Citrus Sinensis ID: 009707

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------53
MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF
ccccccccccccccccEEEEcccccccccccccccccccccccccccccccccEEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccHHHcHHHHHHHHHHHHccccccccccccccccccEEEccEEEccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHcccccccccccccccccEEEEcccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHccccccccccccccccEEcEEEEccHHccHHHHcccccEEEEEEEEcccccccccccccEEEcccccccHHHHHHHHHcccccEEEcccccccccccccHHHHHHHccccEEEcccEEEEEEEEEEEEccccEEEEEEEEEccccHHHHHHHHHHHHcccccEEccEEEcccccccccccccHHHHHHHHHcccc
ccEEEEcHHHHcccccEEccccccccccccHHHEcccccccHHccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccccccccccccEEEccccEEcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccHHccEccccccccHHHHHHcccccccccccccccccccEEEccccccccccEEEEccccccccEHHHHHHHHHHHHcccccccccccccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHcccccEEEccccccccEEEEEEEEHHHHHHcHHHHcccEEEEEEEEEcEEEcccEccccEEEEcccccccHHHHHHHHHHcccccccccccHHHEEccccHHHHHHHcccEEEccccEEEEEEEEEEEccccccEEEEEEEEcccHHHHHHHHHHHHHHcccHHHHHHHHHccccccHHHcccHHHHHHHHHcccc
msllllrpklitssrtlslllppplkdnfikkNVYLLSTKAFsssitstpyplqydmiinnptqpqqsqtrrrparvnstnsdenqnpdgelgfdSWVDKKLEKEaktrqpgsdnaeMTKSMRKYYNKRrqrmygtdsedeygknddgfvelkpEVVEFNRlhkreeelyfydtfaypwekdkHYKMVYQLEKkyfpdqcldkafldpsadQNVKKMRKkaggkseekkynkeddkrlvffddqekksekdsilgedvnvkgevsEKKVEEFFKCLKkvpnkenevgsgepyivsrstelpptwdgpfgtmvlvnkpkgwtsftvcgklrRLVKVkkvghagtldpmaTGLLIVCVGKATKLVDRYQGMIKGYSGVFRlgeatstwdadspviqrepwehikdEDIRKAAASFRgeiwqvppmfsaikvggekmydkarrgesielsprrISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALrrdsigqysaddAWEFKELEEAITKNYF
msllllrpklitssrtlslllppplkdnfIKKNVYLLSTKAFSSSITSTPYPLQYDMIINnptqpqqsqtrrrparvnstnsdenqnpdgelgfDSWVDKKLEkeaktrqpgsdnaemtksMRKYYNKrrqrmygtdsedeygknddgfvelKPEVVEFNrlhkreeelyfyDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKafldpsadqnvkkmrkkaggkseekkynkeddkrlvffddqekksekdsilgedvnvkgevsekKVEEFFKClkkvpnkenevgsgepYIVSRSTELPPTWDGPFGTMVLVNKPKGwtsftvcgklrrLVKVKKVghagtldpmatglLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATstwdadspviqrepwehikdEDIRKAAASfrgeiwqvppmFSAIKVGGEKMYDKARrgesielsprriSIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF
MSLLLLRPKlitssrtlslllppplKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNptqpqqsqtrrrparVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDvnvkgevsekkveeffkCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGklrrlvkvkkvGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF
****LLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMII****************************************************************************************GFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFL***************************************************************EEFFKCLKK*************YIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDK******IELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKEL*********
*******PKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMII*******************************************************************************************ELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAF*******************************************************************************************************GTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAIT****
MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPT***********************NPDGELGFDSWVDKKLE**************MTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSAD*******************NKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF
*SLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPT******************************FDSWVDKKLEKEA*********AEMTKSMRKYYNKRRQRMYG**********DDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSA*************************KRLVFFD**EK*SEKDSILGED*NVKGEVSEKKVEEFFKCLKKV*************************DGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITK**F
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query528 2.2.26 [Sep-21-2011]
A0JUU8306 tRNA pseudouridine syntha yes no 0.399 0.689 0.455 2e-51
Q9RB36229 tRNA pseudouridine syntha yes no 0.403 0.930 0.459 2e-50
Q47RU8293 tRNA pseudouridine syntha yes no 0.405 0.730 0.436 5e-48
A1R520311 tRNA pseudouridine syntha yes no 0.384 0.652 0.463 2e-47
B1MD72298 tRNA pseudouridine syntha yes no 0.405 0.718 0.442 7e-47
Q1BA81297 tRNA pseudouridine syntha yes no 0.392 0.696 0.449 2e-46
A1UET1297 tRNA pseudouridine syntha yes no 0.392 0.696 0.449 2e-46
A3PY88297 tRNA pseudouridine syntha yes no 0.392 0.696 0.449 2e-46
P62190298 tRNA pseudouridine syntha yes no 0.397 0.704 0.443 2e-45
A5U6E6298 tRNA pseudouridine syntha yes no 0.397 0.704 0.443 2e-45
>sp|A0JUU8|TRUB_ARTS2 tRNA pseudouridine synthase B OS=Arthrobacter sp. (strain FB24) GN=truB PE=3 SV=1 Back     alignment and function desciption
 Score =  204 bits (518), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/215 (45%), Positives = 136/215 (63%), Gaps = 4/215 (1%)

Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
           +V+V+KP+GWTS  V G++RRL   +KVGHAGTLDPMATG+L++ + KAT+L+    G  
Sbjct: 5   LVIVDKPQGWTSHDVVGRMRRLAGTRKVGHAGTLDPMATGVLVLGINKATRLLTYIVGTS 64

Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
           K Y+   RLGE+T T DA+  V+       + +  IR A A+  GEI QVP   SAIKV 
Sbjct: 65  KTYTATIRLGESTVTDDAEGEVVSSHSAAAVTEGAIRAAVAALTGEIQQVPSSVSAIKVN 124

Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIF----RVTCSKGTYIRSLCAD 486
           GE+ Y + R GE ++L+ R ++I +FD+     +R   +      V CS GTYIR+L  D
Sbjct: 125 GERAYARVRSGEDVKLAARPVTIHRFDVHAVRPERAGAVLDVDVTVECSSGTYIRALARD 184

Query: 487 FGKALGSCAHLTALRRDSIGQYSADDAWEFKELEE 521
            G+ALG+  HLTALRR  +G Y+ D A   ++L E
Sbjct: 185 LGEALGTGGHLTALRRTQVGPYTLDQARTLEQLAE 219
Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.
Arthrobacter sp. (strain FB24) (taxid: 290399)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: 2EC: 5
>sp|Q9RB36|TRUB_FLAJ1 tRNA pseudouridine synthase B OS=Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|Q47RU8|TRUB_THEFY tRNA pseudouridine synthase B OS=Thermobifida fusca (strain YX) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|A1R520|TRUB_ARTAT tRNA pseudouridine synthase B OS=Arthrobacter aurescens (strain TC1) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|B1MD72|TRUB_MYCA9 tRNA pseudouridine synthase B OS=Mycobacterium abscessus (strain ATCC 19977 / DSM 44196) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|Q1BA81|TRUB_MYCSS tRNA pseudouridine synthase B OS=Mycobacterium sp. (strain MCS) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|A1UET1|TRUB_MYCSK tRNA pseudouridine synthase B OS=Mycobacterium sp. (strain KMS) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|A3PY88|TRUB_MYCSJ tRNA pseudouridine synthase B OS=Mycobacterium sp. (strain JLS) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|P62190|TRUB_MYCTU tRNA pseudouridine synthase B OS=Mycobacterium tuberculosis GN=truB PE=1 SV=1 Back     alignment and function description
>sp|A5U6E6|TRUB_MYCTA tRNA pseudouridine synthase B OS=Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) GN=truB PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query528
255560950513 tRNA-pseudouridine synthase, putative [R 0.946 0.974 0.708 0.0
449450185544 PREDICTED: uncharacterized protein LOC10 0.973 0.944 0.678 0.0
297811569538 hypothetical protein ARALYDRAFT_488288 [ 0.975 0.957 0.666 0.0
225452300520 PREDICTED: uncharacterized protein LOC10 0.946 0.961 0.680 0.0
296087588502 unnamed protein product [Vitis vinifera] 0.922 0.970 0.679 0.0
7573471540 tRNA synthase-like protein [Arabidopsis 0.969 0.948 0.675 0.0
186522847540 tRNA pseudouridine synthase B [Arabidops 0.984 0.962 0.669 0.0
449532619517 PREDICTED: uncharacterized LOC101215528, 0.905 0.924 0.661 0.0
356511706485 PREDICTED: uncharacterized protein LOC10 0.825 0.898 0.686 0.0
413942368497 pseudouridylate synthase/ transporter [Z 0.829 0.881 0.602 1e-162
>gi|255560950|ref|XP_002521488.1| tRNA-pseudouridine synthase, putative [Ricinus communis] gi|223539387|gb|EEF40978.1| tRNA-pseudouridine synthase, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  755 bits (1950), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/531 (70%), Positives = 423/531 (79%), Gaps = 31/531 (5%)

Query: 11  ITSSRTLSLLLPPPL--------KDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNP 62
           +  S +L  LLP P         K   + +   L S      S  STPYP QYDMII+ P
Sbjct: 1   MAKSLSLLFLLPKPTFCPILLSSKPKSLNRACILSSLSRTLFSTVSTPYPFQYDMIISRP 60

Query: 63  TQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSM 122
           +Q Q  Q+R +PARV   +SD +  P+ ELG DSWVD+KL               M KS 
Sbjct: 61  SQSQPPQSRSQPARVTKDDSDCSPEPESELGLDSWVDQKLS--------------MDKSK 106

Query: 123 RKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKD 182
           RKYYNKRR+RMYG+DS+D+    D+GFVELKPEV  F  LHKREEELY YDTFAYPWEKD
Sbjct: 107 RKYYNKRRKRMYGSDSDDDTRNKDEGFVELKPEVAHFGSLHKREEELYMYDTFAYPWEKD 166

Query: 183 KHYKMVYQLEKKYFPDQCLDKAFLDP-----SADQNVKKMRKKAGGKSEEKKYNKEDDKR 237
           KHYKMVYQLEKKYFPDQC DKAFLD      S +++VK+  K+   +      ++E+DK 
Sbjct: 167 KHYKMVYQLEKKYFPDQCFDKAFLDHKDSNFSKNESVKRSSKRVVKRDTNGVGDREEDKG 226

Query: 238 LVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRS 297
           LVFF++++ + E +S    + NV  +V+E+KVEEFFKCLKKVPNK+NE+ +GEPY+V+RS
Sbjct: 227 LVFFEEEKAEIESNS----EKNVAKDVTERKVEEFFKCLKKVPNKKNEIDTGEPYLVTRS 282

Query: 298 TELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG 357
           TELPP WD   GT+VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG
Sbjct: 283 TELPPRWDDTHGTVVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG 342

Query: 358 KATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEI 417
           KATK+VDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASF GEI
Sbjct: 343 KATKVVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFCGEI 402

Query: 418 WQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKG 477
           WQVPPMFSAIKVGGEKMY+KARRGESIELSPRRISIFQF+IERSLEDRQNLIFRV CSKG
Sbjct: 403 WQVPPMFSAIKVGGEKMYEKARRGESIELSPRRISIFQFNIERSLEDRQNLIFRVVCSKG 462

Query: 478 TYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
           TY+RSLCADFGKALGSCAHLTALRRDSIG+YSADDAWEFKELEEAITKNYF
Sbjct: 463 TYVRSLCADFGKALGSCAHLTALRRDSIGEYSADDAWEFKELEEAITKNYF 513

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449450185|ref|XP_004142844.1| PREDICTED: uncharacterized protein LOC101215528 [Cucumis sativus] Back     alignment and taxonomy information
>gi|297811569|ref|XP_002873668.1| hypothetical protein ARALYDRAFT_488288 [Arabidopsis lyrata subsp. lyrata] gi|297319505|gb|EFH49927.1| hypothetical protein ARALYDRAFT_488288 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|225452300|ref|XP_002272379.1| PREDICTED: uncharacterized protein LOC100259460 [Vitis vinifera] Back     alignment and taxonomy information
>gi|296087588|emb|CBI34844.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|7573471|emb|CAB87785.1| tRNA synthase-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|186522847|ref|NP_196950.2| tRNA pseudouridine synthase B [Arabidopsis thaliana] gi|110741670|dbj|BAE98781.1| tRNA synthase - like protein [Arabidopsis thaliana] gi|332004654|gb|AED92037.1| tRNA pseudouridine synthase B [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449532619|ref|XP_004173278.1| PREDICTED: uncharacterized LOC101215528, partial [Cucumis sativus] Back     alignment and taxonomy information
>gi|356511706|ref|XP_003524564.1| PREDICTED: uncharacterized protein LOC100793939 [Glycine max] Back     alignment and taxonomy information
>gi|413942368|gb|AFW75017.1| pseudouridylate synthase/ transporter [Zea mays] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query528
TAIR|locus:2145708540 AT5G14460 [Arabidopsis thalian 0.926 0.905 0.646 3.6e-169
UNIPROTKB|P62190298 truB "tRNA pseudouridine synth 0.403 0.714 0.433 4.8e-39
TIGR_CMR|GSU_1591304 GSU_1591 "tRNA pseudouridine s 0.393 0.684 0.385 5.1e-35
TIGR_CMR|SPO_3837303 SPO_3837 "tRNA pseudouridine s 0.399 0.696 0.392 1.1e-34
UNIPROTKB|Q97QJ3292 truB "tRNA pseudouridine synth 0.403 0.729 0.387 3.6e-34
TIGR_CMR|CBU_1430309 CBU_1430 "tRNA pseudouridine s 0.431 0.737 0.364 1.2e-33
TIGR_CMR|DET_0981300 DET_0981 "tRNA pseudouridine s 0.397 0.7 0.363 6.7e-33
UNIPROTKB|Q9KU78312 truB "tRNA pseudouridine synth 0.369 0.625 0.378 4.7e-32
TIGR_CMR|VC_0645312 VC_0645 "tRNA pseudouridine 55 0.369 0.625 0.378 4.7e-32
UNIPROTKB|P60340314 truB "tRNA pseudouridine 55 sy 0.397 0.668 0.342 8.8e-31
TAIR|locus:2145708 AT5G14460 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1645 (584.1 bits), Expect = 3.6e-169, P = 3.6e-169
 Identities = 334/517 (64%), Positives = 380/517 (73%)

Query:    32 KNVYLLSTKAFSSSITSTPYPLQYDMIINNXXXXXXXXXXXXXXXVNSTNSDENQNPDGE 91
             +N++     +   S TST YPLQYDMIIN                   + + ++  P+  
Sbjct:    32 RNIHKPYLASLFLSTTSTRYPLQYDMIINRPTQSSLSQNRRRPPKAIESGAPDSAEPE-- 89

Query:    92 LGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYG--KNDDGF 149
               FDSWVD KL  E +  +PGS + EM K+ RKYY+KRR+R+YG+DSEDE    K+D+GF
Sbjct:    90 --FDSWVDNKLAMEREQGRPGSGDPEMDKAKRKYYSKRRKRLYGSDSEDENSSRKSDEGF 147

Query:   150 VELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDP- 208
             VELKPEVVEF+RLH+REEELYFYDTFAYPWEKDKHYKMVYQLEKKY+PDQCLDKAFL P 
Sbjct:   148 VELKPEVVEFDRLHQREEELYFYDTFAYPWEKDKHYKMVYQLEKKYYPDQCLDKAFLQPG 207

Query:   209 -----SADQNVKKMRKKA----GGK-SEEKKYNKE----DDKRLVFFDDQEKKSEKDSIL 254
                  S D    + +KK     GGK SE K+   E    DD +LVFFD+ ++K EK    
Sbjct:   208 EVLKKSDDSGKVRGKKKVVAALGGKRSEVKRIGMENCDEDDDKLVFFDEVKEKEEKKK-- 265

Query:   255 GEDXXXXXXXXXXXXXXXXXCLKKVPNKENEV---GSGEPYIVSRSTELPPTWDGPFGTM 311
              ED                  L K PN++      G GEP++V+R+ ELPP WDGP GT+
Sbjct:   266 SEDDVVVVTEKKVEQFFKG--LTKSPNEKGMASGGGDGEPFLVTRNGELPPRWDGPNGTV 323

Query:   312 VLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
             +LVNKPKGWTSFTVCG           GHAGTLDPMATGLLIVCVGKATK+VDRYQGMIK
Sbjct:   324 LLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKVVDRYQGMIK 383

Query:   372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
             GYSGVFRLGEATST DADSPVIQRE WEHIKD+DI+KA  SF GEIWQVPPMFSAIKVGG
Sbjct:   384 GYSGVFRLGEATSTLDADSPVIQRESWEHIKDDDIKKALTSFLGEIWQVPPMFSAIKVGG 443

Query:   432 EKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKAL 491
             EKMY+KARRGE++ELSPRRISIFQFDIERSL+DRQNLIFRV CSKGTYIRSLCAD  KAL
Sbjct:   444 EKMYEKARRGETVELSPRRISIFQFDIERSLDDRQNLIFRVICSKGTYIRSLCADLAKAL 503

Query:   492 GSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
             GSCAHLTALRRDSIG+YSA+DAWEF ELE AITKNYF
Sbjct:   504 GSCAHLTALRRDSIGEYSANDAWEFNELEAAITKNYF 540
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0005215 "transporter activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006396 "RNA processing" evidence=IEA
GO:0009451 "RNA modification" evidence=IEA;ISS
GO:0009982 "pseudouridine synthase activity" evidence=IEA;TAS
GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA
UNIPROTKB|P62190 truB "tRNA pseudouridine synthase B" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_1591 GSU_1591 "tRNA pseudouridine synthase B" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_3837 SPO_3837 "tRNA pseudouridine synthase B" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
UNIPROTKB|Q97QJ3 truB "tRNA pseudouridine synthase B" [Streptococcus pneumoniae TIGR4 (taxid:170187)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1430 CBU_1430 "tRNA pseudouridine synthase B" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0981 DET_0981 "tRNA pseudouridine synthase B" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KU78 truB "tRNA pseudouridine synthase B" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0645 VC_0645 "tRNA pseudouridine 55 synthase" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
UNIPROTKB|P60340 truB "tRNA pseudouridine 55 synthase" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer5.4.990.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query528
cd02573213 cd02573, PseudoU_synth_EcTruB, Pseudouridine synth 1e-101
PRK03287298 PRK03287, truB, tRNA pseudouridine synthase B; Pro 5e-82
pfam01509149 pfam01509, TruB_N, TruB family pseudouridylate syn 2e-72
PRK00130290 PRK00130, truB, tRNA pseudouridine synthase B; Pro 4e-70
TIGR00431209 TIGR00431, TruB, tRNA pseudouridine(55) synthase 2e-69
cd00506210 cd00506, PseudoU_synth_TruB_like, Pseudouridine sy 7e-66
PRK05389305 PRK05389, truB, tRNA pseudouridine synthase B; Pro 1e-65
PRK01550304 PRK01550, truB, tRNA pseudouridine synthase B; Pro 4e-65
PRK02755295 PRK02755, truB, tRNA pseudouridine synthase B; Pro 2e-64
PRK02484294 PRK02484, truB, tRNA pseudouridine synthase B; Pro 3e-63
PRK01851303 PRK01851, truB, tRNA pseudouridine synthase B; Pro 5e-63
COG0130271 COG0130, TruB, Pseudouridine synthase [Translation 9e-62
PRK05033312 PRK05033, truB, tRNA pseudouridine synthase B; Pro 1e-61
PRK00989230 PRK00989, truB, tRNA pseudouridine synthase B; Pro 5e-56
PRK14124308 PRK14124, PRK14124, tRNA pseudouridine synthase B; 2e-53
PRK04642300 PRK04642, truB, tRNA pseudouridine synthase B; Pro 5e-49
PRK00020244 PRK00020, truB, tRNA pseudouridine synthase B; Pro 5e-48
PRK14122312 PRK14122, PRK14122, tRNA pseudouridine synthase B; 3e-47
PRK14123305 PRK14123, PRK14123, tRNA pseudouridine synthase B; 2e-45
cd02572182 cd02572, PseudoU_synth_hDyskerin, Pseudouridine sy 7e-40
PRK02193279 PRK02193, truB, tRNA pseudouridine synthase B; Pro 5e-39
cd02867312 cd02867, PseudoU_synth_TruB_4, Pseudouridine synth 5e-37
PRK04099273 PRK04099, truB, tRNA pseudouridine synthase B; Pro 6e-36
PRK04270300 PRK04270, PRK04270, H/ACA RNA-protein complex comp 3e-35
TIGR00425 322 TIGR00425, CBF5, rRNA pseudouridine synthase, puta 3e-35
PRK01528292 PRK01528, truB, tRNA pseudouridine synthase B; Pro 2e-33
PRK14846 345 PRK14846, truB, tRNA pseudouridine synthase B; Pro 2e-31
cd02868226 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine 5e-07
cd0129187 cd01291, PseudoU_synth, Pseudouridine synthases ca 6e-05
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information 
 Score =  303 bits (778), Expect = e-101
 Identities = 99/211 (46%), Positives = 135/211 (63%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           +L++KP G TS  V  K+RRL+  KKVGH GTLDP+ATG+L + +G+ATKL        K
Sbjct: 3   LLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADK 62

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y    RLGEAT T DA+  +I+  P   + +E+I  A  +F GEI QVPPM+SA+KV G
Sbjct: 63  TYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVDG 122

Query: 432 EKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKAL 491
           +++Y+ AR GE +E  PR+++I+  ++     +     F V CSKGTYIRSL  D GKAL
Sbjct: 123 KRLYELARAGEEVERPPRKVTIYSLELLSFDPENPEADFEVHCSKGTYIRSLARDLGKAL 182

Query: 492 GSCAHLTALRRDSIGQYSADDAWEFKELEEA 522
           G  AHL+ALRR   G ++ + A   +ELE  
Sbjct: 183 GCGAHLSALRRTRSGPFTLEQAITLEELEAL 213

This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine. Length = 213
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal domain) Back     alignment and domain information
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase Back     alignment and domain information
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB family Back     alignment and domain information
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4 Back     alignment and domain information
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative Back     alignment and domain information
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 528
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 100.0
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 100.0
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 100.0
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14123305 tRNA pseudouridine synthase B; Provisional 100.0
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 100.0
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14124308 tRNA pseudouridine synthase B; Provisional 100.0
PRK14122312 tRNA pseudouridine synthase B; Provisional 100.0
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 100.0
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 100.0
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 100.0
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 100.0
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 100.0
TIGR00425 322 CBF5 rRNA pseudouridine synthase, putative. This f 100.0
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 100.0
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 100.0
KOG2559318 consensus Predicted pseudouridine synthase [Transl 100.0
KOG2529395 consensus Pseudouridine synthase [Translation, rib 99.95
KOG2529 395 consensus Pseudouridine synthase [Translation, rib 99.88
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 99.17
TIGR01213388 conserved hypothetical protein TIGR01213. Members 98.71
PRK14554422 putative pseudouridylate synthase; Provisional 98.4
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 98.18
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 98.09
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 98.08
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 98.02
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 97.95
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 97.84
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 97.82
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 97.73
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 97.45
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 97.44
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 97.39
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 97.38
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 97.36
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 97.29
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 97.16
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 97.14
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 96.99
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 96.97
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 96.91
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 96.83
PRK11112257 tRNA pseudouridine synthase C; Provisional 96.82
PF0806859 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 96.82
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 96.78
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 96.73
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 96.66
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 96.53
COG1258398 Predicted pseudouridylate synthase [Translation, r 96.05
TIGR00093128 pseudouridine synthase. This model identifies pane 95.2
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 94.74
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information 
Probab=100.00  E-value=6.5e-76  Score=563.21  Aligned_cols=210  Identities=40%  Similarity=0.680  Sum_probs=203.9

Q ss_pred             eEEEeeCCCCCChHHHHHHHHHHhCCccccccCCCCCCCceEeEEEecccccchhhhcCCCcEEEEEEEEcccccCCCCC
Q 009707          310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD  389 (528)
Q Consensus       310 gIL~VdKP~G~TS~dVV~klRrlL~ikKVGHaGTLDP~ATGVLVVgVGkATKLl~~l~~~~K~Y~at~~LG~eTDT~D~e  389 (528)
                      |||+||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|.+
T Consensus         1 Gil~i~KP~g~tS~~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~aTkl~~~~~~~~K~Y~~~~~lG~~TdT~D~~   80 (210)
T cd00506           1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDTFDAT   80 (210)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHHHhhhHHHhcCCceEEEEEEECCcCCCCCCC
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEeeccCCCCCHHHHHHHHHhCccceeecCCcccccccCChhhHHHHhcCcccccCCceEEEEEEEeeeccCCCceEE
Q 009707          390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLI  469 (528)
Q Consensus       390 GkVie~~p~~hIT~e~LekaL~kF~G~i~QvPP~YSAVKVnGKRAYELARkGe~VELkpR~V~IyeleL~~~l~~~p~~t  469 (528)
                      |+|++++++.|+|.++|++++++|+|+++|+||+|||+|+||+|||||||+|++|++++|+|.||+++++.+....+.+.
T Consensus        81 G~v~~~~~~~~it~e~l~~~l~~f~G~i~Q~pP~ySAvKv~G~raYelAR~G~~v~~~~r~v~I~~i~ll~~~~~~~~~~  160 (210)
T cd00506          81 GQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFNPPHFLLE  160 (210)
T ss_pred             CCEEEEeCCCCCCHHHHHHHHHHCCCeEEEeCCchheEEECCHhHHHHHHCCCccccCcEeEEEEEEEEEEEcCCCcEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999987643336899


Q ss_pred             EEEEecCCccHHHHHHHHHHHhcccceecceEEEEEeccCcccccCHHHH
Q 009707          470 FRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKEL  519 (528)
Q Consensus       470 feV~CSkGTYIRSLa~DIG~aLGt~AhLt~LRRTriG~FtLddA~tLedL  519 (528)
                      |+|.||+||||||||+|||.+|||+|||++||||++|+|+++||+++++|
T Consensus       161 ~~v~cs~GTYIRsL~~Dig~~Lg~~a~l~~L~R~~~G~f~~~~a~~l~~l  210 (210)
T cd00506         161 VEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPFKVENAVTLHHL  210 (210)
T ss_pred             EEEEECCCcCHHHHHHHHHHHhCCcEEEEEEEEEEECCCchhhccchhhC
Confidence            99999999999999999999999999999999999999999999999875

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones Back     alignment and domain information
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>TIGR01213 conserved hypothetical protein TIGR01213 Back     alignment and domain information
>PRK14554 putative pseudouridylate synthase; Provisional Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [] Back     alignment and domain information
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query528
1sgv_A316 Structure Of Trna Psi55 Pseudouridine Synthase (Tru 4e-43
1r3e_A309 Crystal Structure Of Trna Pseudouridine Synthase Tr 3e-33
1ze2_A309 Conformational Change Of Pseudouridine 55 Synthase 3e-33
1ze1_A309 Conformational Change Of Pseudouridine 55 Synthase 3e-33
2ab4_A309 Dissecting The Roles Of A Strictly Conserved Tyrosi 8e-33
1k8w_A327 Crystal Structure Of The E. Coli Pseudouridine Synt 1e-32
1r3f_A314 Crystal Structure Of Trna Pseudouridine Synthase Tr 1e-32
1zl3_A327 Coupling Of Active Site Motions And Rna Binding Len 4e-32
2apo_A 357 Crystal Structure Of The Methanococcus Jannaschii C 6e-22
3u28_A 400 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From 1e-19
2aus_C 334 Crystal Structure Of The Archaeal Box HACA SRNP NOP 1e-16
3lwo_A 340 Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONT 2e-16
2hvy_A 346 Crystal Structure Of An HACA BOX RNP FROM PYROCOCCU 2e-16
3mqk_A 328 Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Cont 3e-16
2ey4_A 333 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Leng 3e-16
3hjw_A 327 Structure Of A Functional Ribonucleoprotein Pseudou 3e-16
2rfk_A 334 Substrate Rna Positioning In The Archaeal HACA Ribo 2e-15
>pdb|1SGV|A Chain A, Structure Of Trna Psi55 Pseudouridine Synthase (Trub) Length = 316 Back     alignment and structure 
Iteration: 1

 Score =  172 bits (436), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 92/214 (42%), Positives = 124/214 (57%), Gaps = 4/214 (1%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
           +V+++KP G TS  V G           GHAGTLDPMATG+L++ + +ATK++       
Sbjct: 8   IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAP 67
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
           K Y+   RLG+ TST DA+  V+Q  P +H+  E I  A    RGEI QVP   SAIKVG
Sbjct: 68  KSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVG 127
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLI---FRVTCSKGTYIRSLCADF 487
           G + Y  AR+G S++L  R I I +F++  +   R  LI     + CS GTYIR+L  D 
Sbjct: 128 GRRAYRLARQGRSVQLEARPIRIDRFELL-AARRRDQLIDIDVEIDCSSGTYIRALARDL 186
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEE 521
           G ALG   H+TALRR  +G++  D A    +L E
Sbjct: 187 GDALGVGGHVTALRRTRVGRFELDQARSLDDLAE 220
>pdb|1R3E|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And Its Rna Complex: Rna-Protein Recognition Through A Combination Of Rigid Docking And Induced Fit Length = 309 Back     alignment and structure
>pdb|1ZE2|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon Its Association With Rna Substrate Length = 309 Back     alignment and structure
>pdb|1ZE1|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon Its Association With Rna Substrate Length = 309 Back     alignment and structure
>pdb|2AB4|A Chain A, Dissecting The Roles Of A Strictly Conserved Tyrosine In Substrate Recognition And Catalysis By Pseudouridine 55 Synthase Length = 309 Back     alignment and structure
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase Trub Bound To A T Stem-Loop Rna Length = 327 Back     alignment and structure
>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And Its Rna Complex: Rna-Protein Recognition Through A Combination Of Rigid Docking And Induced Fit Length = 314 Back     alignment and structure
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding Length = 327 Back     alignment and structure
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5 Nop10 Complex Length = 357 Back     alignment and structure
>pdb|3U28|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From Saccharomyces Cerevisiae Length = 400 Back     alignment and structure
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5 Complex Length = 334 Back     alignment and structure
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING 5BRU Length = 340 Back     alignment and structure
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS FURIOSUS Length = 346 Back     alignment and structure
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing Aca Trinucleotide Length = 328 Back     alignment and structure
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Length = 333 Back     alignment and structure
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine Synthase Bound To A Substrate Rna Length = 327 Back     alignment and structure
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA Ribonucleoprotein Complex Length = 334 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query528
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 1e-104
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 3e-99
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 4e-97
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 9e-71
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 2e-68
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 7e-62
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-07
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 1e-05
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Length = 316 Back     alignment and structure
 Score =  314 bits (808), Expect = e-104
 Identities = 95/225 (42%), Positives = 134/225 (59%), Gaps = 6/225 (2%)

Query: 300 LPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA 359
           +  T  G    +V+++KP G TS  V G+ RR+   ++VGHAGTLDPMATG+L++ + +A
Sbjct: 1   MSATGPG----IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERA 56

Query: 360 TKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQ 419
           TK++       K Y+   RLG+ TST DA+  V+Q  P +H+  E I  A    RGEI Q
Sbjct: 57  TKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQ 116

Query: 420 VPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDI--ERSLEDRQNLIFRVTCSKG 477
           VP   SAIKVGG + Y  AR+G S++L  R I I +F++   R  +   ++   + CS G
Sbjct: 117 VPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSG 176

Query: 478 TYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEA 522
           TYIR+L  D G ALG   H+TALRR  +G++  D A    +L E 
Sbjct: 177 TYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAER 221
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Length = 309 Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Length = 327 Back     alignment and structure
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Length = 357 Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Length = 334 Back     alignment and structure
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Length = 400 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens} Length = 530 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query528
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 100.0
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 100.0
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 100.0
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 100.0
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 100.0
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 100.0
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 98.78
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 98.6
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 97.59
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 97.57
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 96.83
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 96.83
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 96.82
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 96.74
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 96.71
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 96.26
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
Probab=100.00  E-value=1.8e-75  Score=587.19  Aligned_cols=213  Identities=43%  Similarity=0.712  Sum_probs=178.6

Q ss_pred             ceEEEeeCCCCCChHHHHHHHHHHhCCccccccCCCCCCCceEeEEEecccccchhhhcCCCcEEEEEEEEcccccCCCC
Q 009707          309 GTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDA  388 (528)
Q Consensus       309 GgIL~VdKP~G~TS~dVV~klRrlL~ikKVGHaGTLDP~ATGVLVVgVGkATKLl~~l~~~~K~Y~at~~LG~eTDT~D~  388 (528)
                      +|||+||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++|+++.+|+|+++++||.+|||+|.
T Consensus         6 ~Gil~vdKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l~~~~K~Y~~~~~lG~~TdT~D~   85 (316)
T 1sgv_A            6 PGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDA   85 (316)
T ss_dssp             SEEEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGGGGTTTSCEEEEEEEEETEEETTSBT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccccccccccCCCCCeEEEEEEECHHHhHHHHhCcCCcEEEEEEEECCccCCCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEeeccCCCCCHHHHHHHHHhCccceeecCCcccccccCChhhHHHHhcCcccccCCceEEEEEEEeeeccC--CCc
Q 009707          389 DSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLE--DRQ  466 (528)
Q Consensus       389 eGkVie~~p~~hIT~e~LekaL~kF~G~i~QvPP~YSAVKVnGKRAYELARkGe~VELkpR~V~IyeleL~~~l~--~~p  466 (528)
                      +|+|+++.++.|+|.++|+++|++|+|+|+|+||+|||||+||+|||||||+|++||+++|+|+||+|+++.+..  ..|
T Consensus        86 eG~v~~~~~~~~~t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkrlYelAR~G~~ve~~~R~v~I~~i~ll~~~~~~~~p  165 (316)
T 1sgv_A           86 EGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLI  165 (316)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEEEEEEETTEE
T ss_pred             CCCEEEecCCCCCCHHHHHHHHHhccccEEEeCCHHHhcccCChhHHHHHhCCCcccccceEEEEEEEEEEEeeccCCCc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999987632  247


Q ss_pred             eEEEEEEecCCccHHHHHHHHHHHhcccceecceEEEEEeccCcccccCHHHHHH
Q 009707          467 NLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEE  521 (528)
Q Consensus       467 ~~tfeV~CSkGTYIRSLa~DIG~aLGt~AhLt~LRRTriG~FtLddA~tLedL~~  521 (528)
                      .++|+|+||+||||||||+|||.+|||+|||++||||++|+|++++|++|++|.+
T Consensus       166 ~~~~~v~CskGTYIRsLa~DiG~~Lg~~a~~~~LrRt~~G~F~~~~a~tl~~l~~  220 (316)
T 1sgv_A          166 DIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAE  220 (316)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHHTSCEEEEEEEEEEETTEEGGGCBCHHHHHH
T ss_pred             eEEEEEEECCCCcHHHHHHHHHHHhCCCEEEeeEEEEEEccCcHHHccCHHHHhh
Confidence            8999999999999999999999999999999999999999999999999999976
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Back     alignment and structure
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Back     alignment and structure
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens} Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 528
d1sgva2233 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB 4e-64
d1k8wa5242 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB 3e-57
d1r3ea2228 d.265.1.2 (A:10-237) Pseudouridine synthase II Tru 5e-53
d2ey4a2245 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB 5e-45
d2apoa2230 d.265.1.2 (A:17-246) Pseudouridine synthase II Tru 6e-44
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 233 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score =  206 bits (525), Expect = 4e-64
 Identities = 93/213 (43%), Positives = 128/213 (60%), Gaps = 2/213 (0%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           V+++KP G TS  V G+ RR+   ++VGHAGTLDPMATG+L++ + +ATK++       K
Sbjct: 7   VVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPK 66

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y+   RLG+ TST DA+  V+Q  P +H+  E I  A    RGEI QVP   SAIKVGG
Sbjct: 67  SYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGG 126

Query: 432 EKMYDKARRGESIELS--PRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
            + Y  AR+G S++L   P RI  F+    R  +   ++   + CS GTYIR+L  D G 
Sbjct: 127 RRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGD 186

Query: 490 ALGSCAHLTALRRDSIGQYSADDAWEFKELEEA 522
           ALG   H+TALRR  +G++  D A    +L E 
Sbjct: 187 ALGVGGHVTALRRTRVGRFELDQARSLDDLAER 219
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Length = 242 Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Length = 228 Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 245 Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 230 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query528
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 100.0
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 100.0
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 100.0
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 100.0
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 97.98
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 97.81
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 96.96
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 96.85
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=100.00  E-value=6.4e-76  Score=565.61  Aligned_cols=214  Identities=43%  Similarity=0.708  Sum_probs=178.8

Q ss_pred             ceEEEeeCCCCCChHHHHHHHHHHhCCccccccCCCCCCCceEeEEEecccccchhhhcCCCcEEEEEEEEcccccCCCC
Q 009707          309 GTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDA  388 (528)
Q Consensus       309 GgIL~VdKP~G~TS~dVV~klRrlL~ikKVGHaGTLDP~ATGVLVVgVGkATKLl~~l~~~~K~Y~at~~LG~eTDT~D~  388 (528)
                      .|||+||||.|||||+||++||+.++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|.
T Consensus         4 ~G~l~v~KP~G~TS~~~v~~vk~~~~~kKvGh~GTLDP~AtGvL~i~ig~aTK~~~~~~~~~K~Y~~~~~lG~~TdT~D~   83 (233)
T d1sgva2           4 PGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDA   83 (233)
T ss_dssp             SEEEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGGGGTTTSCEEEEEEEEETEEETTSBT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhCcCccccCcCCCCcceeeEEEEechhhhhhhhhccCceEEEEEEEEccccccccc
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEeeccCCCCCHHHHHHHHHhCccceeecCCcccccccCChhhHHHHhcCcccccCCceEEEEEEEeeeccC--CCc
Q 009707          389 DSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLE--DRQ  466 (528)
Q Consensus       389 eGkVie~~p~~hIT~e~LekaL~kF~G~i~QvPP~YSAVKVnGKRAYELARkGe~VELkpR~V~IyeleL~~~l~--~~p  466 (528)
                      +|+|+++.++.|++.++|++++++|+|.++|+||+|||+|+||+|||+|||+|+.+++++|+|.||+++++.+..  ..|
T Consensus        84 ~G~vi~~~~~~~~t~~~i~~~l~~f~G~~~Q~PP~ySAvKv~GkraYelAR~G~~~~~~~r~v~I~~~~l~~~~~~~~~~  163 (233)
T d1sgva2          84 EGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLI  163 (233)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEEEEEEETTEE
T ss_pred             ccceeeeeccccchHHHHHHHHHhcCCcEEeeccHHHHhhccChHHHHHHHhCCcccccccceeeeeEEEEeeccCCCce
Confidence            999999999999999999999999999999999999999999999999999999999999999999999986532  346


Q ss_pred             eEEEEEEecCCccHHHHHHHHHHHhcccceecceEEEEEeccCcccccCHHHHHHH
Q 009707          467 NLIFRVTCSKGTYIRSLCADFGKALGSCAHLTALRRDSIGQYSADDAWEFKELEEA  522 (528)
Q Consensus       467 ~~tfeV~CSkGTYIRSLa~DIG~aLGt~AhLt~LRRTriG~FtLddA~tLedL~~~  522 (528)
                      .++|+|+||+||||||||||||++|||+|||++||||++|+|+++||++|++|.++
T Consensus       164 ~~~~~v~Cs~GTYIRsLa~DiG~~Lg~~A~l~~LrRt~~G~F~~~~a~~l~~l~~~  219 (233)
T d1sgva2         164 DIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAER  219 (233)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHHTSCEEEEEEEEEEETTEEGGGCBCHHHHHHS
T ss_pred             EEEEEEEECchhHHHHHHHHHHHHhCCcEEEEEeEeeeEcCCCHHHccCHHHHhcC
Confidence            89999999999999999999999999999999999999999999999999999864
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure