183 GVELPDNHTADLYVVTLKRMGI 1204 ******9999988888887776 PP == domain 4 score: 6.8 bits; conditional E-value: 0.00068 TruD 375 kGtrRaillrvedlelsaeede.ltleFsLpkGsYATvvlrEi 416 G+rRa l+ + l +++++ l+l+F+Lp+ Y ++lrE+ tr|Q4GZ59|Q4GZ59_TRYB2 1395 GGKRRARTLPAAPYWLPEKNNGcLELSFQLPSSVYPSMLLREV 1437 577777777777666666666669******************6 PP >> tr|Q38BP8|Q38BP8_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.9 0.0 8.8e-09 1.5e-05 210 316 .. 572 679 .. 558 696 .. 0.74 Alignments for each domain: == domain 1 score: 22.9 bits; conditional E-value: 8.8e-09 TruD 210 areavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296 r+++++ + +++a + ++ + r+ lk++ +++++++ ++++p +r +++A +S ++N + s+Rl +++++GD+v+ tr|Q38BP8|Q38BP8_TRYB2 572 LRQFIKRPNVITAARARRASTDPTIRQALKNYELTQGNWEQTVARIPYVWRRRWLNALRSSVWNVMASRRLSLDGASRRVIPGDIVF 658 5666643333444444444444567999999999***************************************99***********9 PP TruD 297 faeer.lpdtdrlqlvteknv 316 e r +++ + +v++++v tr|Q38BP8|Q38BP8_TRYB2 659 RPEYRaDVHHRMIPTVKAEHV 679 998883222222233333333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 8561 (4332363 residues searched) Passed MSV filter: 327 (0.0381965); expected 171.2 (0.02) Passed bias filter: 147 (0.0171709); expected 171.2 (0.02) Passed Vit filter: 21 (0.00245298); expected 8.6 (0.001) Passed Fwd filter: 5 (0.000584044); expected 0.1 (1e-05) Initial search space (Z): 8561 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.05 # Mc/sec: 36045.26 // [ok]