# 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/Trichomonas_vaginalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-67 230.0 2.3 1.4e-62 213.4 0.9 3.2 2 tr|A2EJH2|A2EJH2_TRIVA Uncharacterized protein OS=Trichomona 2.5e-66 225.7 8.4 6.5e-62 211.1 7.0 3.5 2 tr|A2FUM2|A2FUM2_TRIVA Uncharacterized protein OS=Trichomona Domain annotation for each sequence (and alignments): >> tr|A2EJH2|A2EJH2_TRIVA Uncharacterized protein OS=Trichomonas vaginalis OX=5722 GN=TVAG_050450 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.3 0.0 3e-06 0.074 2 32 .. 9 39 .. 8 52 .. 0.86 2 ! 213.4 0.9 5.5e-67 1.4e-62 44 416 .] 115 501 .. 94 501 .. 0.85 Alignments for each domain: == domain 1 score: 13.3 bits; conditional E-value: 3e-06 TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32 +gi y d g++G +++++ DF V+Ei + tr|A2EJH2|A2EJH2_TRIVA 9 VGITEYNNDFAGMNGIIKHRYSDFHVHEIDQ 39 899**************************43 PP == domain 2 score: 213.4 bits; conditional E-value: 5.5e-67 TruD 44 y.lvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.ei.kdvelevvgrarrklrlGdLaG 127 + + + + k+n ++++ +++l+++l+i+++++g+aG KDkrA+TtQ+++ir+v ++le+l ++ ++++ + +a ++++lGdL G tr|A2EJH2|A2EJH2_TRIVA 115 MvISMVICKENTNQQESISKLSKKLNIKKNQIGIAGNKDKRAITTQVMTIRDVGINSLEQLaNLtDKIKCGMFYQAMNPVNLGDLNG 201 33668899********************************************999999998744599******************** PP TruD 128 NkFeirvrdv.aeee......eaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedt 207 N+F++++r++ + e+++ ++ +e+l+ekg + NyfG+QRFG++ + th++G ai+++++++ ++ ++ p e ++ed+ tr|A2EJH2|A2EJH2_TRIVA 202 NHFTLVLRNLtI--PgcetveELREGLKIRMEALSEKG-FINYFGMQRFGTTAMSTHTIGIAILRKEWQKVID-MIMSPIEGNQEDV 284 *********743..334455567777777888899887.******************************9765.7889********* PP TruD 208 reareavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDv 294 ++a++++++t+d+e+a+ ++pk+ +E+++l + ++ k+ + +++++++ + l+ hAyqSy++N++ s+R++r ++v+GD+ tr|A2EJH2|A2EJH2_TRIVA 285 NKAKTIYMKTHDAEKAYALMPKHAATEKSILAAAKKGIKNPFELFKVIDRRQRLLYCHAYQSYVWNHCASARVKRS-G-FKVVPGDI 369 **************************************************************************99.4.48****** PP TruD 295 vifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRai 381 v ++++ +v++ n +++ +++++ +p G+ + +e+l+++g+e+++F+++k el+ G++R++ tr|A2EJH2|A2EJH2_TRIVA 370 VEENRNY-------VTVKAGNESKYS----PFDIVIPLPADGC--------ISPDAEELLKKDGIEQSMFSAQK--ELGLVGDYRKL 435 *777444.......555555544444....5555555544444........3344579***************9..*********** PP TruD 382 llrve................................dlelsaeede.......ltleFsLpkGsYATvvlrEi 416 + +++ + +++eFsL + +YAT+ +rE+ tr|A2EJH2|A2EJH2_TRIVA 436 FAQPTdisfdiiehddndaelidsdidklegrtnkgnH--------VpggkfksAVVEFSLGPSQYATMCMREL 501 ***999******************99998777654321........1222334599****************95 PP >> tr|A2FUM2|A2FUM2_TRIVA Uncharacterized protein OS=Trichomonas vaginalis OX=5722 GN=TVAG_350960 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.8 0.0 3.4e-05 0.85 2 34 .. 10 39 .. 9 51 .. 0.84 2 ! 211.1 7.0 2.6e-66 6.5e-62 43 416 .] 115 488 .. 94 488 .. 0.80 Alignments for each domain: == domain 1 score: 9.8 bits; conditional E-value: 3.4e-05 TruD 2 lgielyvtdtegigGrlrespeDFiVeEieefs 34 +g ++ +++g++G +++++ DF V+Ei + tr|A2FUM2|A2FUM2_TRIVA 10 VGCTRFANESSGFDGIIKHKYSDFHVHEI---D 39 78889999*********************...3 PP == domain 2 score: 211.1 bits; conditional E-value: 2.6e-66 TruD 43 eylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlGdLaG 127 e + +++ k+n+++++++ ++ +l+i ++++gfaG KDkrA TtQ++++r+v +++ k ++++v+ ++ + +l+lGdL G tr|A2FUM2|A2FUM2_TRIVA 115 EITRFTLFKENVNQQEAMAKILARLNITQNQLGFAGNKDKRAATTQYVTVRDVPLQKVVKSlsNLDKVTCGEFCHVTSPLKLGDLSG 201 44778899********************************************999997766699*********************** PP TruD 128 NkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtrearea 213 N+F+i +r++ +k+++e ++++++ g + Ny+G+QRFG+ + th++G i++g++++Av+a + +p e e+++++ea+ a tr|A2FUM2|A2FUM2_TRIVA 202 NRFTIAIRGLkI--G--QKELDEKIKSIQKSG-FINYYGMQRFGTGETATHKIGILIIQGKYDAAVDA-IMNPVEGEEQRIHEAKIA 282 *********833..2..468999999999988.*********************************98.679*************** PP TruD 214 vaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaee 300 + ++ dl++a+e+lp+s Er+++++ +++k+y + ++a++++ ++++vhAyqSy++N++ s+R e+g+ +++e D+v ++ + tr|A2FUM2|A2FUM2_TRIVA 283 F-QRSDLDKAMELLPHSAVAERKIVEAAHDTNKKY-EMFKAVDRRQRMMYVHAYQSYIWNKCASKRAEKGF---KVLETDTVEYKGK 364 *.9************************99966666.56********************************5...689*****99955 PP TruD 301 rlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrve. 386 +++++ +++++ + ++ g+ ++ +++ ++g + e+ r++ +e+g+++e k+ ++ + + +++ tr|A2FUM2|A2FUM2_TRIVA 365 I-KEPTKKSVLQDVVIPLCE-----GDTKDKMI---LDMMKEDGVTTEMFRKIAKEYGINTEYRKFMAFAKDIEYSIVKHDN---Pd 439 4.455555555444444444.....33322222...2566678888888888888888877644433322211111121111...02 PP TruD 387 ...................dlelsaeedeltleFsLpkGsYATvvlrEi 416 ++ +++++++++FsL +G YAT++lrE+ tr|A2FUM2|A2FUM2_TRIVA 440 vqlinndvellnnpklsrvAKNTGNKNSSAVISFSLGSGEYATMFLREL 488 22334457788888898775556677778******************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 50190 (17055200 residues searched) Passed MSV filter: 1987 (0.0395896); expected 1003.8 (0.02) Passed bias filter: 738 (0.0147041); expected 1003.8 (0.02) Passed Vit filter: 35 (0.00069735); expected 50.2 (0.001) Passed Fwd filter: 2 (3.98486e-05); expected 0.5 (1e-05) Initial search space (Z): 50190 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.47u 0.02s 00:00:00.49 Elapsed: 00:00:00.21 # Mc/sec: 33785.54 // [ok]