Citrus Sinensis ID: 015839

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-------40
MKRKREEEKSKANDSNSNGNGNGNGNGNGNGNSSNNMEIVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPVSSDKSESSSEDFSIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
ccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEccccccccccEEEEEEEccccccccHHHHHHHHcccccHHHHHHHHHcccEEEccEEcccccEEccccEEEEEccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHccccccccccccccccccEEEEEEccHHHHHHHHHHHHccccccEEEEEEEEEcccccEEEEcccccccccccccccccccccccccccccEEEEEEEEEEcccEEEEEEEcccccHHHHHHHHcccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccEEcc
cccHHHHHHccccccccccccccccccccccccccccHHHccccccccccccEEEccccccccccEEEEEEEEcHHHcccHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEcccEEEccccEEEEEccccccccccccccEEEEcccEEEEEcccccEEcccccccccHHHHHHHHccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHcccEEEEEEEEEcEccccccEEEcccccccHHHHcEEEEccccccccccccccEEEEEEEEEcccEEEEEEEEEcccccEEEEEHHHccccccccccccccccccccccccHEEHHHHcccEccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHEHHEcc
mkrkreeekskandsnsngngngngngngngnssnnMEIVwqtpanppvkedyifrdgrrnvkpYYFEFISHVKNRWAGKTIVDLFAEefkgrpydyyVSAVKcgriqvdeemvpvsytvkssqkishflhrheppvmawdvsilqkepdvltvckppsvpvhpcgqyrkntVVGILQaehdlaplfpvhrLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVngvfpegeqvVDVNINYnasagrstaesgdslgdtplkgkaactkftristngthsivlcepitgrtHQIRVHLQytgypianDMLYLCEHvthregmsadraaayshhspppvssdksesssedfsidpmctncpnlapkgkrllssnsleDLCYGHMRQYQTSLVMLS
mkrkreeekskandsnsngngngngNGNGNGNSSNNMEIVWQTPANPPVKEDYIFRDGRRNVKPYYFEFIshvknrwagkTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILArnaskadlfrQQIEAGKVIKRYIARVNgvfpegeqvVDVNINYNASAgrstaesgdslgdtpLKGKAACTKftristngthsiVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPVSSDKSESSSEDFSIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
MKRKREEEKSKANDsnsngngngngngngngnssnnMEIVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHspppvssdksesssedfsidpMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
**************************************IVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYN*********************KAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH********************************************************LEDLCYGHMRQY********
************************************************VKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAES*********KGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPVSSDKSESSSEDFSIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
****************SNGNGNGNGNGNGNGNSSNNMEIVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAG*********LGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADR************************SIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
****************************************WQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPVSSDKSESSSEDFSIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
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MKRKREEEKSKANDSNSNGNGNGNGNGNGNGNSSNNMEIVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPVSSDKSESSSEDFSIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTSLVMLS
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 ?
Query399 2.2.26 [Sep-21-2011]
Q0E0Y3393 RNA pseudourine synthase yes no 0.832 0.844 0.675 1e-135
Q9LU60395 RNA pseudourine synthase yes no 0.907 0.916 0.658 1e-134
Q149F1553 RNA pseudouridylate synth yes no 0.634 0.457 0.417 1e-59
Q8IZ73545 RNA pseudouridylate synth yes no 0.634 0.464 0.417 2e-58
Q09709394 Uncharacterized protein C yes no 0.671 0.680 0.407 1e-55
Q12069462 tRNA pseudouridine(32) sy yes no 0.641 0.554 0.391 5e-51
Q12362 591 Bifunctional protein RIB2 no no 0.631 0.426 0.389 5e-50
O16686432 Uncharacterized protein K yes no 0.699 0.645 0.358 2e-46
P53294404 tRNA pseudouridine(31) sy no no 0.654 0.646 0.348 5e-44
Q9HZM9318 Ribosomal large subunit p yes no 0.583 0.732 0.278 1e-19
>sp|Q0E0Y3|PUS7_ORYSJ RNA pseudourine synthase 7 OS=Oryza sativa subsp. japonica GN=Os02g0512300 PE=2 SV=2 Back     alignment and function desciption
 Score =  480 bits (1235), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 233/345 (67%), Positives = 272/345 (78%), Gaps = 13/345 (3%)

Query: 39  IVWQTPANPPVKEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYY 98
           IVWQTPANPP ++DYIFRDGRR V+PYYFEFISHVKNRWAGKTIVDLF +EFKGRP +YY
Sbjct: 8   IVWQTPANPPERQDYIFRDGRRYVRPYYFEFISHVKNRWAGKTIVDLFTDEFKGRPREYY 67

Query: 99  VSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPP 158
           V AVKCGR+QVD++MV   Y V+SSQKISHFLHRHEPPV+  D++ILQ E DV+TVCKP 
Sbjct: 68  VHAVKCGRLQVDDQMVHADYVVQSSQKISHFLHRHEPPVLGGDITILQNEADVVTVCKPA 127

Query: 159 SVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEA 218
           SVPVHPCGQYRKNTVVGILQAEH L PLFPVHRLDRLVSGLLI A+NA KA+ FRQQIEA
Sbjct: 128 SVPVHPCGQYRKNTVVGILQAEHGLVPLFPVHRLDRLVSGLLIFAKNADKAESFRQQIEA 187

Query: 219 GKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRI 278
             + K Y+A+V GVFP+GEQ V+ N+++NA  GRSTAE  D  G  P+ GK ACTKF RI
Sbjct: 188 SLLQKEYVAKVVGVFPDGEQTVNANVHFNAREGRSTAEVCDGDGKAPI-GKQACTKFQRI 246

Query: 279 STNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHR--EGMSADRAAAYS 336
            T+G HSIVLC+P+TGRTHQIRVHL++ GYPIAND +YL E+ + R  +G   +RA   +
Sbjct: 247 CTDGIHSIVLCKPVTGRTHQIRVHLKHIGYPIANDEVYLSENFSPRSSKGTRINRATTLA 306

Query: 337 HHSP---PPVSSD-------KSESSSEDFSIDPMCTNCPNLAPKG 371
              P   P   +D       +   + E+FSIDPMCTNCPNLAP G
Sbjct: 307 CSLPSSDPDSCADLGNNDTNEDTEADEEFSIDPMCTNCPNLAPVG 351

Oryza sativa subsp. japonica (taxid: 39947)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q9LU60|PUS7_ARATH RNA pseudourine synthase 7 OS=Arabidopsis thaliana GN=At5g51140 PE=2 SV=1 Back     alignment and function description
>sp|Q149F1|RUSD2_MOUSE RNA pseudouridylate synthase domain-containing protein 2 OS=Mus musculus GN=Rpusd2 PE=2 SV=2 Back     alignment and function description
>sp|Q8IZ73|RUSD2_HUMAN RNA pseudouridylate synthase domain-containing protein 2 OS=Homo sapiens GN=RPUSD2 PE=1 SV=2 Back     alignment and function description
>sp|Q09709|YA32_SCHPO Uncharacterized protein C18B11.02c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC18B11.02c PE=3 SV=1 Back     alignment and function description
>sp|Q12069|PUS9_YEAST tRNA pseudouridine(32) synthase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUS9 PE=1 SV=1 Back     alignment and function description
>sp|Q12362|RIB2_YEAST Bifunctional protein RIB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIB2 PE=1 SV=1 Back     alignment and function description
>sp|O16686|YK27_CAEEL Uncharacterized protein K07E8.7 OS=Caenorhabditis elegans GN=K07E8.7 PE=3 SV=1 Back     alignment and function description
>sp|P53294|PUS6_YEAST tRNA pseudouridine(31) synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUS6 PE=1 SV=1 Back     alignment and function description
>sp|Q9HZM9|RLUC_PSEAE Ribosomal large subunit pseudouridine synthase C OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) 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 ?
Query399
255540129385 ribosomal pseudouridine synthase, putati 0.907 0.940 0.727 1e-160
224134072388 predicted protein [Populus trichocarpa] 0.909 0.935 0.745 1e-157
359491112386 PREDICTED: RNA pseudourine synthase 7-li 0.849 0.878 0.782 1e-150
449440959393 PREDICTED: RNA pseudourine synthase 7-li 0.834 0.847 0.776 1e-149
297734463374 unnamed protein product [Vitis vinifera] 0.832 0.887 0.790 1e-148
357464999380 RNA pseudourine synthase [Medicago trunc 0.827 0.868 0.763 1e-146
356516519381 PREDICTED: RNA pseudourine synthase 7-li 0.822 0.860 0.761 1e-144
297795919392 pseudouridine synthase family protein [A 0.899 0.915 0.655 1e-135
218190831393 hypothetical protein OsI_07380 [Oryza sa 0.832 0.844 0.678 1e-133
334188313410 RNA pseudourine synthase 7 [Arabidopsis 0.907 0.882 0.658 1e-133
>gi|255540129|ref|XP_002511129.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223550244|gb|EEF51731.1| ribosomal pseudouridine synthase, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  570 bits (1468), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 288/396 (72%), Positives = 312/396 (78%), Gaps = 34/396 (8%)

Query: 1   MKRKREEEKSKANDSNSNGNGNGNGNGNGNGNSSNNMEIVWQTPANPPVKEDYIFRDGRR 60
           MKRKREEE                        + N+MEIVWQTPANPP K DYIFRDGRR
Sbjct: 1   MKRKREEE------------------------NKNDMEIVWQTPANPPEKHDYIFRDGRR 36

Query: 61  NVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTV 120
           +V+PYYFEFISH KNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVD E VPVSY V
Sbjct: 37  HVRPYYFEFISHAKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDGETVPVSYIV 96

Query: 121 KSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAE 180
           KSSQKISHFLHRHEPPV AWD+ +L K+PDV+TV KP +VPVHPCGQYRKNTVVGILQAE
Sbjct: 97  KSSQKISHFLHRHEPPVTAWDIPVLYKDPDVVTVYKPATVPVHPCGQYRKNTVVGILQAE 156

Query: 181 HDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVV 240
           H+LAPLFPVHRLDRLVSGLLILARNA KADLFRQ+IEAG V K+Y+A+V GVFPE EQVV
Sbjct: 157 HNLAPLFPVHRLDRLVSGLLILARNALKADLFRQEIEAGMVQKQYVAKVVGVFPEDEQVV 216

Query: 241 DVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIR 300
            VNINYNA  GRSTAE G+S  D+P KGK ACTKFTRISTNGTHSIVLC+PITGRTHQIR
Sbjct: 217 GVNINYNAREGRSTAEVGNSCVDSPPKGKTACTKFTRISTNGTHSIVLCKPITGRTHQIR 276

Query: 301 VHLQYTGYPIANDMLYLCEHVTHR--EGMSADRAAAYSHHSPPP---VSSDKSESSSEDF 355
           VHLQYTG+PIAND LYL EH   R  EGMSADRAA  S +   P    S    E+S +DF
Sbjct: 277 VHLQYTGHPIANDFLYLSEHAASRSAEGMSADRAACSSSYCVTPQDFCSDTHEENSVQDF 336

Query: 356 SIDPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQY 391
           SIDPMCTNCPNLAPKG      +  E+  + H  QY
Sbjct: 337 SIDPMCTNCPNLAPKG-----YDVYEECLWLHCVQY 367

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224134072|ref|XP_002321729.1| predicted protein [Populus trichocarpa] gi|222868725|gb|EEF05856.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359491112|ref|XP_003634223.1| PREDICTED: RNA pseudourine synthase 7-like isoform 2 [Vitis vinifera] gi|359491114|ref|XP_002280549.2| PREDICTED: RNA pseudourine synthase 7-like isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|449440959|ref|XP_004138251.1| PREDICTED: RNA pseudourine synthase 7-like [Cucumis sativus] gi|449501468|ref|XP_004161375.1| PREDICTED: RNA pseudourine synthase 7-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297734463|emb|CBI15710.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|357464999|ref|XP_003602781.1| RNA pseudourine synthase [Medicago truncatula] gi|355491829|gb|AES73032.1| RNA pseudourine synthase [Medicago truncatula] Back     alignment and taxonomy information
>gi|356516519|ref|XP_003526941.1| PREDICTED: RNA pseudourine synthase 7-like [Glycine max] Back     alignment and taxonomy information
>gi|297795919|ref|XP_002865844.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297311679|gb|EFH42103.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|218190831|gb|EEC73258.1| hypothetical protein OsI_07380 [Oryza sativa Indica Group] Back     alignment and taxonomy information
>gi|334188313|ref|NP_001190513.1| RNA pseudourine synthase 7 [Arabidopsis thaliana] gi|332008660|gb|AED96043.1| RNA pseudourine synthase 7 [Arabidopsis thaliana] 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 ?
Query399
FB|FBgn0051719 739 RluA-1 "RluA-1" [Drosophila me 0.666 0.359 0.439 7.3e-59
FB|FBgn0032256547 RluA-2 "RluA-2" [Drosophila me 0.676 0.493 0.431 3.3e-56
MGI|MGI:1918066553 Rpusd2 "RNA pseudouridylate sy 0.634 0.457 0.421 4.2e-56
UNIPROTKB|F1PK69552 RPUSD2 "Uncharacterized protei 0.634 0.458 0.432 6.8e-56
RGD|1306147553 Rpusd2 "RNA pseudouridylate sy 0.634 0.457 0.414 1.4e-55
UNIPROTKB|Q8IZ73545 RPUSD2 "RNA pseudouridylate sy 0.634 0.464 0.421 3.7e-55
UNIPROTKB|F1P0G3456 RPUSD2 "Uncharacterized protei 0.641 0.561 0.420 1.3e-54
DICTYBASE|DDB_G0281097578 DDB_G0281097 "pseudouridine sy 0.581 0.401 0.369 1.4e-54
UNIPROTKB|F1N088552 RPUSD2 "Uncharacterized protei 0.634 0.458 0.417 2.6e-54
POMBASE|SPAC18B11.02c394 SPAC18B11.02c "tRNA pseudourid 0.679 0.687 0.407 5.5e-54
FB|FBgn0051719 RluA-1 "RluA-1" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 604 (217.7 bits), Expect = 7.3e-59, P = 7.3e-59
 Identities = 124/282 (43%), Positives = 170/282 (60%)

Query:    53 YIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEE 112
             Y   +G R V PYYF F +  K RW G+ I+D+F+ EF+  P + Y   ++ G + V+ E
Sbjct:   288 YYMENGLRKVYPYYFTFTTFTKGRWVGEKILDIFSREFRAHPTEEYERCIQTGTLTVNFE 347

Query:   113 MVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNT 172
              VP+ Y +K +  +++ +HRHE PV    + I+  + D++ V KP S+PVHPCG+YR NT
Sbjct:   348 KVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNT 407

Query:   173 VVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGV 232
             VV IL  E +L  L  +HRLDRL SGLL+  R+  KA    QQI   +V K YI RV GV
Sbjct:   408 VVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGV 467

Query:   233 FPEG----EQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVL 288
             FP+G    ++ ++V ++Y     + +A           KGK   T F ++S NGT S+VL
Sbjct:   468 FPDGIVECKEPIEV-VSYKIGVCKVSA-----------KGKDCTTTFQKLSQNGTTSVVL 515

Query:   289 CEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSAD 330
             C+P+TGR HQIRVHLQY GYPI ND LY  E     +G S D
Sbjct:   516 CKPLTGRMHQIRVHLQYLGYPILNDPLYNHEVFGPLKGRSGD 557
GO:0008835 "diaminohydroxyphosphoribosylaminopyrimidine deaminase activity" evidence=ISS
GO:0009231 "riboflavin biosynthetic process" evidence=ISS
GO:0009982 "pseudouridine synthase activity" evidence=IEA
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
FB|FBgn0032256 RluA-2 "RluA-2" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
MGI|MGI:1918066 Rpusd2 "RNA pseudouridylate synthase domain containing 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1PK69 RPUSD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1306147 Rpusd2 "RNA pseudouridylate synthase domain containing 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q8IZ73 RPUSD2 "RNA pseudouridylate synthase domain-containing protein 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1P0G3 RPUSD2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0281097 DDB_G0281097 "pseudouridine synthase family protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|F1N088 RPUSD2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
POMBASE|SPAC18B11.02c SPAC18B11.02c "tRNA pseudouridine synthase (predicted)" [Schizosaccharomyces pombe (taxid:4896)] 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) ?
Q9LU60PUS7_ARATH5, ., 4, ., 9, 9, ., -0.65860.90720.9164yesno
Q0E0Y3PUS7_ORYSJ5, ., 4, ., 9, 9, ., -0.67530.83200.8447yesno

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:
fgenesh4_pg.C_LG_XV000757
hypothetical protein (388 aa)
(Populus trichocarpa)
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 ?
Query399
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 7e-89
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 4e-55
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 6e-47
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 3e-42
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 2e-28
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 2e-25
cd02558246 cd02558, PSRA_1, Pseudouridine synthase, a subgrou 4e-22
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 1e-17
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 3e-17
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine is 4e-15
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy 7e-12
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 8e-11
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; 7e-08
cd02553167 cd02553, PseudoU_synth_RsuA, Pseudouridine synthas 1e-04
cd02870146 cd02870, PseudoU_synth_RsuA_like, Pseudouridine sy 0.003
>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2 Back     alignment and domain information 
 Score =  267 bits (685), Expect = 7e-89
 Identities = 98/192 (51%), Positives = 123/192 (64%), Gaps = 9/192 (4%)

Query: 127 SHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPL 186
           SH +HRHEPPV    + I+ ++ D+L V KP  +PVHP G+YR NTV  IL++E+ L  L
Sbjct: 1   SHTVHRHEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTEL 60

Query: 187 FPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINY 246
            P HRLDRL SGLL+ A+ +  A   +QQI + +V K Y+ARV G FP+GE VVD  I  
Sbjct: 61  RPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGL 120

Query: 247 NASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNG--THSIVLCEPITGRTHQIRVHLQ 304
            +  G       D       KGK A T F R+S NG    S+VLC+PITGRTHQIRVHLQ
Sbjct: 121 VSPKGGL---RNDVDE----KGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQ 173

Query: 305 YTGYPIANDMLY 316
           Y G+PI ND +Y
Sbjct: 174 YLGHPIVNDPIY 185

Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs. Length = 213
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase 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|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C Back     alignment and domain information
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>gnl|CDD|211327 cd02553, PseudoU_synth_RsuA, Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>gnl|CDD|211347 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases, RsuA subfamily Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 399
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 100.0
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 100.0
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 100.0
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 100.0
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 100.0
PRK11112257 tRNA pseudouridine synthase C; Provisional 100.0
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 100.0
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 100.0
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 100.0
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 100.0
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 100.0
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 99.97
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.97
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.96
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.96
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.96
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.95
TIGR00093128 pseudouridine synthase. This model identifies pane 99.93
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.93
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 98.91
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 98.82
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 98.36
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 98.16
COG1188100 Ribosome-associated heat shock protein implicated 97.75
smart0036360 S4 S4 RNA-binding domain. 97.55
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.45
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 97.12
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 97.11
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 97.08
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.07
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 97.05
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 97.01
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 96.98
CHL00113201 rps4 ribosomal protein S4; Reviewed 96.94
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 96.94
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 96.89
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 96.89
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 96.74
PRK14124308 tRNA pseudouridine synthase B; Provisional 96.73
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 96.71
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 96.63
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 96.6
PRK14123305 tRNA pseudouridine synthase B; Provisional 96.6
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 96.59
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 96.58
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 96.54
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 96.51
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 96.5
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 96.5
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 96.5
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 96.49
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 96.48
PRK05327203 rpsD 30S ribosomal protein S4; Validated 96.47
COG2302257 Uncharacterized conserved protein, contains S4-lik 96.45
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 96.33
PRK14122312 tRNA pseudouridine synthase B; Provisional 96.23
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 96.1
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 95.84
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 95.84
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 95.5
PRK1150770 ribosome-associated protein; Provisional 95.39
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 95.39
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 95.28
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 95.27
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 93.76
COG250173 S4-like RNA binding protein [Replication, recombin 93.38
PLN00189194 40S ribosomal protein S9; Provisional 92.8
PTZ00155181 40S ribosomal protein S9; Provisional 90.5
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 90.11
PRK0177795 hypothetical protein; Validated 86.79
PRK04313237 30S ribosomal protein S4e; Validated 86.66
PF1445181 Ub-Mut7C: Mut7-C ubiquitin 85.83
PTZ00223273 40S ribosomal protein S4; Provisional 83.34
PLN00036261 40S ribosomal protein S4; Provisional 83.33
PTZ00118262 40S ribosomal protein S4; Provisional 82.2
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=1.8e-59  Score=463.90  Aligned_cols=333  Identities=38%  Similarity=0.567  Sum_probs=271.6

Q ss_pred             CCCceeeCCeecccceeeeeehhccccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839           50 KEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF  129 (399)
Q Consensus        50 ~~~~~~~~~~r~v~P~~~~~~~~v~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~  129 (399)
                      ..+|++++|+|++.|||++|.++++.+|.++.+.++|+.+|...++.+++..|+.|.|++||+.+...+.++.+|.|.+.
T Consensus        14 ~~~~~~~~~~~~v~pyy~~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~   93 (371)
T KOG1919|consen   14 EISVYIDGGLRKVAPYYFTYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHT   93 (371)
T ss_pred             ccceeecCCcceeeeEEEeeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEe
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCeeeccceeeccCCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchh
Q 015839          130 LHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKA  209 (399)
Q Consensus       130 ~~~~e~pv~~~~~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a  209 (399)
                      +|+|+|++....+.|+|||++|+|||||+|++|||++.+..|++..++........+++|||||+.|||||+||++.+.+
T Consensus        94 vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~  173 (371)
T KOG1919|consen   94 VHRHEPPVAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAA  173 (371)
T ss_pred             eccCCCCccccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhccccccccccccCccccceEEEEechhHh
Confidence            99999999888999999999999999999999999999999999999887655567899999999999999999999999


Q ss_pred             HHHHHHHhhchhhhhh-heeeccccC-CCceEEeeeeeeccc-CCccccccCCCCCCCCCCCcccccceEEeecCCeeeE
Q 015839          210 DLFRQQIEAGKVIKRY-IARVNGVFP-EGEQVVDVNINYNAS-AGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSI  286 (399)
Q Consensus       210 ~~L~~~~~~~~v~K~Y-lA~V~G~~~-~~~~~i~~~i~~~~~-~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~sl  286 (399)
                      ..+.++|+++.+.|.| +|.|.|.|+ .+...+..++..... .+.....+.   ..+...++.|+|.|+++.+++..++
T Consensus       174 ~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~~~~~l~~~~---~~~~~~~k~a~T~~~~~~~~~~ss~  250 (371)
T KOG1919|consen  174 DKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNAVG---VRDEVAAKDAKTLFKVLSYDGGSSL  250 (371)
T ss_pred             HHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCccccccccceEeeecc---cccccccccceeEEEEcccCCceEE
Confidence            9999999999999999 799999999 555577776654322 011111111   1111358999999999999998999


Q ss_pred             EEeecccCceeEEEEEeeeeCcccccCceeecccccc--ccCCCccccccccc-------cCCCCCCCCCcCCCCCcccc
Q 015839          287 VLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH--REGMSADRAAAYSH-------HSPPPVSSDKSESSSEDFSI  357 (399)
Q Consensus       287 V~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~--~~~~~~~~~~~~~~-------~lp~~~~~~~~~~~~~~~~~  357 (399)
                      |+|.|+||||||||+||+++|+||+||.+|++...|+  +.-.........+.       .-....+.|..........+
T Consensus       251 V~~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~  330 (371)
T KOG1919|consen  251 VECRPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKKKSLEEEIQRLIDVHLLENWLGFHPRTGPLI  330 (371)
T ss_pred             EEeeccCCcHHHHHHHHHHhCCCcCCCcccccccccccCCCCCCCCCccccCccccccccchhhccccccccccccccch
Confidence            9999999999999999999999999999998877776  21111111110110       00001111221222333667


Q ss_pred             CccCcCCCCCCcccccccccCchhhhhhhhhhceeee
Q 015839          358 DPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTS  394 (399)
Q Consensus       358 ~~~C~~c~~~~~~~~~~~~~~~~~~l~lha~~y~~~~  394 (399)
                      +++|.+|..+        ..+ ++.+|||||+|....
T Consensus       331 ~~~~~~C~~~--------~~~-Dl~~~lha~~y~~~~  358 (371)
T KOG1919|consen  331 EELCQECKVP--------IDN-DLELFLHALKYEMKG  358 (371)
T ss_pred             hhhhhhCCCC--------CCc-hHhHhhhhcccccCC
Confidence            8899999975        122 789999999998764

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional 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
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like 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
>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
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; 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
>PRK10475 23S rRNA pseudouridine synthase F; 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
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like 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
>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
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein 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
>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
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type 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
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 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
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 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
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] 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
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] 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
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>PRK01777 hypothetical protein; Validated Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PF14451 Ub-Mut7C: Mut7-C ubiquitin Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional 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 ?
Query399
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 3e-16
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 2e-15
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 1e-09
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 3e-08
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 8e-07
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 9e-07
>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 = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 83/173 (47%), Gaps = 6/173 (3%)
Query: 144 ILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILA 203
           IL ++  +L + KP    VH         + G+     +   L  VHRLDR  SG+L++A
Sbjct: 7   ILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVA 66
Query: 204 RNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGD 263
           +  S      +Q+    + K Y+A V G +    + V   +  N        +SG+ +  
Sbjct: 67  KKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKN------ILQSGERIVR 120
Query: 264 TPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLY 316
              +GK + T+F         ++V C P+TGRTHQIRVH QY G+PIA D  Y
Sbjct: 121 VSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY 173
>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|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349 Back     alignment and structure
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 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 ?
Query399
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 3e-37
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 4e-31
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 2e-24
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
>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
 Score =  133 bits (338), Expect = 3e-37
 Identities = 53/169 (31%), Positives = 83/169 (49%), Gaps = 10/169 (5%)

Query: 150 DVLTVCKPPSVPVHP-CGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARN-AS 207
            +L + KP    VH   G      + G+     +   L  VHRLDR  SG+L++A+  ++
Sbjct: 10  HILVLNKPSGTAVHGGSGLSF-GVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSA 68

Query: 208 KADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLK 267
              L  +Q+    + K Y+A V G +    + V   +       ++  +SG+ +     +
Sbjct: 69  LRSL-HEQLREKGMQKDYLALVRGQWQSHVKSVQAPL------LKNILQSGERIVRVSQE 121

Query: 268 GKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLY 316
           GK + T+F         ++V C P+TGRTHQIRVH QY G+PIA D  Y
Sbjct: 122 GKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY 170
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query399
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 100.0
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 100.0
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 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; 99.97
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.58
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.22
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.07
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 97.84
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 97.81
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 97.63
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 97.35
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 97.19
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 97.11
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 97.08
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 97.04
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 96.8
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 96.4
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 96.14
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 96.09
2aus_C334 Pseudouridine synthase; isomerase, structural prot 95.95
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 95.93
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 95.74
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 95.39
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 93.91
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 93.03
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 82.45
>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=1.2e-54  Score=428.47  Aligned_cols=262  Identities=21%  Similarity=0.249  Sum_probs=163.2

Q ss_pred             ccccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCee-eeeeEEEecccccccccccCCCC-ee--eccceeeccC
Q 015839           73 VKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEM-VPVSYTVKSSQKISHFLHRHEPP-VM--AWDVSILQKE  148 (399)
Q Consensus        73 v~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~-v~~~~~v~~gD~I~~~~~~~e~p-v~--~~~~~IlyEd  148 (399)
                      +...+.++||++||++.+..+||+.++++|++|+|+|||++ +.++++|++||.|.+.....+++ ..  ..++.|+|||
T Consensus        10 v~~~~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed   89 (325)
T 1v9f_A           10 VSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYED   89 (325)
T ss_dssp             ------------------------------------------------------------------CCCCCCCCCEEEEC
T ss_pred             ECCccCCchHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeEEEEC
Confidence            56677899999999998768999999999999999999998 58999999999999876543211 11  1246799999


Q ss_pred             CCeEEeecCCCcccccCcccccceEEEEeecc----cCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhh
Q 015839          149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAE----HDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKR  224 (399)
Q Consensus       149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~----~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~  224 (399)
                      ++|||||||+||+|||++.....|+++.|...    ....++++|||||++||||||||||+++++.|+++|+++.+.|+
T Consensus        90 ~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~  169 (325)
T 1v9f_A           90 EDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE  169 (325)
T ss_dssp             SSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEE
T ss_pred             CCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeEE
Confidence            99999999999999998877677887766321    12246899999999999999999999999999999999999999


Q ss_pred             hheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEee
Q 015839          225 YIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQ  304 (399)
Q Consensus       225 YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla  304 (399)
                      |+|+|.|.++. ++.|+.+|..+........ +       ..+|+.|.|.|++++...+.|+|+|+|+||||||||+||+
T Consensus       170 Y~a~v~G~~~~-~g~i~~~i~~~~~~~~~~~-v-------~~~gk~a~t~~~vl~~~~~~slv~~~l~TGR~HQIRvhla  240 (325)
T 1v9f_A          170 YEAVAIGHMTA-GGTVDEPISRHPTKRTHMA-V-------HPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMA  240 (325)
T ss_dssp             EEEEEESCCCC-CEEEECCEEECSSCTTCEE-E-------CTTSBCCEEEEEEEEECSSEEEEEEEESCCCTTHHHHHHH
T ss_pred             EEEEEeCCCCC-CCEEeeeeeECCCCCEEEE-E-------CCCCeeEEEEEEEeEEcCCeEEEEEEECCCCcHHHHHHHH
Confidence            99999999987 7899999987654322221 1       1378999999999998878999999999999999999999


Q ss_pred             eeCcccccCceeeccccc------------cccCCCccccccccccCCCCC
Q 015839          305 YTGYPIANDMLYLCEHVT------------HREGMSADRAAAYSHHSPPPV  343 (399)
Q Consensus       305 ~lG~PIvGD~~Yg~~~~~------------~~~~~~~~~~~~~~~~lp~~~  343 (399)
                      ++||||+||.+||+....            ......++|+..+.|.+|.+-
T Consensus       241 ~lG~PI~GD~~Yg~~~~~~~~~~~~~~~~~~~~~r~~LHA~~L~f~hP~~~  291 (325)
T 1v9f_A          241 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISG  291 (325)
T ss_dssp             HTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTC
T ss_pred             hCCCceeCChhhCCccccccccchhhhhhccCCcChhhheeeeEeeCCCCC
Confidence            999999999999975210            012456888999999998763
>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
>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
>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
>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
>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
>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
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* 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 399
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 1e-19
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 2e-13
>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 = 85.0 bits (209), Expect = 1e-19
 Identities = 53/187 (28%), Positives = 86/187 (45%), Gaps = 6/187 (3%)

Query: 144 ILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILA 203
           I+ ++  +L + KP    VH         + G+     +   L  VHRLDR  SG+L++A
Sbjct: 3   IMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVA 62

Query: 204 RNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGD 263
           +  S      +Q+    + K Y+A V G +    + V   +       ++  +SG+ +  
Sbjct: 63  KKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPL------LKNILQSGERIVR 116

Query: 264 TPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH 323
              +GK + T+F         ++V C P+TGRTHQIRVH QY G+PIA D  Y       
Sbjct: 117 VSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDR 176

Query: 324 REGMSAD 330
           +   +  
Sbjct: 177 QLTEAGT 183
>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 ?
Query399
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 99.95
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 99.93
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 98.74
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 98.58
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 98.46
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 97.89
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 96.73
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 96.56
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 96.48
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 96.39
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 96.29
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 95.86
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 95.85
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 95.62
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 92.25
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 92.12
>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=1.7e-46  Score=350.16  Aligned_cols=193  Identities=30%  Similarity=0.371  Sum_probs=158.5

Q ss_pred             eeeccCCCeEEeecCCCcccccCcccccceEEEEeec-ccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchh
Q 015839          143 SILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQA-EHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKV  221 (399)
Q Consensus       143 ~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~-~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v  221 (399)
                      .|||||++|||||||+||+|||+.....+ ++..+.. ......+++|||||++||||||||+|.++++.|+++|+++.+
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~~-~~~~l~~~~~~~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v   80 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM   80 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBCC-HHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCS
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcch-HHHHHHHhCCCCcccceeeeccceeeeeeeeecchHHHHHHHHHHhcccc
Confidence            38999999999999999999997665543 3333332 223355789999999999999999999999999999999999


Q ss_pred             hhhhheeeccccCCCceEEeeeeeecccCCc-cccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEE
Q 015839          222 IKRYIARVNGVFPEGEQVVDVNINYNASAGR-STAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIR  300 (399)
Q Consensus       222 ~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~-~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR  300 (399)
                      .|+|+|+|.|.++...+.++.++..+..... ..+.+       ..+++.|.|.|++++..+..|+|+|+|+||||||||
T Consensus        81 ~K~Y~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~gk~a~t~~~~l~~~~~~slv~~~~~TGRtHQIR  153 (227)
T d1v9ka_          81 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRV-------SQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIR  153 (227)
T ss_dssp             EEEEEEEEESCCCTTCCEECCCEEEEECTTSCEEEEE-------CTTSBCCCEEEEEEEECSSEEEEEEEESSCCTTHHH
T ss_pred             cceecccccCccccccCccccccccccccceeeeeec-------CCCCcccceeehhhhhcCCcEEEEEEeccCchHHHH
Confidence            9999999999999888888888765433222 22222       257899999999999999999999999999999999


Q ss_pred             EEeeeeCcccccCceeeccccc-------cccCCCccccccccccCCCCC
Q 015839          301 VHLQYTGYPIANDMLYLCEHVT-------HREGMSADRAAAYSHHSPPPV  343 (399)
Q Consensus       301 ~hla~lG~PIvGD~~Yg~~~~~-------~~~~~~~~~~~~~~~~lp~~~  343 (399)
                      +||+++||||+||.+||....+       ......++++..+.|.+|.+-
T Consensus       154 vHla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~rl~LHa~~L~f~hP~t~  203 (227)
T d1v9ka_         154 VHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTG  203 (227)
T ss_dssp             HHHHHTTCCBTTCTTTSCHHHHHHHHHTTCCCCSCCEEEEEEEEECTTTC
T ss_pred             HHHhhcCceeccCcccccccccccchhcccCcchHHHHccccEeECCCCC
Confidence            9999999999999999975321       123456788999999998763
>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
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} 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
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} 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
>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