Citrus Sinensis ID: 042463

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
KFKQTQSYRSEDKSQKFSPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV
ccccccccccccccccccccccccEEEEEHHHHHHHHHccccHHHHccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccHHHHHHHHHcccEEEcccccccccccccccccccccccccEEccccEEEcccccccccccccccccccccccccHHHHHHHHccEEEEcccEEEEEccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHcccHHHHHHHHHHHHccccccccHHHHHHHccccccEEEEEEEccccccccEEEccccccccccccEEEEEEcccccccccccEEEEEEEEEEccccEEEEEEEEcccHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEcccccHHHccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHccccc
ccccccccccccccccccccccccHEHHHHHHHHHHHccccccHHHHHEEccccccccccEEEEccccccccccccccccccccccccccccccccHHccHHccccHHHHHHHHHcccccHHHHHHHHHcccEEEcccEccccccHccccccccEEccccEEccccEEEEcccccccccccccccccccccccccccHHHHHHHEEEccccEEEEEcccccEEcccccccccHHHHHHHHHHccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHccccccHHHHHccccHHHHHHHHHHHcccccccccEEEccccccccccccEEEEEEEcccccccccccEEEHHHHHHccccEEEEEEEcccccccHHEHHHHHHccccccccccccccHHHcccccccccccccccccccccccccHHHHHHHHHHHcHHHHHHHHHcccccHHHHHHHccccccEEEEEccccHHHHHHHHHHHHccc
kfkqtqsyrsedksqkfspflglnfYRIEYEFNMMWKKQAEFIWLSSIrhysrispprpavirvsekkvahlgppkagpkprqllslppfpghnlpgkhwgrqchVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANmgdsfveqgqmkpirkiktnevmepgariflpvsmvegriskrydtipsgtlnpnadeIDYLRRLVKYRDSailvlnkppkvplkghlpvhnSMDALAAAALSydynegpklvhrldressglllmgrTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIgspkekqgiihaplskvllddgktERIILAQNSGLEASQEAMTEYRVlgpmingcswielrpltcrkhqLRVHCaealgtpivgdykygwfvhrrwkqmprvdieptsgkpyklrrpdgldvqkgsvlskvpllhlhcrelksdnlfptlsskpdgpdlLRFVASMPSHMKISWNLMSSYLV
kfkqtqsyrsedksqkfspflgLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAhlgppkagpkprqLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFveqgqmkpirkiktnevmepgariFLPVSMVEGRISKrydtipsgtlnpnadEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAqnsgleasQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEalgtpivgdykYGWFVHRrwkqmprvdieptsgkpyklrrpdgLDVQKGSVLSKVPLLHLHCRELKSdnlfptlsskpdGPDLLRFVASMpshmkiswnlmssylv
KFKQTQSYRSEDKSQKFSPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDalaaaalSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV
*****************SPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRIS*************************************HNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDI*****************VQKGSVLSKVPLLHLHCRELKSDNLF***********LLRFVA******KISWN*******
******************PFLGLNFYRIEYEFNMMWKKQAEFIWLS**********************************************************HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFV**G*M**IRKIKTNEVMEPGARIFLPVSMV*******************ADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTE***********ASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTL***PDGPDLLRFVASMPSHMKISWNLMSSYLV
**************QKFSPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV
*************SQKFSPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAHLGPPK*****RQLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFV*QGQMKPIRKIKTNEVMEPGARIFLPVSMVE************GTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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KFKQTQSYRSEDKSQKFSPFLGLNFYRIEYEFNMMWKKQAEFIWLSSIRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFPGHNLPGKHWGRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV
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 ?
Query490 2.2.26 [Sep-21-2011]
Q5XET6478 RNA pseudourine synthase yes no 0.928 0.951 0.695 0.0
Q0J4D4475 RNA pseudourine synthase yes no 0.879 0.907 0.666 1e-167
Q9LT72477 RNA pseudourine synthase no no 0.797 0.819 0.363 1e-64
Q69K07448 RNA pseudourine synthase no no 0.516 0.564 0.370 2e-44
Q28C59324 RNA pseudouridylate synth yes no 0.475 0.719 0.314 2e-22
O66114219 Uncharacterized RNA pseud no no 0.346 0.776 0.333 2e-18
Q68XB2303 Ribosomal large subunit p yes no 0.332 0.537 0.338 4e-17
Q9ZDR7303 Ribosomal large subunit p yes no 0.336 0.544 0.321 8e-17
Q1RJX7301 Ribosomal large subunit p yes no 0.334 0.544 0.340 1e-16
Q4UKQ3305 Ribosomal large subunit p yes no 0.332 0.534 0.343 1e-16
>sp|Q5XET6|PUS3_ARATH RNA pseudourine synthase 3, mitochondrial OS=Arabidopsis thaliana GN=At1g78910 PE=2 SV=1 Back     alignment and function desciption
 Score =  661 bits (1706), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 333/479 (69%), Positives = 388/479 (81%), Gaps = 24/479 (5%)

Query: 35  MWKKQAEF--IWLSS-IRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFP 91
           MWK +  F  I+L+  IR YSR++PP  +VIRV+   VAHLGPPK GP PRQL+SLPPFP
Sbjct: 1   MWKAKTCFRQIYLTVLIRRYSRVAPPPSSVIRVTNN-VAHLGPPKQGPLPRQLISLPPFP 59

Query: 92  GHNLPGKHWGRQC-------HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSF 144
           GH LPGK+ G          HVTA+SWVKYYF+E+ D  IQ+HF KGLVQME     D+ 
Sbjct: 60  GHPLPGKNAGADGDDGDSGGHVTAISWVKYYFEEIYDKAIQTHFTKGLVQMEFRGRRDAS 119

Query: 145 VE-QGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRR 203
            E +    P+RKIK NEVM+ G +I+LPVS+ E RISKRYDTIPSGTL PNADEI YL+R
Sbjct: 120 REKEDGAIPMRKIKHNEVMQIGDKIWLPVSIAEMRISKRYDTIPSGTLYPNADEIAYLQR 179

Query: 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLL 263
           LV+++DSAI+VLNKPPK+P+KG++P+HNSMDALAAAALS+  +EGP+LVHRLDRE+SGLL
Sbjct: 180 LVRFKDSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGLL 239

Query: 264 LMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLS 323
           +MGRTKES+  L  +FSD     S  KAWN ACEAMYQ+YWALVIGSPKEK+G+I APLS
Sbjct: 240 VMGRTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLS 299

Query: 324 KVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCA 383
           KVLLDDGKT+R++LAQ SG EASQ+A+TEY+VLGP INGCSW+ELRP+T RKHQLRVHCA
Sbjct: 300 KVLLDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHCA 359

Query: 384 EALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLH 443
           EALGTPIVGDYKYGWFVH+RWKQMP+VDIEPT+GKPYKLRRP+GLDVQKGSVLSKVPLLH
Sbjct: 360 EALGTPIVGDYKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKVPLLH 419

Query: 444 LHCRELKSDNLF------------PTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV 490
           LHCRE+   N+             P  +   D PDLLRFVASMPSHMKISWNLMSSYLV
Sbjct: 420 LHCREMVLPNIAKFLHVMNQQETEPLHTGIIDKPDLLRFVASMPSHMKISWNLMSSYLV 478

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q0J4D4|PUS3_ORYSJ RNA pseudourine synthase 3, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0520100 PE=2 SV=1 Back     alignment and function description
>sp|Q9LT72|PUS4_ARATH RNA pseudourine synthase 4, mitochondrial OS=Arabidopsis thaliana GN=At3g19440 PE=2 SV=1 Back     alignment and function description
>sp|Q69K07|PUS4_ORYSJ RNA pseudourine synthase 4, mitochondrial OS=Oryza sativa subsp. japonica GN=Os09g0103500 PE=2 SV=1 Back     alignment and function description
>sp|Q28C59|RUSD4_XENTR RNA pseudouridylate synthase domain-containing protein 4 OS=Xenopus tropicalis GN=rpusd4 PE=2 SV=1 Back     alignment and function description
>sp|O66114|Y505_ZYMMO Uncharacterized RNA pseudouridine synthase ZMO0505 OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=ZMO0505 PE=3 SV=2 Back     alignment and function description
>sp|Q68XB2|RLUC_RICTY Ribosomal large subunit pseudouridine synthase C OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|Q9ZDR7|RLUC_RICPR Ribosomal large subunit pseudouridine synthase C OS=Rickettsia prowazekii (strain Madrid E) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|Q1RJX7|RLUC_RICBR Ribosomal large subunit pseudouridine synthase C OS=Rickettsia bellii (strain RML369-C) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|Q4UKQ3|RLUC_RICFE Ribosomal large subunit pseudouridine synthase C OS=Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) GN=rluC 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 ?
Query490
225443375479 PREDICTED: RNA pseudourine synthase 3, m 0.895 0.916 0.769 0.0
297735761481 unnamed protein product [Vitis vinifera] 0.895 0.912 0.763 0.0
449441766471 PREDICTED: RNA pseudourine synthase 3, m 0.906 0.942 0.709 0.0
449490137471 PREDICTED: RNA pseudourine synthase 3, m 0.906 0.942 0.711 0.0
356562211554 PREDICTED: RNA pseudourine synthase 3, m 0.906 0.801 0.721 0.0
42563328478 RNA pseudourine synthase 3 [Arabidopsis 0.928 0.951 0.695 0.0
297839759477 hypothetical protein ARALYDRAFT_477057 [ 0.928 0.953 0.690 0.0
255571790468 ribosomal pseudouridine synthase, putati 0.918 0.961 0.742 0.0
3834304491 Contains similarity to gi|1786244 hypoth 0.928 0.926 0.676 0.0
125604035509 hypothetical protein OsJ_27960 [Oryza sa 0.879 0.846 0.666 1e-165
>gi|225443375|ref|XP_002267010.1| PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  706 bits (1821), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/468 (76%), Positives = 400/468 (85%), Gaps = 29/468 (6%)

Query: 48  IRHYSRISPPRPA----VIRVSEKKVAHLGPPKAGPKPRQLLSLPPFPGHNLPGKHW--- 100
           +RHYSRI+PPRPA    VIRVS   VA LG PK GPKPRQLLSLPPFP H LPGK     
Sbjct: 16  VRHYSRIAPPRPASAAPVIRVSNN-VAQLGSPKEGPKPRQLLSLPPFPAHPLPGKSLVNV 74

Query: 101 -GRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVE-QGQMKPIRKIKT 158
            G   HVTA+SW+KYYFDE+  SV+QSHFNKGLV ME +N+ DS +E +GQ+KP+RKIK 
Sbjct: 75  SGLPTHVTAISWIKYYFDEIPGSVVQSHFNKGLVHMERSNLDDSSLEKEGQIKPLRKIKP 134

Query: 159 NEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKP 218
           NEVME G RI++PVS+ E RISKR+DTIPSGTL+PNADEI+YL+RLV Y+D AILVLNKP
Sbjct: 135 NEVMEAGTRIYVPVSVAEARISKRFDTIPSGTLHPNADEIEYLQRLVTYKDPAILVLNKP 194

Query: 219 PKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWL 278
           PKVPLKG+LPVHNSMDALAAAAL++DY EGPKLVHRLDRESSGLLLMGRTKESV+ L WL
Sbjct: 195 PKVPLKGNLPVHNSMDALAAAALTFDYEEGPKLVHRLDRESSGLLLMGRTKESVAHLHWL 254

Query: 279 FSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILA 338
           FSD+NK+KSLSKAW+DACEA  QRYWALVIGSPK+K+G+IHAPLSKVLLDDGKTER+ILA
Sbjct: 255 FSDINKAKSLSKAWDDACEATCQRYWALVIGSPKQKEGVIHAPLSKVLLDDGKTERVILA 314

Query: 339 QNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGW 398
             SGLEASQEA+TEYRVLGPMINGCSWIEL P T RKHQLRVHCAEALGTPIVGDYKYGW
Sbjct: 315 NQSGLEASQEAITEYRVLGPMINGCSWIELCPRTSRKHQLRVHCAEALGTPIVGDYKYGW 374

Query: 399 FVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCREL--------- 449
           FVHRRWKQMPRVD+EPT+GKPYK+RRP+GLDVQKGSVLSKVPLLHLHCREL         
Sbjct: 375 FVHRRWKQMPRVDLEPTTGKPYKMRRPEGLDVQKGSVLSKVPLLHLHCRELILPNIAKFL 434

Query: 450 -------KSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSYLV 490
                  K+ N +P LS K   PD+LRFVASMP+HMKISWNLMSSYLV
Sbjct: 435 PILDPKPKNQNQYPKLSLK---PDILRFVASMPNHMKISWNLMSSYLV 479

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297735761|emb|CBI18448.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449441766|ref|XP_004138653.1| PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449490137|ref|XP_004158518.1| PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356562211|ref|XP_003549365.1| PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|42563328|ref|NP_178012.2| RNA pseudourine synthase 3 [Arabidopsis thaliana] gi|75110951|sp|Q5XET6.1|PUS3_ARATH RecName: Full=RNA pseudourine synthase 3, mitochondrial; AltName: Full=RNA pseudouridylate synthase 3; AltName: Full=RNA-uridine isomerase 3; Flags: Precursor gi|53850479|gb|AAU95416.1| At1g78910 [Arabidopsis thaliana] gi|56790228|gb|AAW30031.1| At1g78910 [Arabidopsis thaliana] gi|332198052|gb|AEE36173.1| RNA pseudourine synthase 3 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297839759|ref|XP_002887761.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp. lyrata] gi|297333602|gb|EFH64020.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|255571790|ref|XP_002526838.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223533842|gb|EEF35573.1| ribosomal pseudouridine synthase, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|3834304|gb|AAC83020.1| Contains similarity to gi|1786244 hypothetical 24.9 kD protein in surA-hepA intergenic region yab0 from Escherichia coli genome gb|AE000116, and to hypothetical YABO family PF|00849 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|125604035|gb|EAZ43360.1| hypothetical protein OsJ_27960 [Oryza sativa Japonica Group] 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 ?
Query490
TAIR|locus:2037593478 AT1G78910 [Arabidopsis thalian 0.926 0.949 0.683 3.8e-172
TAIR|locus:2090689477 AT3G19440 [Arabidopsis thalian 0.759 0.779 0.376 3.8e-62
DICTYBASE|DDB_G0285543718 DDB_G0285543 [Dictyostelium di 0.228 0.155 0.4 4.4e-30
TIGR_CMR|SPO_0516347 SPO_0516 "ribosomal large subu 0.491 0.694 0.307 5.5e-28
UNIPROTKB|E1BYI6354 RPUSD4 "Uncharacterized protei 0.391 0.542 0.319 2.1e-19
MGI|MGI:1919239377 Rpusd4 "RNA pseudouridylate sy 0.534 0.694 0.25 6.9e-13
ZFIN|ZDB-GENE-040801-238358 zgc:92006 "zgc:92006" [Danio r 0.518 0.709 0.310 9.7e-13
UNIPROTKB|Q5E9Z1377 RPUSD4 "RNA pseudouridylate sy 0.434 0.564 0.308 1.5e-12
RGD|1311268377 Rpusd4 "RNA pseudouridylate sy 0.534 0.694 0.253 1.5e-12
UNIPROTKB|Q96CM3377 RPUSD4 "RNA pseudouridylate sy 0.455 0.591 0.289 5.6e-12
TAIR|locus:2037593 AT1G78910 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1673 (594.0 bits), Expect = 3.8e-172, P = 3.8e-172
 Identities = 328/480 (68%), Positives = 385/480 (80%)

Query:    35 MWKKQAEF--IWLSS-IRHYSRISPPRPAVIRVSEKKVAHLGPPKAGPKPRQLLSLPPFP 91
             MWK +  F  I+L+  IR YSR++PP  +VIRV+   VAHLGPPK GP PRQL+SLPPFP
Sbjct:     1 MWKAKTCFRQIYLTVLIRRYSRVAPPPSSVIRVTNN-VAHLGPPKQGPLPRQLISLPPFP 59

Query:    92 GHNLPGKHWGRQC-------HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSF 144
             GH LPGK+ G          HVTA+SWVKYYF+E+ D  IQ+HF KGLVQME     D+ 
Sbjct:    60 GHPLPGKNAGADGDDGDSGGHVTAISWVKYYFEEIYDKAIQTHFTKGLVQMEFRGRRDAS 119

Query:   145 VEQ--GQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLR 202
              E+  G + P+RKIK NEVM+ G +I+LPVS+ E RISKRYDTIPSGTL PNADEI YL+
Sbjct:   120 REKEDGAI-PMRKIKHNEVMQIGDKIWLPVSIAEMRISKRYDTIPSGTLYPNADEIAYLQ 178

Query:   203 RLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDYNEGPKLVHRLDRESSGL 262
             RLV+++DSAI+VLNKPPK+P+KG++P+HNSMD       S+  +EGP+LVHRLDRE+SGL
Sbjct:   179 RLVRFKDSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGL 238

Query:   263 LLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPL 322
             L+MGRTKES+  L  +FSD     S  KAWN ACEAMYQ+YWALVIGSPKEK+G+I APL
Sbjct:   239 LVMGRTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPL 298

Query:   323 SKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHC 382
             SKVLLDDGKT+R++LAQ SG EASQ+A+TEY+VLGP INGCSW+ELRP+T RKHQLRVHC
Sbjct:   299 SKVLLDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHC 358

Query:   383 AEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLL 442
             AEALGTPIVGDYKYGWFVH+RWKQMP+VDIEPT+GKPYKLRRP+GLDVQKGSVLSKVPLL
Sbjct:   359 AEALGTPIVGDYKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKVPLL 418

Query:   443 HLHCRELKSDNLFPTL------SSKP------DGPDLLRFVASMPSHMKISWNLMSSYLV 490
             HLHCRE+   N+   L       ++P      D PDLLRFVASMPSHMKISWNLMSSYLV
Sbjct:   419 HLHCREMVLPNIAKFLHVMNQQETEPLHTGIIDKPDLLRFVASMPSHMKISWNLMSSYLV 478
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0005739 "mitochondrion" evidence=ISM
GO:0009451 "RNA modification" evidence=IEA
GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS
TAIR|locus:2090689 AT3G19440 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0285543 DDB_G0285543 [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_0516 SPO_0516 "ribosomal large subunit pseudouridine synthase C" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
UNIPROTKB|E1BYI6 RPUSD4 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:1919239 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040801-238 zgc:92006 "zgc:92006" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q5E9Z1 RPUSD4 "RNA pseudouridylate synthase domain-containing protein 4" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
RGD|1311268 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q96CM3 RPUSD4 "RNA pseudouridylate synthase domain-containing protein 4" [Homo sapiens (taxid:9606)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q0J4D4PUS3_ORYSJ5, ., 4, ., 9, 9, ., -0.66660.87950.9073yesno
Q5XET6PUS3_ARATH5, ., 4, ., 9, 9, ., -0.69510.92850.9518yesno

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:
GSVIVG00029606001
SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (481 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query490
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 2e-44
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 3e-40
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 1e-26
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 6e-24
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine is 6e-19
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 6e-15
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 2e-14
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 3e-14
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy 2e-12
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 4e-12
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 1e-11
cd02558246 cd02558, PSRA_1, Pseudouridine synthase, a subgrou 3e-09
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; 2e-08
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information 
 Score =  154 bits (390), Expect = 2e-44
 Identities = 68/200 (34%), Positives = 97/200 (48%), Gaps = 28/200 (14%)

Query: 212 ILVLNKPPKV---PLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRT 268
           +LV+NKP  +   P  GH      ++AL    L       P LVHRLD+++SGLLL+ + 
Sbjct: 1   LLVVNKPAGLPVHPGPGH-LTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKN 59

Query: 269 KESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLD 328
           K++ + L+  F    K + + K            Y ALV G P E +G I APL      
Sbjct: 60  KKAAAKLSKQF----KERKVKK-----------TYLALVDGKPPEDEGTIDAPL------ 98

Query: 329 DGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGT 388
            G+ +R   A+    E  + A+T Y+VL       + +EL+  T R HQ+RVH A ++G 
Sbjct: 99  -GRKKRKKRARVVVSEDGKPAITHYKVLERF-GNVTLVELQLETGRTHQIRVHLA-SIGH 155

Query: 389 PIVGDYKYGWFVHRRWKQMP 408
           PIVGD KYG           
Sbjct: 156 PIVGDPKYGGKASDSPGLKR 175

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 185
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase Back     alignment and domain information
>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C Back     alignment and domain information
>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2 Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 490
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 100.0
PRK11112257 tRNA pseudouridine synthase C; Provisional 100.0
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 100.0
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 100.0
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 100.0
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 100.0
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 100.0
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 100.0
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 99.97
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 99.97
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 99.97
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 99.97
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.96
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.96
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 99.95
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 99.95
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.94
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.93
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.92
TIGR00093128 pseudouridine synthase. This model identifies pane 99.9
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.89
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 98.83
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 98.69
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 98.26
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 98.1
COG1188100 Ribosome-associated heat shock protein implicated 97.6
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.56
smart0036360 S4 S4 RNA-binding domain. 97.45
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 97.32
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.21
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 97.2
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.2
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 97.17
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 97.17
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 97.04
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 96.99
PRK14123305 tRNA pseudouridine synthase B; Provisional 96.99
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 96.96
PRK14846345 truB tRNA pseudouridine synthase B; Provisional 96.96
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 96.94
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 96.91
PRK14124308 tRNA pseudouridine synthase B; Provisional 96.91
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 96.9
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 96.89
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 96.89
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 96.88
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 96.87
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 96.86
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 96.83
PRK14122312 tRNA pseudouridine synthase B; Provisional 96.73
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 96.68
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 96.67
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 96.64
CHL00113201 rps4 ribosomal protein S4; Reviewed 96.58
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 96.44
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 96.43
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 96.28
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 96.2
PRK05327203 rpsD 30S ribosomal protein S4; Validated 96.08
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 96.05
COG2302257 Uncharacterized conserved protein, contains S4-lik 95.54
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 95.46
PRK1150770 ribosome-associated protein; Provisional 95.0
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 94.47
COG250173 S4-like RNA binding protein [Replication, recombin 92.53
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 92.1
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 91.87
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 87.08
PRK04313237 30S ribosomal protein S4e; Validated 80.03
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=5.5e-56  Score=445.54  Aligned_cols=278  Identities=30%  Similarity=0.438  Sum_probs=217.9

Q ss_pred             CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463          103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR  182 (490)
Q Consensus       103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~  182 (490)
                      ..++|+++||+..++ +||+.++++|++|+|+||           |+     +++.++++..||+|.+........    
T Consensus        10 ~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vN-----------g~-----~v~~~~~l~~gd~i~~~~~~~~~~----   68 (289)
T COG0564          10 EAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVN-----------GK-----KVKPSYKLKPGDVVRIPLPEEPEE----   68 (289)
T ss_pred             hcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEEC-----------CE-----EccCCeeeCCCCEEEEeccccccc----
Confidence            357899999999666 999999999999999999           73     666999999999999966432210    


Q ss_pred             ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccC--CCCCccccCCCcCCc
Q 042463          183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDY--NEGPKLVHRLDRESS  260 (490)
Q Consensus       183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~--~~~l~~VHRLDr~TS  260 (490)
                            .  .+.+.++   ...|||||+++||||||+||+||++. .+. ..+++..++....  ..++++||||||+||
T Consensus        69 ------~--~~~~~~~---~l~IlyED~~llVvnKP~Gl~vhp~~-~~~-~~tl~~~l~~~~~~~~~~~~~vHRLDkdTS  135 (289)
T COG0564          69 ------E--KLVPEDI---PLDILYEDEDLLVVNKPAGLVVHPGG-GHH-EGTLVNALLRHCQDGVERPGIVHRLDKDTS  135 (289)
T ss_pred             ------c--cccccCC---CccEEEecCCEEEEECCCCCcCcCCC-CCc-cHhHHHHHHHhccccCCceeeeccCCCCCc
Confidence                  0  0111111   13599999999999999999999873 332 2455554443322  567999999999999


Q ss_pred             eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463          261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN  340 (490)
Q Consensus       261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~  340 (490)
                      ||||+|||..++..|+.+|+++               .+.|+|+|+|.|.++..+|.|+.||.+......  .+.+... 
T Consensus       136 Glll~AK~~~a~~~l~~~f~~r---------------~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~--~~~v~~~-  197 (289)
T COG0564         136 GLLLVAKNREAARELSEQFKQR---------------KVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRK--KMAVVKE-  197 (289)
T ss_pred             eEEEEECCHHHHHHHHHHHhcC---------------cCcEEEEEEEECcccCCCCEEeeeeecCCcCCc--eEEEecc-
Confidence            9999999999999999999997               599999999999999888999999988643322  2222211 


Q ss_pred             CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463          341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY  420 (490)
Q Consensus       341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~  420 (490)
                         ..++.|+|+|++++...+..||++|+|+||||||||+||+ ++||||+||.+||...  .                 
T Consensus       198 ---~~gk~A~T~~~~l~~~~~~~tlv~~~~~TGRTHQIRVHl~-~lghPI~GD~~Yg~~~--~-----------------  254 (289)
T COG0564         198 ---GSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLA-HLGHPIVGDPLYGGKD--K-----------------  254 (289)
T ss_pred             ---CCCCceEEEEEehhccCCceEEEEEEeCCCCHhHHHHHHH-HCCCCeeCCcccCCch--h-----------------
Confidence               1179999999999974333699999999999999999999 8999999999999731  0                 


Q ss_pred             eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCch
Q 042463          421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPS  476 (490)
Q Consensus       421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~  476 (490)
                                   +......|++|||+.|.|  .||.+      ++.+.|+||+|.
T Consensus       255 -------------~~~~~~~r~~LHA~~l~f--~hp~t------~~~~~~~a~~p~  289 (289)
T COG0564         255 -------------SAGAGLKRQALHAYKLSF--THPLT------GEELEFEAPLPE  289 (289)
T ss_pred             -------------hcccCcchhhhhhceeEc--cCCCC------CCEEEEecCCCC
Confidence                         000114589999999999  56766      557999999984

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional 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
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine 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
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] 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
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional 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
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] 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
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like 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
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA Back     alignment and domain information
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [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
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>PRK00989 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
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 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
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein 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
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated 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 ?
Query490
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 4e-11
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 9e-11
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 1e-10
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 4e-05
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 1e-04
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 4e-04
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 Back     alignment and structure 
Iteration: 1

 Score = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 88/204 (43%), Gaps = 45/204 (22%)
Query: 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDYNEGPK----------LVH 253
           ++ Y D  ILVLNKP    + G                S+   EG +          LVH
Sbjct: 6   VILYEDDHILVLNKPSGTAVHG------------GSGLSFGVIEGLRALRPEARFLELVH 53
Query: 254 RLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKE 313
           RLDR++SG+LL+ + + ++             +SL +   +  + M + Y ALV G  + 
Sbjct: 54  RLDRDTSGVLLVAKKRSAL-------------RSLHEQLRE--KGMQKDYLALVRGQWQS 98
Query: 314 KQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTC 373
               + APL K +L  G  ERI+     G  +      E R     +  CS     P+T 
Sbjct: 99  HVKSVQAPLLKNILQSG--ERIVRVSQEGKPSETRFKVEERYAFATLVRCS-----PVTG 151
Query: 374 RKHQLRVHCAEALGTPIVGDYKYG 397
           R HQ+RVH   A G PI  D +YG
Sbjct: 152 RTHQIRVHTQYA-GHPIAFDDRYG 174
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of Pseudouridine Synthase Rluc From Escherichia Coli Length = 228 Back     alignment and structure
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-induced Rna Structure Length = 217 Back     alignment and structure
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325 Back     alignment and structure
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 Back     alignment and structure
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349 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 ?
Query490
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 2e-33
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 3e-29
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 5e-17
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-13
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-04
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217 Back     alignment and structure
 Score =  124 bits (315), Expect = 2e-33
 Identities = 57/203 (28%), Positives = 84/203 (41%), Gaps = 50/203 (24%)

Query: 207 YRDSAILVLNKPPK---VPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLL 263
           Y+D  I+V+NKP     VP +      +S+                + VHRLD  +SG++
Sbjct: 16  YQDDHIMVVNKPSGLLSVPGRLE-EHKDSVMTRIQRDY-----PQAESVHRLDMATSGVI 69

Query: 264 LMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLS 323
           ++  TK +   L   F +    +   K           +Y A V G P   +G++  PL 
Sbjct: 70  VVALTKAAERELKRQFRE----REPKK-----------QYVARVWGHPSPAEGLVDLPLI 114

Query: 324 ---------KVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCR 374
                    KV  + GK                 A TEY V+    +  + + L+P+T R
Sbjct: 115 CDWPNRPKQKVCYETGK----------------PAQTEYEVVEYAADNTARVVLKPITGR 158

Query: 375 KHQLRVHCAEALGTPIVGDYKYG 397
            HQLRVH   ALG PI+GD  Y 
Sbjct: 159 SHQLRVHML-ALGHPILGDRFYA 180
>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 Length = 228 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 Length = 325 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 ?
Query490
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 100.0
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 100.0
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 100.0
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 100.0
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 100.0
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 99.95
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 97.97
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 97.83
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 97.41
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 97.24
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 97.09
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 97.05
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 97.01
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 96.95
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 96.58
2aus_C334 Pseudouridine synthase; isomerase, structural prot 96.53
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 96.52
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 96.44
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 96.41
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 96.34
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 96.33
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 95.98
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 95.56
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 95.02
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 90.21
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 89.66
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 83.14
>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
Probab=100.00  E-value=3.9e-54  Score=439.28  Aligned_cols=299  Identities=22%  Similarity=0.294  Sum_probs=176.0

Q ss_pred             CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463          103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR  182 (490)
Q Consensus       103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~  182 (490)
                      ..++||++||++.++.+||+.++++|++|+|+||           |+    ..+++++.|.+||.|.+.....+.     
T Consensus        14 ~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VN-----------G~----~v~~~~~~v~~gD~I~v~~~~~~~-----   73 (325)
T 1v9f_A           14 QLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVN-----------GK----VCDKPKEKVLGGEQVAINAEIEEE-----   73 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCchHHHHHHhhccccCHHHHHHHHHCCCEEEC-----------CE----EccCCCCEeCCCCEEEEecccccc-----
Confidence            3468999999998878999999999999999999           74    137889999999999996432110     


Q ss_pred             ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHH-hccCCCCCccccCCCcCCc
Q 042463          183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAAL-SYDYNEGPKLVHRLDRESS  260 (490)
Q Consensus       183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~-~~~~~~~l~~VHRLDr~TS  260 (490)
                            ....+..     +...|+|||++|+|||||+||+||+.... ..++...+.... ......++++|||||++||
T Consensus        74 ------~~~~~~~-----~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TS  142 (325)
T 1v9f_A           74 ------ARFEPQD-----IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTT  142 (325)
T ss_dssp             --------CCCCC-----CCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCE
T ss_pred             ------ccCCccc-----CCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceeeecCCCCCCe
Confidence                  0001111     12349999999999999999999976542 234433332221 1112346899999999999


Q ss_pred             eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463          261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN  340 (490)
Q Consensus       261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~  340 (490)
                      ||||||+|+++++.|+++|.++               .+.|+|+|+|.|.+++ +|.|+.||.+....  . .++.+.  
T Consensus       143 Glll~ak~~~~~~~l~~~~~~~---------------~v~K~Y~a~v~G~~~~-~g~i~~~i~~~~~~--~-~~~~v~--  201 (325)
T 1v9f_A          143 GLMVVAKTVPAQTRLVESLQRR---------------EITREYEAVAIGHMTA-GGTVDEPISRHPTK--R-THMAVH--  201 (325)
T ss_dssp             EEEEEESSHHHHHHHHHHHHTT---------------CSEEEEEEEEESCCCC-CEEEECCEEECSSC--T-TCEEEC--
T ss_pred             eEEEEEcCHHHHHHHHHHHHcC---------------CeeEEEEEEEeCCCCC-CCEEeeeeeECCCC--C-EEEEEC--
Confidence            9999999999999999999986               5999999999999987 89999999875322  1 122221  


Q ss_pred             CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463          341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY  420 (490)
Q Consensus       341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~  420 (490)
                         .+++.|.|+|++++. ..++|+++|+|.||||||||+||+ ++||||+||.+||+..  .   .             
T Consensus       202 ---~~gk~a~t~~~vl~~-~~~~slv~~~l~TGR~HQIRvhla-~lG~PI~GD~~Yg~~~--~---~-------------  258 (325)
T 1v9f_A          202 ---PMGKPAVTHYRIMEH-FRVHTRLRLRLETGRTHQIRVHMA-HITHPLVGDPVYGGRP--R---P-------------  258 (325)
T ss_dssp             ---TTSBCCEEEEEEEEE-CSSEEEEEEEESCCCTTHHHHHHH-HTTCCBTTCTTTTCCC--C---C-------------
T ss_pred             ---CCCeeEEEEEEEeEE-cCCeEEEEEEECCCCcHHHHHHHH-hCCCceeCChhhCCcc--c---c-------------
Confidence               357899999999995 457899999999999999999999 8999999999999621  0   0             


Q ss_pred             eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhhc
Q 042463          421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSY  488 (490)
Q Consensus       421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~~  488 (490)
                          +.............++|++|||++|.|.  ||.+      ++.+.|+||+|++|+.+|+.|+.+
T Consensus       259 ----~~~~~~~~~~~~~~~~r~~LHA~~L~f~--hP~~------~~~~~~~aplp~~~~~~l~~l~~~  314 (325)
T 1v9f_A          259 ----PKGASEAFISTLRKFDRQALHATMLRLY--HPIS------GIEMEWHAPIPQDMVELIEVMRAD  314 (325)
T ss_dssp             ----CTTCCHHHHHHHHHCCSCSEEEEEEEEE--CTTT------CCEEEEECCCCHHHHHHHHHHHHH
T ss_pred             ----ccccchhhhhhccCCcChhhheeeeEee--CCCC------CCEEEEEecCcHHHHHHHHHhccc
Confidence                0000000000001135799999999994  6766      557999999999999999988753
>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
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {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
>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
>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
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} 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
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6 Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus} Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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
>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
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>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
>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
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Back     alignment and structure
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} 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 490
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 3e-12
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 2e-08
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

 Score = 63.8 bits (154), Expect = 3e-12
 Identities = 65/286 (22%), Positives = 97/286 (33%), Gaps = 68/286 (23%)

Query: 204 LVKYRDSAILVLNKPPKVPLKGHLPVH----NSMDALAAAALSYDYNEGPKLVHRLDRES 259
           ++ Y D  ILVLNKP          VH     S   +             +LVHRLDR++
Sbjct: 2   VIMYEDDHILVLNKPS------GTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDT 55

Query: 260 SGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIH 319
           SG+LL+ + + ++  L     +               + M + Y ALV G  +     + 
Sbjct: 56  SGVLLVAKKRSALRSLHEQLRE---------------KGMQKDYLALVRGQWQSHVKSVQ 100

Query: 320 APLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLR 379
           APL K +L  G+  RI+     G  +      E R         + +   P+T R HQ+R
Sbjct: 101 APLLKNILQSGE--RIVRVSQEGKPSETRFKVEER-----YAFATLVRCSPVTGRTHQIR 153

Query: 380 VHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKV 439
           VH               G  +    +   R      +     L R               
Sbjct: 154 VHT-----------QYAGHPIAFDDRYGDREFDRQLTEAGTGLNR--------------- 187

Query: 440 PLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLM 485
             L LH   LK    F      P   +++R  A M   +K     M
Sbjct: 188 --LFLHAAALK----FT----HPGTGEVMRIEAPMDEGLKRCLQKM 223
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250 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 ?
Query490
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 100.0
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 99.93
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 99.89
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 98.45
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 98.4
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 98.0
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 97.86
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 96.96
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 96.87
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 96.75
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 96.63
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 96.46
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 95.17
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 94.7
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 94.41
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 92.58
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 86.55
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.1e-51  Score=394.61  Aligned_cols=224  Identities=29%  Similarity=0.380  Sum_probs=178.8

Q ss_pred             eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463          204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN  283 (490)
Q Consensus       204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~  283 (490)
                      .|||||+++||||||+||+||++.....++...+..  .......+++|||||++||||||||||.+++..|+++|+++ 
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~~~~~~l~~--~~~~~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~~~f~~~-   78 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA--LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK-   78 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHH--HSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTT-
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcchHHHHHHH--hCCCCcccceeeeccceeeeeeeeecchHHHHHHHHHHhcc-
Confidence            499999999999999999999875544443333322  12344568899999999999999999999999999999997 


Q ss_pred             cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCc
Q 042463          284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGC  363 (490)
Q Consensus       284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~  363 (490)
                                    .+.|+|+|+|.|.++...+.++.++.......+.  .++..    ..+++.|.|.|++++. ..++
T Consensus        79 --------------~v~K~Y~a~~~G~~~~~~~~~~~~~~~~~~~~~~--~~~~~----~~~gk~a~t~~~~l~~-~~~~  137 (227)
T d1v9ka_          79 --------------GMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE--RIVRV----SQEGKPSETRFKVEER-YAFA  137 (227)
T ss_dssp             --------------CSEEEEEEEEESCCCTTCCEECCCEEEEECTTSC--EEEEE----CTTSBCCCEEEEEEEE-CSSE
T ss_pred             --------------cccceecccccCccccccCcccccccccccccee--eeeec----CCCCcccceeehhhhh-cCCc
Confidence                          5999999999999998889998888765433322  22221    2457899999999996 5679


Q ss_pred             eEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcchhh
Q 042463          364 SWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLH  443 (490)
Q Consensus       364 slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~rl~  443 (490)
                      +||+|+|.||||||||+||| ++||||+||.+||+...+...                           .......+|++
T Consensus       138 slv~~~~~TGRtHQIRvHla-~lG~PIvGD~~Yg~~~~~~~~---------------------------~~~~~~~~rl~  189 (227)
T d1v9ka_         138 TLVRCSPVTGRTHQIRVHTQ-YAGHPIAFDDRYGDREFDRQL---------------------------TEAGTGLNRLF  189 (227)
T ss_dssp             EEEEEEESSCCTTHHHHHHH-HTTCCBTTCTTTSCHHHHHHH---------------------------HHTTCCCCSCC
T ss_pred             EEEEEEeccCchHHHHHHHh-hcCceeccCcccccccccccc---------------------------hhcccCcchHH
Confidence            99999999999999999999 899999999999974322100                           00011245899


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhh
Q 042463          444 LHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSS  487 (490)
Q Consensus       444 LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~  487 (490)
                      |||++|+|  .||.|      |+.+.|+||+|++|+.+|+.|++
T Consensus       190 LHa~~L~f--~hP~t------~~~~~~~aplP~~f~~~l~~Lk~  225 (227)
T d1v9ka_         190 LHAAALKF--THPGT------GEVMRIEAPMDEGLKRCLQKMRN  225 (227)
T ss_dssp             EEEEEEEE--ECTTT------CCEEEEECCCCHHHHHHHHHHHH
T ss_pred             HHccccEe--ECCCC------CCEEEEEecCcHHHHHHHHHHHh
Confidence            99999999  46766      55799999999999999999975
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {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
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} 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
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} 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
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure