Citrus Sinensis ID: 031054

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------
MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS
ccccccccccccccccccccccEEEcccccccccccEEEEccHHHHHHHccccccccEEEEEEEcccccHHHHHHHHcccEEccEEEcccEEEEccccccccccEEEEEEEccccHHHHHHHHHccccccEEEEEEEEccccccccccccEEEccHHHHHHHHccc
ccccccccEEEEccccccccccEcEccEccccccEEEEEEccHHHHHHHccccccccEEEEEEEEccccHHHHHHHHcccEEccccccccEEEEEEccccccEEEEEEEEEccccHHHHHHHHHHcccEEEEEEEEcccccccccccccccccccHHHHHHHHHcc
MSLFDDYLKSwdkrnpglprprlftvgrldvattgliivtndgdfaqavshpssklQKEYIATIDGAVNKRHLIAISegtviegthctpdvvellppqpdiprpririvvheGRNHEVRELVKNAGlklyslkrlriggfrlpsdlgigmHVELKqsdlklmgwks
MSLFDDYLKswdkrnpglprprlftvgRLDVATTGLIIVTNDGDFAQAvshpssklqKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVellppqpdiprpRIRIVVHegrnhevrelvknaglklyslkRLRIGGFrlpsdlgigmhvelkqsdlklmgwks
MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLppqpdiprpririVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS
*******L**W******LPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHP*SKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELK***********
MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGW**
MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS
*****DYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGW**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS
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 ?
Query166 2.2.26 [Sep-21-2011]
O67444249 Uncharacterized RNA pseud yes no 0.813 0.542 0.369 2e-16
P57369250 Ribosomal large subunit p yes no 0.837 0.556 0.302 3e-15
O66829238 Uncharacterized RNA pseud no no 0.819 0.571 0.321 6e-15
Q9HZ55 386 Ribosomal large subunit p yes no 0.843 0.362 0.333 1e-14
O51155249 Uncharacterized RNA pseud yes no 0.728 0.485 0.307 2e-14
P42395257 Ribosomal large subunit p yes no 0.933 0.603 0.322 3e-14
P35159244 Ribosomal large subunit p yes no 0.680 0.463 0.345 5e-14
Q8PQN3190 Ribosomal large subunit p yes no 0.753 0.657 0.338 2e-13
P0AA46231 Ribosomal small subunit p yes no 0.795 0.571 0.292 4e-13
P0AA43231 Ribosomal small subunit p N/A no 0.795 0.571 0.292 4e-13
>sp|O67444|Y1464_AQUAE Uncharacterized RNA pseudouridine synthase aq_1464 OS=Aquifex aeolicus (strain VF5) GN=aq_1464 PE=3 SV=1 Back     alignment and function desciption
 Score = 85.1 bits (209), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/138 (36%), Positives = 77/138 (55%), Gaps = 3/138 (2%)

Query: 22  RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
           R+F VGRLD  T GL+I+TNDG+ A  + HP  KL K Y+A ++G V+++ L  + +G  
Sbjct: 98  RVFPVGRLDYNTEGLLILTNDGELANRILHPRYKLPKVYLALVEGKVDQKTLKRMKQGIE 157

Query: 82  IEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFR 141
           +E     PD + ++  + +     + I  HEGR H V+  +   G K+  LKR+ IG  +
Sbjct: 158 LEDGFAKPDNIRIV--RYEGKNTLLEITFHEGRKHLVKRFLGAFGHKVKRLKRIAIGPIK 215

Query: 142 LPSDLGIGMHVELKQSDL 159
           L   L  G   EL Q +L
Sbjct: 216 L-GKLSPGKWRELNQGEL 232

Aquifex aeolicus (strain VF5) (taxid: 224324)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|P57369|RLUB_BUCAI Ribosomal large subunit pseudouridine synthase B OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=rluB PE=3 SV=1 Back     alignment and function description
>sp|O66829|Y554_AQUAE Uncharacterized RNA pseudouridine synthase aq_554 OS=Aquifex aeolicus (strain VF5) GN=aq_554 PE=3 SV=1 Back     alignment and function description
>sp|Q9HZ55|RLUB_PSEAE Ribosomal large subunit pseudouridine synthase B OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=rluB PE=3 SV=1 Back     alignment and function description
>sp|O51155|Y129_BORBU Uncharacterized RNA pseudouridine synthase BB_0129 OS=Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) GN=BB_0129 PE=3 SV=1 Back     alignment and function description
>sp|P42395|RLUB_BUCAP Ribosomal large subunit pseudouridine synthase B OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN=rluB PE=3 SV=2 Back     alignment and function description
>sp|P35159|RLUB_BACSU Ribosomal large subunit pseudouridine synthase B OS=Bacillus subtilis (strain 168) GN=rluB PE=1 SV=2 Back     alignment and function description
>sp|Q8PQN3|RLUE_XANAC Ribosomal large subunit pseudouridine synthase E OS=Xanthomonas axonopodis pv. citri (strain 306) GN=rluE PE=3 SV=2 Back     alignment and function description
>sp|P0AA46|RSUA_SHIFL Ribosomal small subunit pseudouridine synthase A OS=Shigella flexneri GN=rsuA PE=3 SV=1 Back     alignment and function description
>sp|P0AA43|RSUA_ECOLI Ribosomal small subunit pseudouridine synthase A OS=Escherichia coli (strain K12) GN=rsuA PE=1 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 ?
Query166
296085982 296 unnamed protein product [Vitis vinifera] 1.0 0.560 0.825 3e-78
225448976 393 PREDICTED: uncharacterized RNA pseudouri 1.0 0.422 0.825 5e-78
224100741 397 predicted protein [Populus trichocarpa] 0.993 0.415 0.806 2e-76
297823807 412 pseudouridine synthase family protein [A 1.0 0.402 0.783 1e-73
449444626 398 PREDICTED: uncharacterized RNA pseudouri 1.0 0.417 0.795 5e-73
30687794 410 suppressor of variegation1 causing pseud 1.0 0.404 0.777 8e-73
359486558 335 PREDICTED: uncharacterized RNA pseudouri 0.933 0.462 0.825 1e-71
356535605 399 PREDICTED: uncharacterized RNA pseudouri 1.0 0.416 0.753 4e-69
388509884 408 unknown [Medicago truncatula] 0.993 0.404 0.721 4e-66
357113998 405 PREDICTED: ribosomal large subunit pseud 0.975 0.4 0.709 4e-63
>gi|296085982|emb|CBI31423.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  295 bits (756), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 137/166 (82%), Positives = 155/166 (93%)

Query: 1   MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEY 60
           + LFDDYLKSW+K+NPG+P+PR+FTVGRLDVATTGLII+TNDGDFAQ +SHPSSKL KEY
Sbjct: 131 LCLFDDYLKSWNKQNPGVPKPRIFTVGRLDVATTGLIILTNDGDFAQKLSHPSSKLSKEY 190

Query: 61  IATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRE 120
           IATIDG VNKRHLIAISEGTVIEG HCTPD VELLPPQP+I +PR+R+VVHEGRNHEVRE
Sbjct: 191 IATIDGVVNKRHLIAISEGTVIEGVHCTPDSVELLPPQPNISKPRLRVVVHEGRNHEVRE 250

Query: 121 LVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS 166
           LVK+AGL+++SLKR+RIGGFRLPSDLG G HVELKQ DLK +GWKS
Sbjct: 251 LVKSAGLQIHSLKRIRIGGFRLPSDLGHGKHVELKQGDLKALGWKS 296

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225448976|ref|XP_002270186.1| PREDICTED: uncharacterized RNA pseudouridine synthase aq_1464 isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224100741|ref|XP_002311995.1| predicted protein [Populus trichocarpa] gi|222851815|gb|EEE89362.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297823807|ref|XP_002879786.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297325625|gb|EFH56045.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449444626|ref|XP_004140075.1| PREDICTED: uncharacterized RNA pseudouridine synthase aq_1464-like [Cucumis sativus] gi|449490423|ref|XP_004158601.1| PREDICTED: uncharacterized RNA pseudouridine synthase aq_1464-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|30687794|ref|NP_181447.2| suppressor of variegation1 causing pseudouridine synthase-like protein [Arabidopsis thaliana] gi|21617894|gb|AAM66944.1| unknown [Arabidopsis thaliana] gi|26450440|dbj|BAC42334.1| unknown protein [Arabidopsis thaliana] gi|330254545|gb|AEC09639.1| suppressor of variegation1 causing pseudouridine synthase-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|359486558|ref|XP_003633453.1| PREDICTED: uncharacterized RNA pseudouridine synthase aq_1464 isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356535605|ref|XP_003536335.1| PREDICTED: uncharacterized RNA pseudouridine synthase aq_1464-like [Glycine max] Back     alignment and taxonomy information
>gi|388509884|gb|AFK43008.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|357113998|ref|XP_003558788.1| PREDICTED: ribosomal large subunit pseudouridine synthase B-like [Brachypodium distachyon] 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 ?
Query166
TAIR|locus:2056108410 SVR1 "SUPPRESSOR OF VARIEGATIO 1.0 0.404 0.722 2e-63
TAIR|locus:210230674 AT3G43340 [Arabidopsis thalian 0.445 1.0 0.648 1.7e-20
TIGR_CMR|GSU_1403247 GSU_1403 "ribosomal large subu 0.813 0.546 0.326 7.7e-16
UNIPROTKB|Q3AAS7241 rluB "Pseudouridine synthase" 0.716 0.493 0.355 1.3e-15
TIGR_CMR|CHY_1938241 CHY_1938 "ribosomal large subu 0.716 0.493 0.355 1.3e-15
TIGR_CMR|DET_0789249 DET_0789 "pseudouridine syntha 0.704 0.469 0.333 4.2e-15
TIGR_CMR|CBU_1059244 CBU_1059 "pseudouridine syntha 0.855 0.581 0.328 1.1e-14
UNIPROTKB|Q9KSS7321 rluB "Ribosomal large subunit 0.843 0.436 0.335 2.3e-14
TIGR_CMR|VC_1179321 VC_1179 "pseudouridine synthas 0.843 0.436 0.335 2.3e-14
TIGR_CMR|CHY_1531231 CHY_1531 "ribosomal small subu 0.825 0.593 0.304 1e-13
TAIR|locus:2056108 SVR1 "SUPPRESSOR OF VARIEGATION 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 647 (232.8 bits), Expect = 2.0e-63, P = 2.0e-63
 Identities = 120/166 (72%), Positives = 140/166 (84%)

Query:     1 MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEY 60
             +SLFD+YL SWDKRNPG P+PRLFTVGRLDVATTGLI+VTNDGDFAQ +SHPSS L KEY
Sbjct:   245 ISLFDEYLSSWDKRNPGTPKPRLFTVGRLDVATTGLIVVTNDGDFAQKLSHPSSSLPKEY 304

Query:    61 IATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRE 120
             I T+ G ++KRHL+AISEGT++EG HC PD VEL+             VVHEGRNHEVRE
Sbjct:   305 ITTVVGDIHKRHLMAISEGTMVEGVHCVPDSVELMPKQHDIPRARLRIVVHEGRNHEVRE 364

Query:   121 LVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWKS 166
             LVKNAGL+++SLKR+RIGGFRLPSDLG+G HVELKQS+LK +GWK+
Sbjct:   365 LVKNAGLEVHSLKRVRIGGFRLPSDLGLGKHVELKQSELKALGWKN 410
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0009451 "RNA modification" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0009982 "pseudouridine synthase activity" evidence=IEA;TAS
GO:0016866 "intramolecular transferase activity" evidence=IEA
GO:0000488 "maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)" evidence=IMP
GO:0000489 "maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)" evidence=IMP
GO:0009501 "amyloplast" evidence=TAS
GO:0032544 "plastid translation" evidence=IMP
TAIR|locus:2102306 AT3G43340 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_1403 GSU_1403 "ribosomal large subunit pseudouridine synthase B" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|Q3AAS7 rluB "Pseudouridine synthase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1938 CHY_1938 "ribosomal large subunit pseudouridine synthase B" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0789 DET_0789 "pseudouridine synthase, RsuA family" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1059 CBU_1059 "pseudouridine synthase family protein" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KSS7 rluB "Ribosomal large subunit pseudouridine synthase B" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_1179 VC_1179 "pseudouridine synthase family 1 protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1531 CHY_1531 "ribosomal small subunit pseudouridine synthase A" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer5.4.990.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query166
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylat 5e-37
cd02870146 cd02870, PseudoU_synth_RsuA_like, Pseudouridine sy 1e-33
cd02553167 cd02553, PseudoU_synth_RsuA, Pseudouridine synthas 9e-33
cd02556167 cd02556, PseudoU_synth_RluB, Pseudouridine synthas 1e-22
TIGR00093128 TIGR00093, TIGR00093, pseudouridine synthase 1e-22
cd02554164 cd02554, PseudoU_synth_RluF, Pseudouridine synthas 7e-22
cd02566168 cd02566, PseudoU_synth_RluE, Pseudouridine synthas 2e-17
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 5e-15
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 6e-15
PRK10839232 PRK10839, PRK10839, 16S rRNA pseudouridylate synth 3e-13
PRK10700289 PRK10700, PRK10700, 23S rRNA pseudouridylate synth 6e-13
cd02555177 cd02555, PSSA_1, Pseudouridine synthase, a subgrou 3e-12
PRK11394217 PRK11394, PRK11394, 23S rRNA pseudouridine synthas 3e-11
PRK10475290 PRK10475, PRK10475, 23S rRNA pseudouridine synthas 4e-08
>gnl|CDD|224108 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
 Score =  127 bits (321), Expect = 5e-37
 Identities = 54/159 (33%), Positives = 83/159 (52%), Gaps = 6/159 (3%)

Query: 5   DDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATI 64
            D L     R     + RLF VGRLD  T GL+++TNDG+ A  + HPSS+++KEY+  +
Sbjct: 88  FDLLPERLPR-----KKRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSEVEKEYLVRV 142

Query: 65  DGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKN 124
           +G V +  L  + +G  ++     P     L  +P      +RI + EGRN +VR + + 
Sbjct: 143 EGPVTEEDLEKLRKGVTLDDGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEA 202

Query: 125 AGLKLYSLKRLRIGGFRLPS-DLGIGMHVELKQSDLKLM 162
            GL++  LKR+RIG   L    L  G   EL   ++  +
Sbjct: 203 VGLEVLRLKRIRIGPLSLGDLPLPPGEWRELTLEEIAQL 241

Length = 248
>gnl|CDD|211347 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases, RsuA subfamily 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|211330 cd02556, PseudoU_synth_RluB, Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>gnl|CDD|232821 TIGR00093, TIGR00093, pseudouridine synthase Back     alignment and domain information
>gnl|CDD|211328 cd02554, PseudoU_synth_RluF, Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>gnl|CDD|211334 cd02566, PseudoU_synth_RluE, Pseudouridine synthase, Escherichia coli RluE 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|236774 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>gnl|CDD|182659 PRK10700, PRK10700, 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>gnl|CDD|211329 cd02555, PSSA_1, Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>gnl|CDD|236698 PRK10475, PRK10475, 23S rRNA pseudouridine synthase F; 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 166
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 100.0
TIGR00093128 pseudouridine synthase. This model identifies pane 100.0
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 100.0
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 100.0
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 100.0
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 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
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 100.0
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 99.97
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 99.97
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 99.97
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 99.96
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 99.96
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 99.96
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 99.96
PRK11112257 tRNA pseudouridine synthase C; Provisional 99.96
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 99.96
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 99.96
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 99.95
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.92
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 99.85
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 98.64
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 98.15
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.53
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 97.51
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.34
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.26
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 97.15
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 97.0
PRK14123305 tRNA pseudouridine synthase B; Provisional 96.99
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 96.78
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 96.74
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 96.72
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 96.69
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 96.65
PRK14124308 tRNA pseudouridine synthase B; Provisional 96.6
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 96.58
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 96.54
PRK03287 298 truB tRNA pseudouridine synthase B; Provisional 96.54
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 96.5
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 96.49
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 96.47
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 96.42
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 96.23
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 96.2
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 95.82
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 95.73
PRK14122 312 tRNA pseudouridine synthase B; Provisional 95.53
KOG2559318 consensus Predicted pseudouridine synthase [Transl 95.3
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 90.52
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 89.89
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information 
Probab=100.00  E-value=5.1e-43  Score=268.20  Aligned_cols=134  Identities=35%  Similarity=0.581  Sum_probs=121.6

Q ss_pred             CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054           21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD  100 (166)
Q Consensus        21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (166)
                      +++++|||||++||||||||||++++++|+++++.++|+|+|+|+|.++++.+..+..++..++++.+++.++++...  
T Consensus        34 ~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~~~~~i~K~Y~a~V~g~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~~~--  111 (167)
T cd02556          34 PRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVTDEQLKSLKKGVELEDGFAGFKSIQLEGGE--  111 (167)
T ss_pred             CceEEcCcCCCCCeeEEEEECCHHHHHHHhCCcCCCCeEEEEEECccCCHHHHHHHHcCCEECCCcCcceEEEEEecC--
Confidence            467999999999999999999999999999999999999999999999988887778888777777778888887542  


Q ss_pred             CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031054          101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ  156 (166)
Q Consensus       101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~  156 (166)
                      .++++++|+|.|||+||||+||+++||||+.|+|++||++.|.++|++|+||+|+|
T Consensus       112 ~~~sll~v~l~tGR~HQIR~~~a~~G~pV~~L~R~~ig~~~l~~~L~~G~~r~l~~  167 (167)
T cd02556         112 GKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRGQWEELPP  167 (167)
T ss_pred             CCcEEEEEEEEeCCCHHHHHHHHHcCCeEeEEEEEEECCcccCCCCCCCceEECCC
Confidence            24689999999999999999999999999999999999999965899999999986

This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>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
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE 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
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu 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
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] 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
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD 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
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like 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
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like 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
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like 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
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional 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
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 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
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query166
1vio_A243 Crystal Structure Of Pseudouridylate Synthase Lengt 1e-12
1ksk_A234 Structure Of Rsua Length = 234 6e-11
3dh3_A290 Crystal Structure Of Rluf In Complex With A 22 Nucl 7e-07
2oml_A189 Crystal Structure Of E. Coli Pseudouridine Synthase 2e-06
2olw_A217 Crystal Structure Of E. Coli Pseudouridine Synthase 3e-06
2gml_A237 Crystal Structure Of Catalytic Domain Of E.Coli Rlu 3e-06
>pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase Length = 243 Back     alignment and structure 
Iteration: 1

 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 8/141 (5%)
Query: 22  RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
           +L + GRLDV TTGL+++T+DG ++  ++ P    +K Y+ T+   V + +  A +EG +
Sbjct: 96  KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGIL 155
Query: 82  IEGTH--CTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKLYSLKRLRIGG 139
           + G      P  +E+L              + EGR H+V+ +    G K+  L R +IG 
Sbjct: 156 LRGEKEPTKPAKLEIL------DDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGD 209
Query: 140 FRLPSDLGIGMHVELKQSDLK 160
             L   L  G +  L QS+++
Sbjct: 210 VVLDESLEEGEYRPLTQSEIE 230
>pdb|1KSK|A Chain A, Structure Of Rsua Length = 234 Back     alignment and structure
>pdb|3DH3|A Chain A, Crystal Structure Of Rluf In Complex With A 22 Nucleotide Rna Substrate Length = 290 Back     alignment and structure
>pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue Length = 189 Back     alignment and structure
>pdb|2OLW|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue Length = 217 Back     alignment and structure
>pdb|2GML|A Chain A, Crystal Structure Of Catalytic Domain Of E.Coli Rluf Length = 237 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 ?
Query166
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 5e-38
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 6e-38
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 9e-38
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 4e-37
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 2e-35
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 1e-34
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Length = 237 Back     alignment and structure
 Score =  128 bits (325), Expect = 5e-38
 Identities = 40/144 (27%), Positives = 69/144 (47%), Gaps = 8/144 (5%)

Query: 18  LPRP-RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAI 76
           +    R+F +GRLD  + GLI +TN GD    +    +  +KEY+ T+D  + +  +  +
Sbjct: 41  VNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGM 100

Query: 77  SEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136
           S G  I GT      V+   P         RI + +G N ++R + ++ G ++  L+R R
Sbjct: 101 SAGVPILGTVTKKCKVKKEAPF------VFRITLVQGLNRQIRRMCEHFGYEVKKLERTR 154

Query: 137 IGGFRLPSDLGIGMHVELKQSDLK 160
           I    L S + +G   +L   +L 
Sbjct: 155 IMNVSL-SGIPLGEWRDLTDDELI 177
>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} Length = 290 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* Length = 234 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 Length = 243 Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189 Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Length = 217 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query166
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 100.0
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 100.0
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 100.0
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 99.97
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 99.97
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 99.96
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 96.8
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 96.67
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 96.59
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 96.46
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 96.33
2aus_C334 Pseudouridine synthase; isomerase, structural prot 96.33
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=2.3e-43  Score=282.14  Aligned_cols=137  Identities=28%  Similarity=0.450  Sum_probs=128.5

Q ss_pred             CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054           21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD  100 (166)
Q Consensus        21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (166)
                      .+++||||||++||||||||||++++++|+++.+.|+|+|+|+|+|.++++.+..+..|+.++++..+++.++++.    
T Consensus        45 ~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~p~~~v~K~Y~a~V~G~~~~~~i~~l~~Gv~l~~~~~~~a~~~~l~----  120 (237)
T 2gml_A           45 KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEA----  120 (237)
T ss_dssp             SCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHHHSCEEEEEEESSCCCHHHHHHHSSCCEETTEECCCCEEEEEE----
T ss_pred             CCeeEecCCCCCCeeEEEEEcCHHHHHHHhCccCCCCEEEEEEEcccCCHHHHHHHHcCeEeCCcccccEEEEEeC----
Confidence            4689999999999999999999999999999988999999999999999988888888998888888889998874    


Q ss_pred             CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhccc
Q 031054          101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGW  164 (166)
Q Consensus       101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~~  164 (166)
                        .++++|+|.|||+||||+||+++||||++|+|++||++.| ++|++|+||+|+++|+..|+.
T Consensus       121 --~s~l~i~L~tGR~HQIRr~~a~lG~pV~~L~R~~iG~l~L-~~L~~G~~R~Lt~~E~~~l~~  181 (237)
T 2gml_A          121 --PFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWRDLTDDELIDLFK  181 (237)
T ss_dssp             --TTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEEEETTEEC-TTCCTTCEEECCHHHHHHHHT
T ss_pred             --CEEEEEEEecCCcHHHHHHHHHcCCCEeeeEEEEECCEec-CCCCCCCEEECCHHHHHHHHH
Confidence              4799999999999999999999999999999999999999 599999999999999998864
>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
>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
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {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
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>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
>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
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Back     alignment and structure
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Back     alignment and structure
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Back     alignment and structure

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 166
d1kska4172 d.265.1.3 (A:60-231) Ribosomal small subunit pseud 4e-22
d1vioa1174 d.265.1.3 (A:58-231) Ribosomal small subunit pseud 4e-16
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Length = 172 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 small subunit pseudouridine 516 synthase RsuA
species: Escherichia coli [TaxId: 562]

 Score = 85.2 bits (210), Expect = 4e-22
 Identities = 38/141 (26%), Positives = 68/141 (48%), Gaps = 4/141 (2%)

Query: 20  RPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEG 79
             +L   GRLD+ TTGL+++T+DG ++  ++ P    +K Y+ T++  V        ++G
Sbjct: 33  AWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKG 92

Query: 80  TVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGG 139
             +           L    P     ++R+ + EGR H+V+ +    G  +  L R RIGG
Sbjct: 93  VQLHNEKDLTKPAVLEVITP----TQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGG 148

Query: 140 FRLPSDLGIGMHVELKQSDLK 160
             L +DL  G +  L + ++ 
Sbjct: 149 ITLDADLAPGEYRPLTEEEIA 169
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Length = 174 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 ?
Query166
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 100.0
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 100.0
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 99.96
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 99.96
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 97.53
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 97.14
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 96.94
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 96.92
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 96.67
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} 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 small subunit pseudouridine 516 synthase RsuA
species: Haemophilus influenzae [TaxId: 727]

Probab=100.00  E-value=1.1e-40  Score=253.39  Aligned_cols=137  Identities=31%  Similarity=0.557  Sum_probs=124.2

Q ss_pred             CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcc--cceeEEEEcCCC
Q 031054           21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTH--CTPDVVELLPPQ   98 (166)
Q Consensus        21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~   98 (166)
                      .++++|||||++||||||||+|+++++.++++...++|+|.+.+.+.++++.+..+..++.++|..  ..++.++..+  
T Consensus        36 ~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~~~~~~~k~y~v~v~~~~~~~~~~~l~~~v~~~g~~~~~~~~~~~~~~--  113 (174)
T d1vioa1          36 GKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILD--  113 (174)
T ss_dssp             GGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSCCCTTHHHHHHHCCCCTTCSSCCCCCEEEECS--
T ss_pred             CceEEEecCChhHhceEEEeecccccccccccccceeeeeeeEEecccchhhHHHHhCCceecCccccceeeeecccc--
Confidence            468999999999999999999999999999999999999999999999999999999998887754  4456666654  


Q ss_pred             CCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhcc
Q 031054           99 PDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMG  163 (166)
Q Consensus        99 ~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~  163 (166)
                          .+.++++|.|||+||||+||+++||||++|+|++||+++|+.+|++|+||+|+++|++.|.
T Consensus       114 ----~~~~~i~l~tGR~hQIR~~~~~~g~pI~~L~Ri~~g~~~L~~~L~~G~~r~l~~~Ei~~ll  174 (174)
T d1vioa1         114 ----DYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV  174 (174)
T ss_dssp             ----SSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHHHTC
T ss_pred             ----CcEEEEEEecccchHHHHHHHHcCCEEEEEEEEEEcccccCCCCCCCCcEECCHHHHHhhC
Confidence                3579999999999999999999999999999999999999447999999999999999873
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {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
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} 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
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure