Citrus Sinensis ID: 011455

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-----
MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLST
ccccccccccccccccEEEEcccccccccccccccccccccccccccccccccEEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccHHHcHHHHHHHHHHHHccccccccccccccccccEEcccEEEEcccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHccccccccccccccccEEEEEccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEEccccccHHHHHHHHHHHHccccccccccccccccEEcEEEEccHHcHHHHHcccccEEEEEEEEccccccccccccEEEEEccccccHHHHHHHHHccccccEEcccccccccccccHHHHHHHccccccccccEEEEEEEEEEEEEccEEEEEEcccccEEEEEEEccc
ccEEEEcHHHHcccccEEccccccccccccHHHEcccccccHHccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccHHccccccccEEEccccEEcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccHHccEcccccccccHHHcccccccccccccccccccccEEEccccccccccEEEEccccccccEHHHcHHHHHHHHcccccccccccccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHcccccEEEccccccccEEEEEEEEHHHHHHcHHHHcccEEEEEEEEEcEEEcccEccccEEEEcccccccHHHHHHHHHHcccccccccccHHHHHccccHHHHHHHcccEEEccccEEEEEEEEEEEccccEEEEEEEEccEEEEEEEEccc
msllllrpklitssrtlslllppplkdnfikkNVYLLSTKAFsssitstpyplqydmiinnptqpqqsqtrrrparvnstnsdenqnpdgelgfdSWVDKKLEKEaktrqpgsdnaeMTKSMRKYYNKRrqrmygtdsedeygknddgfvelkpEVVEFNRlhkreeelyfydtfaypwekdkHYKMVYQLEKkyfpdqcldkafldpsadQNVKKMRKkaggkseekkynkeddkrlvffddqekksekdsilgedvnvkgevsEKKVEEFFKCLKkvpnkenevgsgepyivsrstelpptwdgpfgtmvlvnkpkgwtsftvcgklrRLVKVkkvghagtldpmaTGLLIVCVGKATKLVDRYQGMIKGYSGVFRlgeatstwdadspviqrepwehikdEDIRKAAASFRgeiwqvppmfsaikvggekmydkarrgesielsprrISIFQFDIERSLEDRfffflfplplklldvIHLST
msllllrpklitssrtlslllppplkdnfIKKNVYLLSTKAFSSSITSTPYPLQYDMIINnptqpqqsqtrrrparvnstnsdenqnpdgelgfDSWVDKKLEkeaktrqpgsdnaemtksMRKYYNKrrqrmygtdsedeygknddgfvelKPEVVEFNrlhkreeelyfyDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKafldpsadqnvkkmrkkaggkseekkynkeddkrlvffddqekksekdsilgedvnvkgevsekKVEEFFKClkkvpnkenevgsgepYIVSRSTELPPTWDGPFGTMVLVNKPKGwtsftvcgklrrLVKVKKVghagtldpmatglLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATstwdadspviqrepwehikdEDIRKAAASfrgeiwqvppmFSAIKVGGEKMYDKARrgesielsprriSIFQFDIERSLEDRFFFFLfplplklldvihlst
MSLLLLRPKlitssrtlslllppplKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNptqpqqsqtrrrparVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDvnvkgevsekkveeffkCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGklrrlvkvkkvGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRfffflfplplkllDVIHLST
****LLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMII****************************************************************************************GFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFL***************************************************************EEFFKCLKK*************YIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKA*****IELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHL**
*******PKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMII*******************************************************************************************ELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAF********************************************************************************************************TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS*
MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPT***********************NPDGELGFDSWVDKKLE**************MTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSAD*******************NKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLST
*SLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPT******************************FDSWVDKKLEKEA*********AEMTKSMRKYYNKRRQRMYGTD******KNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPS**************************KRLVFFD***K*SEKDSILGED**VKGEVSEKKVEEFFKCLKKV*************************DGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS*
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSLLLLRPKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLST
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 ?
Query485 2.2.26 [Sep-21-2011]
A0JUU8 306 tRNA pseudouridine syntha yes no 0.329 0.522 0.45 7e-36
A1R520 311 tRNA pseudouridine syntha yes no 0.307 0.479 0.463 1e-34
Q1BA81 297 tRNA pseudouridine syntha yes no 0.296 0.484 0.486 3e-34
A1UET1 297 tRNA pseudouridine syntha yes no 0.296 0.484 0.486 3e-34
A3PY88 297 tRNA pseudouridine syntha yes no 0.296 0.484 0.486 3e-34
Q47RU8 293 tRNA pseudouridine syntha yes no 0.305 0.505 0.445 3e-34
Q9RB36229 tRNA pseudouridine syntha yes no 0.313 0.663 0.446 1e-33
B1MD72 298 tRNA pseudouridine syntha yes no 0.305 0.496 0.452 9e-33
Q650L8233 tRNA pseudouridine syntha yes no 0.309 0.643 0.461 2e-32
Q5LJ29233 tRNA pseudouridine syntha yes no 0.309 0.643 0.461 2e-32
>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 =  152 bits (383), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 72/160 (45%), Positives = 102/160 (63%)

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 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFL 470
           GE+ Y + R GE ++L+ R ++I +FD+     +R    L
Sbjct: 125 GERAYARVRSGEDVKLAARPVTIHRFDVHAVRPERAGAVL 164
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|A1R520|TRUB_ARTAT tRNA pseudouridine synthase B OS=Arthrobacter aurescens (strain TC1) 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|Q47RU8|TRUB_THEFY tRNA pseudouridine synthase B OS=Thermobifida fusca (strain YX) GN=truB PE=3 SV=1 Back     alignment and function description
>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|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|Q650L8|TRUB_BACFR tRNA pseudouridine synthase B OS=Bacteroides fragilis (strain YCH46) GN=truB PE=3 SV=1 Back     alignment and function description
>sp|Q5LJ29|TRUB_BACFN tRNA pseudouridine synthase B OS=Bacteroides fragilis (strain ATCC 25285 / NCTC 9343) 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 ?
Query485
255560950513 tRNA-pseudouridine synthase, putative [R 0.901 0.851 0.675 1e-176
449532619517 PREDICTED: uncharacterized LOC101215528, 0.929 0.872 0.646 1e-168
449450185544 PREDICTED: uncharacterized protein LOC10 0.929 0.829 0.646 1e-168
297811569538 hypothetical protein ARALYDRAFT_488288 [ 0.931 0.840 0.637 1e-166
7573471540 tRNA synthase-like protein [Arabidopsis 0.942 0.846 0.641 1e-160
225452300520 PREDICTED: uncharacterized protein LOC10 0.901 0.840 0.649 1e-160
186522847540 tRNA pseudouridine synthase B [Arabidops 0.942 0.846 0.641 1e-159
296087588502 unnamed protein product [Vitis vinifera] 0.874 0.844 0.647 1e-159
356511706485 PREDICTED: uncharacterized protein LOC10 0.773 0.773 0.643 1e-142
226501514490 pseudouridylate synthase/ transporter [Z 0.773 0.765 0.566 1e-127
>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 =  625 bits (1611), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 316/468 (67%), Positives = 361/468 (77%), Gaps = 31/468 (6%)

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 WQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDR 465
           WQVPPMFSAIKVGGEKMY+KARRGESIELSPRRISIFQF+IERSLEDR
Sbjct: 403 WQVPPMFSAIKVGGEKMYEKARRGESIELSPRRISIFQFNIERSLEDR 450

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449532619|ref|XP_004173278.1| PREDICTED: uncharacterized LOC101215528, partial [Cucumis sativus] Back     alignment and taxonomy information
>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|7573471|emb|CAB87785.1| tRNA synthase-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|225452300|ref|XP_002272379.1| PREDICTED: uncharacterized protein LOC100259460 [Vitis vinifera] 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|296087588|emb|CBI34844.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356511706|ref|XP_003524564.1| PREDICTED: uncharacterized protein LOC100793939 [Glycine max] Back     alignment and taxonomy information
>gi|226501514|ref|NP_001150630.1| pseudouridylate synthase/ transporter [Zea mays] gi|195640714|gb|ACG39825.1| 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 ?
Query485
TAIR|locus:2145708540 AT5G14460 [Arabidopsis thalian 0.878 0.788 0.612 8.3e-138
UNIPROTKB|P62190 298 truB "tRNA pseudouridine synth 0.311 0.506 0.444 2.2e-27
TIGR_CMR|SPO_3837 303 SPO_3837 "tRNA pseudouridine s 0.282 0.452 0.442 3.6e-24
TIGR_CMR|DET_0981 300 DET_0981 "tRNA pseudouridine s 0.290 0.47 0.382 6.4e-24
TIGR_CMR|GSU_1591 304 GSU_1591 "tRNA pseudouridine s 0.305 0.486 0.364 7.5e-23
UNIPROTKB|Q97QJ3 292 truB "tRNA pseudouridine synth 0.303 0.503 0.385 2.2e-22
UNIPROTKB|Q9KU78 312 truB "tRNA pseudouridine synth 0.307 0.477 0.36 3.7e-22
TIGR_CMR|VC_0645 312 VC_0645 "tRNA pseudouridine 55 0.307 0.477 0.36 3.7e-22
ASPGD|ASPL0000051985 392 AN0072 [Emericella nidulans (t 0.237 0.293 0.444 1.7e-21
TIGR_CMR|CBU_1430 309 CBU_1430 "tRNA pseudouridine s 0.334 0.524 0.339 1.8e-21
TAIR|locus:2145708 AT5G14460 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1349 (479.9 bits), Expect = 8.3e-138, P = 8.3e-138
 Identities = 278/454 (61%), Positives = 322/454 (70%)

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 EKMYDKARRGESIELSPRRISIFQFDIERSLEDR 465
             EKMY+KARRGE++ELSPRRISIFQFDIERSL+DR
Sbjct:   444 EKMYEKARRGETVELSPRRISIFQFDIERSLDDR 477
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|SPO_3837 SPO_3837 "tRNA pseudouridine synthase B" [Ruegeria pomeroyi DSS-3 (taxid:246200)] 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
TIGR_CMR|GSU_1591 GSU_1591 "tRNA pseudouridine synthase B" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|Q97QJ3 truB "tRNA pseudouridine synthase B" [Streptococcus pneumoniae TIGR4 (taxid:170187)] 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
ASPGD|ASPL0000051985 AN0072 [Emericella nidulans (taxid:162425)] 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

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

Your Input:
fgenesh2_kg.6__1422__AT5G14460.1
annotation not avaliable (538 aa)
(Arabidopsis lyrata)
Predicted Functional Partners:
Al_scaffold_0009_187
annotation not avaliable (88 aa)
•  •  • 0.932
fgenesh2_kg.1__1879__AT1G17220.1
annotation not avaliable (1027 aa)
•  •  • 0.914
fgenesh2_kg.6__3088__AT4G11160.1
annotation not avaliable (746 aa)
•  •  • 0.894
scaffold_300355.1
annotation not avaliable (922 aa)
•  •  • 0.870
fgenesh1_pm.C_scaffold_1040000001
annotation not avaliable (104 aa)
•  •  • 0.868
fgenesh2_kg.3__716__AT3G06950.1
annotation not avaliable (323 aa)
  •• •• 0.820
fgenesh2_kg.6__1433__AT5G14580.1
annotation not avaliable (992 aa)
•  •  • 0.782
fgenesh2_kg.6__3223__AT4G04350.1
At4g04350-like protein (972 aa)
•  •  • 0.740
fgenesh2_kg.4__1993__AT2G39140.1
annotation not avaliable (412 aa)
• ••  • 0.682
Al_scaffold_0004_707
annotation not avaliable (411 aa)
•  •  • 0.610

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 ?
Query485
cd02573213 cd02573, PseudoU_synth_EcTruB, Pseudouridine synth 4e-71
pfam01509149 pfam01509, TruB_N, TruB family pseudouridylate syn 9e-65
PRK03287 298 PRK03287, truB, tRNA pseudouridine synthase B; Pro 3e-58
PRK02755 295 PRK02755, truB, tRNA pseudouridine synthase B; Pro 1e-49
PRK00130 290 PRK00130, truB, tRNA pseudouridine synthase B; Pro 6e-48
TIGR00431209 TIGR00431, TruB, tRNA pseudouridine(55) synthase 2e-47
PRK01550 304 PRK01550, truB, tRNA pseudouridine synthase B; Pro 6e-46
cd00506210 cd00506, PseudoU_synth_TruB_like, Pseudouridine sy 1e-45
PRK05389 305 PRK05389, truB, tRNA pseudouridine synthase B; Pro 7e-45
PRK02484 294 PRK02484, truB, tRNA pseudouridine synthase B; Pro 3e-42
PRK05033 312 PRK05033, truB, tRNA pseudouridine synthase B; Pro 3e-40
PRK01851 303 PRK01851, truB, tRNA pseudouridine synthase B; Pro 4e-40
PRK00989230 PRK00989, truB, tRNA pseudouridine synthase B; Pro 2e-39
COG0130 271 COG0130, TruB, Pseudouridine synthase [Translation 1e-38
PRK14124 308 PRK14124, PRK14124, tRNA pseudouridine synthase B; 3e-37
PRK14122 312 PRK14122, PRK14122, tRNA pseudouridine synthase B; 1e-35
PRK04642 300 PRK04642, truB, tRNA pseudouridine synthase B; Pro 2e-33
PRK14123 305 PRK14123, PRK14123, tRNA pseudouridine synthase B; 4e-33
cd02867 312 cd02867, PseudoU_synth_TruB_4, Pseudouridine synth 6e-33
PRK00020244 PRK00020, truB, tRNA pseudouridine synthase B; Pro 1e-30
PRK02193 279 PRK02193, truB, tRNA pseudouridine synthase B; Pro 3e-25
PRK04099273 PRK04099, truB, tRNA pseudouridine synthase B; Pro 3e-24
cd02572182 cd02572, PseudoU_synth_hDyskerin, Pseudouridine sy 3e-24
PRK01528 292 PRK01528, truB, tRNA pseudouridine synthase B; Pro 3e-21
TIGR00425 322 TIGR00425, CBF5, rRNA pseudouridine synthase, puta 3e-20
PRK14846 345 PRK14846, truB, tRNA pseudouridine synthase B; Pro 2e-19
PRK04270 300 PRK04270, PRK04270, H/ACA RNA-protein complex comp 6e-19
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 =  224 bits (574), Expect = 4e-71
 Identities = 69/147 (46%), Positives = 99/147 (67%)

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 EKMYDKARRGESIELSPRRISIFQFDI 458
           +++Y+ AR GE +E  PR+++I+  ++
Sbjct: 123 KRLYELARAGEEVERPPRKVTIYSLEL 149

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|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal domain) Back     alignment and domain information
>gnl|CDD|235113 PRK03287, 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|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|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional 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|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235333 PRK05033, 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|179199 PRK00989, 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|172614 PRK14124, PRK14124, 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|179870 PRK04642, truB, 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|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4 Back     alignment and domain information
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179739 PRK04099, truB, 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|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative Back     alignment and domain information
>gnl|CDD|237834 PRK14846, 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|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 485
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 100.0
PRK00130 290 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 100.0
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 100.0
PRK02755 295 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14124 308 tRNA pseudouridine synthase B; Provisional 100.0
PRK05033 312 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02484 294 truB tRNA pseudouridine synthase B; Provisional 100.0
cd02573 277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 100.0
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01550 304 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04642 300 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14123 305 tRNA pseudouridine synthase B; Provisional 100.0
PRK01851 303 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04099 273 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK05389 305 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK03287 298 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01528 292 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02193 279 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14122 312 tRNA pseudouridine synthase B; Provisional 100.0
cd02867 312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 100.0
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 100.0
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 100.0
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 100.0
COG0130 271 TruB Pseudouridine synthase [Translation, ribosoma 100.0
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 100.0
PRK04270 300 H/ACA RNA-protein complex component Cbf5p; Reviewe 100.0
TIGR00425 322 CBF5 rRNA pseudouridine synthase, putative. This f 100.0
KOG2529395 consensus Pseudouridine synthase [Translation, rib 99.96
KOG2559 318 consensus Predicted pseudouridine synthase [Transl 99.95
KOG2529 395 consensus Pseudouridine synthase [Translation, rib 99.63
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 98.35
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 97.43
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 97.35
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 97.32
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 97.26
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 97.26
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 97.13
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 97.08
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 96.88
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 96.87
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 96.82
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 96.7
PRK11112257 tRNA pseudouridine synthase C; Provisional 96.68
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 96.63
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 96.6
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 96.53
PF0806859 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 96.46
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 96.43
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 96.4
TIGR01213388 conserved hypothetical protein TIGR01213. Members 96.31
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 96.24
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 96.18
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 95.91
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 95.76
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 95.65
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 95.27
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 95.16
PRK14554422 putative pseudouridylate synthase; Provisional 94.2
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 87.93
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information 
Probab=100.00  E-value=9.4e-57  Score=424.50  Aligned_cols=166  Identities=42%  Similarity=0.701  Sum_probs=161.1

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455          307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW  386 (485)
Q Consensus       307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~  386 (485)
                      +|| |++||||.|||||+||++||++++.+||||+|||||+|+|||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus         1 ~~G-~l~v~KP~g~tS~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~~G~~TdT~   79 (209)
T TIGR00431         1 ING-VLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLGVRTDTL   79 (209)
T ss_pred             CCe-EEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHhhhhHHHcCCCCeEEEEEEECCcCCCC
Confidence            356 9999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455          387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF  466 (485)
Q Consensus       387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~  466 (485)
                      |++|+|+++.++. ++.++|++++++|+|+++|+||+|||+||||+|||||||+|+.||+++|+|+||+|++++      
T Consensus        80 D~~G~i~~~~~~~-~~~~~l~~~l~~f~G~~~Q~PP~ySA~Kv~G~raYelAR~g~~v~~~~r~v~I~~i~ll~------  152 (209)
T TIGR00431        80 DPDGQIVETRPVN-PTTEDVEAALPTFRGEIEQIPPMYSALKVNGKRLYEYARQGIEVERKARPVTVYDLQFLK------  152 (209)
T ss_pred             CCCCCEEEecCCC-CCHHHHHHHHHHccCcEEEECChhhEEeeCCHhHHHHHHCCCccccCcceeEEEEEEEEE------
Confidence            9999999999987 478999999999999999999999999999999999999999999999999999999998      


Q ss_pred             ccccCCCCeeEEEEeeec
Q 011455          467 FFFLFPLPLKLLDVIHLS  484 (485)
Q Consensus       467 ~~~~F~~P~ftLEV~~~~  484 (485)
                          |+.|.|+++|+|-+
T Consensus       153 ----~~~~~~~~~v~cs~  166 (209)
T TIGR00431       153 ----YEGPELTLEVHCSK  166 (209)
T ss_pred             ----EcCCcEEEEEEECC
Confidence                89999999999964

TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB 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
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14122 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
>PRK14846 truB tRNA pseudouridine synthase B; Provisional 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
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis] 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
>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
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like 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
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [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
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family 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
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional 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
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate 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
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>TIGR01213 conserved hypothetical protein TIGR01213 Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional 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
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>PRK14554 putative pseudouridylate synthase; Provisional 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query485
1sgv_A 316 Structure Of Trna Psi55 Pseudouridine Synthase (Tru 9e-30
1r3e_A 309 Crystal Structure Of Trna Pseudouridine Synthase Tr 2e-22
1ze2_A 309 Conformational Change Of Pseudouridine 55 Synthase 2e-22
1ze1_A 309 Conformational Change Of Pseudouridine 55 Synthase 3e-22
2ab4_A 309 Dissecting The Roles Of A Strictly Conserved Tyrosi 6e-22
1r3f_A 314 Crystal Structure Of Trna Pseudouridine Synthase Tr 3e-21
1k8w_A 327 Crystal Structure Of The E. Coli Pseudouridine Synt 4e-21
1zl3_A 327 Coupling Of Active Site Motions And Rna Binding Len 1e-20
3u28_A 400 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From 1e-10
2apo_A 357 Crystal Structure Of The Methanococcus Jannaschii C 8e-08
3lwo_A 340 Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONT 1e-06
2hvy_A 346 Crystal Structure Of An HACA BOX RNP FROM PYROCOCCU 1e-06
2aus_C 334 Crystal Structure Of The Archaeal Box HACA SRNP NOP 1e-06
2ey4_A 333 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Leng 1e-06
3mqk_A 328 Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Cont 1e-06
3hjw_A 327 Structure Of A Functional Ribonucleoprotein Pseudou 1e-06
2rfk_A 334 Substrate Rna Positioning In The Archaeal HACA Ribo 8e-06
>pdb|1SGV|A Chain A, Structure Of Trna Psi55 Pseudouridine Synthase (Trub) Length = 316 Back     alignment and structure 
Iteration: 1

 Score =  128 bits (321), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 65/148 (43%), Positives = 89/148 (60%)
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 GEKMYDKARRGESIELSPRRISIFQFDI 458
           G + Y  AR+G S++L  R I I +F++
Sbjct: 128 GRRAYRLARQGRSVQLEARPIRIDRFEL 155
>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|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|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|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding Length = 327 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|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5 Nop10 Complex Length = 357 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|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5 Complex Length = 334 Back     alignment and structure
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Length = 333 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|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 ?
Query485
1sgv_A 316 TRNA pseudouridine synthase B; hinged motion, tRNA 2e-73
1r3e_A 309 TRNA pseudouridine synthase B; RNA modification, p 2e-69
1k8w_A 327 TRNA pseudouridine synthase B; protein-RNA complex 1e-67
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 3e-44
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 3e-43
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 7e-36
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
>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 =  233 bits (596), Expect = 2e-73
 Identities = 70/159 (44%), Positives = 99/159 (62%), Gaps = 4/159 (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 458
           VP   SAIKVGG + Y  AR+G S++L  R I I +F++
Sbjct: 117 VPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFEL 155
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query485
1k8w_A 327 TRNA pseudouridine synthase B; protein-RNA complex 100.0
1r3e_A 309 TRNA pseudouridine synthase B; RNA modification, p 100.0
1sgv_A 316 TRNA pseudouridine synthase B; hinged motion, tRNA 100.0
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 100.0
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 100.0
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 100.0
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 97.43
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 97.21
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 96.94
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 96.85
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 96.57
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 96.45
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 96.43
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 96.4
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 95.45
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 94.54
>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
Probab=100.00  E-value=1.8e-56  Score=444.08  Aligned_cols=176  Identities=32%  Similarity=0.543  Sum_probs=165.4

Q ss_pred             CCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEE
Q 011455          297 STELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGV  376 (485)
Q Consensus       297 ~~~~p~~W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at  376 (485)
                      +.+.+..|..++| ||+||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++
T Consensus        14 ~~~~~~~~~~~~G-il~vdKP~G~TS~dvv~~vr~~l~~kKvGH~GTLDP~AtGvL~i~~G~aTKl~~~l~~~~K~Y~a~   92 (327)
T 1k8w_A           14 SGHIEGRHMDING-VLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVI   92 (327)
T ss_dssp             --------CCCCE-EEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGTHHHHTSCEEEEEE
T ss_pred             ccccccccCCCCe-EEEEECCCCCCHHHHHHHHHHhhccceeccCCCCCCCCeeEEEEEECHHHhHHHHhccCCcEEEEE
Confidence            3456788999999 999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEE
Q 011455          377 FRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQF  456 (485)
Q Consensus       377 ~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsI  456 (485)
                      ++||.+|||+|++|+|++++++ ++|.++|+++|++|+|.|+|+||||||||+||||||||||+|+.||+++|+|+||+|
T Consensus        93 ~~lG~~TdT~D~eG~v~~~~~~-~~t~e~i~~~l~~f~G~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i  171 (327)
T 1k8w_A           93 ARLGQRTDTSDADGQIVEERPV-TFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYEL  171 (327)
T ss_dssp             EEETEEESSSBTTSCEEEECCC-CCCHHHHHHHHHTTSEEEEECCCSSSCCEETTEEHHHHHHTTCCCCCCCEEEEEEEE
T ss_pred             EEECCcccCCCCCCCEEeecCC-CCCHHHHHHHHHhccceEEEeCChhheeccCCccHHHHHhCCCcccccceEEEEEEE
Confidence            9999999999999999999999 899999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeecccccccccCCCCeeEEEEeeec
Q 011455          457 DIERSLEDRFFFFLFPLPLKLLDVIHLS  484 (485)
Q Consensus       457 kLi~~l~dr~~~~~F~~P~ftLEV~~~~  484 (485)
                      +|++          |++|.|+|+|.|.+
T Consensus       172 ~ll~----------~~~~~~~~~v~Csk  189 (327)
T 1k8w_A          172 LFIR----------HEGNELELEIHCSK  189 (327)
T ss_dssp             EEEE----------EETTEEEEEEEECT
T ss_pred             EEEE----------eeCCEEEEEEEEcC
Confidence            9998          78999999999964
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} 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
>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
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} 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

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 485
d1sgva2233 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB 3e-40
d1k8wa5242 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB 6e-38
d1r3ea2228 d.265.1.2 (A:10-237) Pseudouridine synthase II Tru 5e-35
d2ey4a2245 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB 4e-30
d2apoa2230 d.265.1.2 (A:17-246) Pseudouridine synthase II Tru 8e-25
>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 =  142 bits (359), Expect = 3e-40
 Identities = 68/147 (46%), Positives = 95/147 (64%)

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 EKMYDKARRGESIELSPRRISIFQFDI 458
            + Y  AR+G S++L  R I I +F++
Sbjct: 127 RRAYRLARQGRSVQLEARPIRIDRFEL 153
>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 ?
Query485
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 100.0
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 100.0
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 100.0
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 100.0
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 100.0
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 96.92
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 96.83
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 94.86
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 94.62
>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=7e-56  Score=418.56  Aligned_cols=170  Identities=42%  Similarity=0.614  Sum_probs=134.3

Q ss_pred             CceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCC
Q 011455          308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD  387 (485)
Q Consensus       308 nGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~D  387 (485)
                      +| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|++||+++++++.+|+|++++.||.+|||+|
T Consensus         4 ~G-~l~v~KP~G~TS~~~v~~vk~~~~~kKvGh~GTLDP~AtGvL~i~ig~aTK~~~~~~~~~K~Y~~~~~lG~~TdT~D   82 (233)
T d1sgva2           4 PG-IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTED   82 (233)
T ss_dssp             SE-EEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGGGGTTTSCEEEEEEEEETEEETTSB
T ss_pred             CE-EEEEEcCCCCCHHHHHHHHHHHhCcCccccCcCCCCcceeeEEEEechhhhhhhhhccCceEEEEEEEEcccccccc
Confidence            46 99999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccc
Q 011455          388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFF  467 (485)
Q Consensus       388 ieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~  467 (485)
                      ++|+|+++.++.|++.++|++++++|+|.++|+||+|||+|+||||||+|||+|+.+++++|+|+||+|+|+...     
T Consensus        83 ~~G~vi~~~~~~~~t~~~i~~~l~~f~G~~~Q~PP~ySAvKv~GkraYelAR~G~~~~~~~r~v~I~~~~l~~~~-----  157 (233)
T d1sgva2          83 AEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAAR-----  157 (233)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEEEEE-----
T ss_pred             cccceeeeeccccchHHHHHHHHHhcCCcEEeeccHHHHhhccChHHHHHHHhCCcccccccceeeeeEEEEeec-----
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999721     


Q ss_pred             cccCCCCeeEEEEeeec
Q 011455          468 FFLFPLPLKLLDVIHLS  484 (485)
Q Consensus       468 ~~~F~~P~ftLEV~~~~  484 (485)
                       .....|.|+++|+|-+
T Consensus       158 -~~~~~~~~~~~v~Cs~  173 (233)
T d1sgva2         158 -RRDQLIDIDVEIDCSS  173 (233)
T ss_dssp             -EETTEEEEEEEEEESC
T ss_pred             -cCCCceEEEEEEEECc
Confidence             1235689999999964
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} 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
>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
>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