Citrus Sinensis ID: 026613

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------

MLSSITASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS

cccccccccccccccccHHHHHHHHHcHHHHHHHHccccccEEEEEEEcEEcccccEEEcccccccccccccEEEEEEEccccccccccEEEEEEEEEccccEEEEEEEcccccHHHHHHHHcccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccEEEEEEccccHHHHHHHHHHcc

cccccccccEEEEEcccccEEEEEEccHHHHHHHHcccccEEEEEEEEccccccccEEEcccccccccccccEEEEEEEccccccccccEEEEEEEEcccccEEEEEEEcccccccEEEEEHHHHcccccccccccccccEccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHccccccccccEEEEcccccccccccEEEEEccccHHHHHHHHHHcc

MLSSITASHVYEKCIAVSSGIITVErvmykdndneKRILQRWYWALVVgtprcskgvisaplgkvvvdngksdritvvnndqimSAQHAVTRYqvikpschgytwlklspltgrkhqlRVHCAevlgtpivgdykygwqthrkwkqfhpsdlskdsneeipkektlhfgldlesgsilekqprlhlhckemtlpnvSQAIQKVQLssgcdvskletlklvaplpshmqrswdvlns

mlssitashvyekciavssgiitvERVMYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQfhpsdlskdsneeIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLklvaplpshmqrswdvlns

******ASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQF*******************HFGLDLE**SILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVA***************

***SITASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDR**********SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS

***SITASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		236	2.2.26 [Sep-21-2011]
Q9LT72		477	RNA pseudourine synthase	yes	no	0.813	0.402	0.590	1e-58
Q0J4D4		475	RNA pseudourine synthase	yes	no	0.826	0.410	0.475	1e-51
Q5XET6		478	RNA pseudourine synthase	no	no	0.809	0.399	0.46	5e-50
Q69K07		448	RNA pseudourine synthase	no	no	0.360	0.189	0.517	3e-19
Q28C59		324	RNA pseudouridylate synth	yes	no	0.618	0.450	0.307	6e-13
Q4QQT0		377	RNA pseudouridylate synth	yes	no	0.686	0.429	0.287	3e-12
Q68XB2		303	Ribosomal large subunit p	yes	no	0.538	0.419	0.293	3e-11
Q96CM3		377	RNA pseudouridylate synth	yes	no	0.593	0.371	0.288	6e-11
Q6DBR0		358	RNA pseudouridylate synth	yes	no	0.559	0.368	0.327	7e-11
O66114		219	Uncharacterized RNA pseud	no	no	0.389	0.420	0.363	1e-09

>sp\|Q9LT72\|PUS4_ARATH RNA pseudourine synthase 4, mitochondrial OS=Arabidopsis thaliana GN=At3g19440 PE=2 SV=1	Back alignment and function desciption

 Score =  226 bits (575), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 117/198 (59%), Positives = 152/198 (76%), Gaps = 6/198 (3%)

Query: 39  LQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKP 98
           L+R Y ALV+G P   +G ISAPL KVVVD+GKS+RITV +N +++S QHA+T Y+VI+ 
Sbjct: 278 LKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNGELVSTQHAITEYRVIES 337

Query: 99  SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNE 158
           S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H+  + F    +S ++N 
Sbjct: 338 SPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHKAREPF----VSSENNP 393

Query: 159 EIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLK 218
              K+ +  FGLDL+ G +  KQP LHLH K++ LPN+SQ ++K+Q+SS  D+S L++LK
Sbjct: 394 T--KQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLEKMQVSSDSDISDLDSLK 451

Query: 219 LVAPLPSHMQRSWDVLNS 236
             APLPSHMQ S+++L S
Sbjct: 452 FDAPLPSHMQLSFNLLKS 469

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp\|Q0J4D4\|PUS3_ORYSJ RNA pseudourine synthase 3, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0520100 PE=2 SV=1	Back alignment and function description

>sp\|Q5XET6\|PUS3_ARATH RNA pseudourine synthase 3, mitochondrial OS=Arabidopsis thaliana GN=At1g78910 PE=2 SV=1	Back alignment and function description

>sp\|Q69K07\|PUS4_ORYSJ RNA pseudourine synthase 4, mitochondrial OS=Oryza sativa subsp. japonica GN=Os09g0103500 PE=2 SV=1	Back alignment and function description

>sp\|Q28C59\|RUSD4_XENTR RNA pseudouridylate synthase domain-containing protein 4 OS=Xenopus tropicalis GN=rpusd4 PE=2 SV=1	Back alignment and function description

>sp\|Q4QQT0\|RUSD4_RAT RNA pseudouridylate synthase domain-containing protein 4 OS=Rattus norvegicus GN=Rpusd4 PE=2 SV=1	Back alignment and function description

>sp\|Q68XB2\|RLUC_RICTY Ribosomal large subunit pseudouridine synthase C OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=rluC PE=3 SV=1	Back alignment and function description

>sp\|Q96CM3\|RUSD4_HUMAN RNA pseudouridylate synthase domain-containing protein 4 OS=Homo sapiens GN=RPUSD4 PE=2 SV=1	Back alignment and function description

>sp\|Q6DBR0\|RUSD4_DANRE RNA pseudouridylate synthase domain-containing protein 4 OS=Danio rerio GN=rpusd4 PE=2 SV=1	Back alignment and function description

>sp\|O66114\|Y505_ZYMMO Uncharacterized RNA pseudouridine synthase ZMO0505 OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=ZMO0505 PE=3 SV=2	Back alignment and function description

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
Query		236
225428918		476	PREDICTED: RNA pseudourine synthase 4, m	0.872	0.432	0.733	9e-88
255555275		536	ribosomal pseudouridine synthase, putati	0.868	0.382	0.694	1e-77
224105621		324	predicted protein [Populus trichocarpa]	0.898	0.654	0.666	1e-77
356495831		427	PREDICTED: RNA pseudourine synthase 4, m	0.864	0.477	0.668	4e-76
358343831		430	RNA pseudourine synthase [Medicago trunc	0.889	0.488	0.652	8e-74
449438639		466	PREDICTED: RNA pseudourine synthase 4, m	0.830	0.420	0.617	1e-66
449526979		471	PREDICTED: RNA pseudourine synthase 4, m	0.826	0.414	0.615	2e-66
357154257		465	PREDICTED: RNA pseudourine synthase 4, m	0.851	0.432	0.556	2e-58
297830600		477	pseudouridine synthase family protein [A	0.813	0.402	0.595	1e-57
326504872		472	predicted protein [Hordeum vulgare subsp	0.851	0.425	0.551	3e-57

>gi\|225428918\|ref\|XP_002282614.1\| PREDICTED: RNA pseudourine synthase 4, mitochondrial [Vitis vinifera] gi\|296090438\|emb\|CBI40257.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  328 bits (842), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 151/206 (73%), Positives = 179/206 (86%)

Query: 31  DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAV 90
           D D +KRILQR YWALV+G+PR  +G+ISAPLGKVVVD+GKS+RIT+V+N Q MS+QHA+
Sbjct: 271 DIDTKKRILQRRYWALVIGSPRRPRGLISAPLGKVVVDDGKSERITIVDNVQTMSSQHAI 330

Query: 91  TRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPS 150
           T Y+VIK SCHGYTWL+LSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ HRKWKQ   S
Sbjct: 331 TEYRVIKSSCHGYTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHRKWKQLFQS 390

Query: 151 DLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCD 210
           ++ K+ +E +   KT  FGLDLESGSIL+KQP LHLHCK+M LPNVS A+Q +QLS+ CD
Sbjct: 391 NIEKNLDENLSNRKTHPFGLDLESGSILDKQPHLHLHCKQMVLPNVSLALQNLQLSAECD 450

Query: 211 VSKLETLKLVAPLPSHMQRSWDVLNS 236
           +S+LE+L+ VAPLPSHMQRSWD+LNS
Sbjct: 451 LSELESLEFVAPLPSHMQRSWDILNS 476

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255555275\|ref\|XP_002518674.1\| ribosomal pseudouridine synthase, putative [Ricinus communis] gi\|223542055\|gb\|EEF43599.1\| ribosomal pseudouridine synthase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224105621\|ref\|XP_002313876.1\| predicted protein [Populus trichocarpa] gi\|222850284\|gb\|EEE87831.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356495831\|ref\|XP_003516775.1\| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Glycine max]	Back alignment and taxonomy information

>gi\|358343831\|ref\|XP_003635999.1\| RNA pseudourine synthase [Medicago truncatula] gi\|355501934\|gb\|AES83137.1\| RNA pseudourine synthase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449438639\|ref\|XP_004137095.1\| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449526979\|ref\|XP_004170490.1\| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357154257\|ref\|XP_003576723.1\| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Brachypodium distachyon]	Back alignment and taxonomy information

>gi\|297830600\|ref\|XP_002883182.1\| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi\|297329022\|gb\|EFH59441.1\| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|326504872\|dbj\|BAK06727.1\| predicted protein [Hordeum vulgare subsp. vulgare]	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
Query		236
TAIR\|locus:2090689		477	AT3G19440 [Arabidopsis thalian	0.813	0.402	0.590	3.5e-59
TAIR\|locus:2037593		478	AT1G78910 [Arabidopsis thalian	0.809	0.399	0.465	1.4e-48
DICTYBASE\|DDB_G0285543		718	DDB_G0285543 [Dictyostelium di	0.444	0.146	0.444	9.4e-19
TIGR_CMR\|SPO_0516		347	SPO_0516 "ribosomal large subu	0.423	0.288	0.358	9.2e-12
UNIPROTKB\|E1BYI6		354	RPUSD4 "Uncharacterized protei	0.559	0.372	0.311	2e-11
UNIPROTKB\|F1S6H1		376	LOC100737111 "Uncharacterized	0.622	0.390	0.308	6e-11
TIGR_CMR\|CHY_1505		305	CHY_1505 "ribosomal large subu	0.411	0.318	0.383	8e-11
RGD\|1311268		377	Rpusd4 "RNA pseudouridylate sy	0.631	0.395	0.304	3.8e-10
TIGR_CMR\|NSE_0556		305	NSE_0556 "ribosomal large subu	0.398	0.308	0.366	4.1e-10
MGI\|MGI:1919239		377	Rpusd4 "RNA pseudouridylate sy	0.631	0.395	0.292	2.6e-09

TAIR\|locus:2090689 AT3G19440 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 117/198 (59%), Positives = 152/198 (76%)

Query:    39 LQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKP 98
             L+R Y ALV+G P   +G ISAPL KVVVD+GKS+RITV +N +++S QHA+T Y+VI+ 
Sbjct:   278 LKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNGELVSTQHAITEYRVIES 337

Query:    99 SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNE 158
             S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H+  + F    +S ++N 
Sbjct:   338 SPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHKAREPF----VSSENNP 393

Query:   159 EIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLK 218
                K+ +  FGLDL+ G +  KQP LHLH K++ LPN+SQ ++K+Q+SS  D+S L++LK
Sbjct:   394 T--KQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLEKMQVSSDSDISDLDSLK 451

Query:   219 LVAPLPSHMQRSWDVLNS 236
               APLPSHMQ S+++L S
Sbjct:   452 FDAPLPSHMQLSFNLLKS 469

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS

GO:0019243 "methylglyoxal catabolic process to D-lactate" evidence=RCA

TAIR\|locus:2037593 AT1G78910 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0285543 DDB_G0285543 [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_0516 SPO_0516 "ribosomal large subunit pseudouridine synthase C" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BYI6 RPUSD4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S6H1 LOC100737111 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_1505 CHY_1505 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

RGD\|1311268 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

TIGR_CMR\|NSE_0556 NSE_0556 "ribosomal large subunit pseudouridine synthase C" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]	Back alignment and assigned GO terms

MGI\|MGI:1919239 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

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 Level	EC number	Confidence of Prediction
3rd Layer	5.4.99	LOW CONFIDENCE prediction!

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
Query		236
cd02869		185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	1e-26
COG0564		289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	5e-26
TIGR00005		299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	1e-21
pfam00849		149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	1e-11
cd02563		223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	8e-10
PRK11025		317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	4e-08
cd02550		154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	5e-08
PRK11112		257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	5e-08
PRK10158		219	PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy	2e-07
cd02558		246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	3e-07
cd02557		213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	1e-06
PRK11180		325	PRK11180, rluD, 23S rRNA pseudouridine synthase D;	5e-05

>gnl\|CDD\|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family	Back alignment and domain information

 Score =  100 bits (252), Expect = 1e-26
 Identities = 37/103 (35%), Positives = 55/103 (53%), Gaps = 9/103 (8%)

Query: 35  EKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQ 94
           ++R +++ Y ALV G P   +G I APLG+          ++          + A+T Y+
Sbjct: 71  KERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS-------EDGKPAITHYK 123

Query: 95  VIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
           V++      T ++L   TGR HQ+RVH A  +G PIVGD KYG
Sbjct: 124 VLERFG-NVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYG 164

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 185

>gnl\|CDD\|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family	Back alignment and domain information

>gnl\|CDD\|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase	Back alignment and domain information

>gnl\|CDD\|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C	Back alignment and domain information

>gnl\|CDD\|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional	Back alignment and domain information

>gnl\|CDD\|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family	Back alignment and domain information

>gnl\|CDD\|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional	Back alignment and domain information

>gnl\|CDD\|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional	Back alignment and domain information

>gnl\|CDD\|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family	Back alignment and domain information

>gnl\|CDD\|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2	Back alignment and domain information

>gnl\|CDD\|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		236
PRK11025		317	23S rRNA pseudouridylate synthase C; Provisional	100.0
COG0564		289	RluA Pseudouridylate synthases, 23S RNA-specific [	100.0
PRK11112		257	tRNA pseudouridine synthase C; Provisional	100.0
PRK11180		325	rluD 23S rRNA pseudouridine synthase D; Provisiona	100.0
TIGR00005		299	rluA_subfam pseudouridine synthase, RluA family. m	100.0
TIGR01621		217	RluA-like pseudouridine synthase Rlu family protei	100.0
cd02563		223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	100.0
PRK10158		219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	100.0
cd02558		246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	100.0
cd02557		213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	100.0
cd02869		185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	100.0
cd02550		154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.95
TIGR00093		128	pseudouridine synthase. This model identifies pane	99.94
KOG1919		371	consensus RNA pseudouridylate synthases [RNA proce	99.94
cd02870		146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.93
PF00849		164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.93
cd02556		167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.93
cd02553		167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.92
PRK10839		232	16S rRNA pseudouridylate synthase A; Provisional	99.92
cd02566		168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.9
cd02555		177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.88
PRK11394		217	23S rRNA pseudouridine synthase E; Provisional	99.87
PRK10700		289	23S rRNA pseudouridylate synthase B; Provisional	99.77
cd02554		164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.74
PRK10475		290	23S rRNA pseudouridine synthase F; Provisional	99.67
COG1187		248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.65
cd02868		226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	97.92
cd01291		87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	96.68

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional	Back alignment and domain information

Probab=100.00  E-value=2.7e-44  Score=318.79  Aligned_cols=174  Identities=28%  Similarity=0.398  Sum_probs=140.5

Q ss_pred             ccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613            8 SHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI   83 (236)
Q Consensus         8 ~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~   83 (236)
                      +++|||||++||||||||||..+    +.+|.++.|+|+|+|+|.|.++...|+|+.||.+.....+  .++....    
T Consensus       137 ~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~--~~~~~~~----  210 (317)
T PRK11025        137 LELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSG--ERIVRVS----  210 (317)
T ss_pred             CceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccCC--ceEEecC----
Confidence            57899999999999999999543    3367899999999999999998778999999986532111  1221111    


Q ss_pred             ccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCcccccc
Q 026613           84 MSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKE  163 (236)
Q Consensus        84 ~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (236)
                      .+++.|.|+|++++.. .++|||+|+|.||||||||+|||+ +||||+||.+||.....               ..+.  
T Consensus       211 ~~gk~a~T~~~~l~~~-~~~sLv~~~~~TGRtHQIRvhla~-lG~PIlGD~~Yg~~~~~---------------~~~~--  271 (317)
T PRK11025        211 QEGKPSETRFKVEERY-AFATLVRASPVTGRTHQIRVHTQY-AGHPIAFDDRYGDREFD---------------QQLT--  271 (317)
T ss_pred             CCCccceEEEEEeEEc-CCcEEEEEEeCCCCHHHHHHHHHH-CCCCEECCcccCCcccc---------------hhhh--
Confidence            2479999999999987 789999999999999999999997 99999999999964210               0000  


Q ss_pred             cccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHhc
Q 026613          164 KTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  235 (236)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l~  235 (236)
                                    .....+++|||++|.|+||               .+++.+.|+||+|++|..+++.|.
T Consensus       272 --------------~~~~~r~~LHa~~l~f~~P---------------~~~~~~~~~aplP~~~~~~l~~l~  314 (317)
T PRK11025        272 --------------GTGLNRLFLHAAALKFTHP---------------GTGEVMRIEAPLDEQLKRCLQKLR  314 (317)
T ss_pred             --------------ccCCcchhhhcCcceeeCC---------------CCCCeEEEEcCCCHHHHHHHHHHh
Confidence                          0013579999999999998               689999999999999999988764

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK11112 tRNA pseudouridine synthase C; Provisional	Back alignment and domain information

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional	Back alignment and domain information

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family	Back alignment and domain information

>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621	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

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; 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

>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family	Back alignment and domain information

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family	Back alignment and domain information

>TIGR00093 pseudouridine synthase	Back alignment and domain information

>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]	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

>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family	Back alignment and domain information

>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like	Back alignment and domain information

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like	Back alignment and domain information

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional	Back alignment and domain information

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE	Back alignment and domain information

>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family	Back alignment and domain information

>PRK11394 23S rRNA pseudouridine synthase E; Provisional	Back alignment and domain information

>PRK10700 23S rRNA pseudouridylate synthase B; 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

>PRK10475 23S rRNA pseudouridine synthase F; 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

>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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		236
2i82_A		217	Crystal Structure Of Pseudouridine Synthase Rlua: I		3e-06
1xpi_A		231	Crystal Structure Of The Catalytic Domain Of E. Col		7e-06
1v9k_A		228	The Crystal Structure Of The Catalytic Domain Of Ps		1e-05

>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

Iteration: 1

Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust. Identities = 39/134 (29%), Positives = 59/134 (44%), Gaps = 30/134 (22%) Query: 17 VSSGIITVERVMYKDNDNEKRILQR----WYWALVVGTPRCSKGVISAPL---------G 63 +SG+I V + + +++ +R Y A V G P ++G++ PL Sbjct: 64 ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQ 123 Query: 64 KVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCA 123 KV + GK A T Y+V++ + + L P+TGR HQLRVH Sbjct: 124 KVCYETGKP----------------AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXL 167 Query: 124 EVLGTPIVGDYKYG 137 LG PI+GD Y Sbjct: 168 -ALGHPILGDRFYA 180

PyMOL of 2i82

>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231

Back alignment and structure

>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

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		236
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	2e-25
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	1e-23
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	9e-17

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217	Back alignment and structure

 Score = 98.0 bits (245), Expect = 2e-25
 Identities = 35/112 (31%), Positives = 50/112 (44%), Gaps = 26/112 (23%)

Query: 35  EKRILQRWYWALVVGTPRCSKGVISAPLG---------KVVVDNGKSDRITVVNNDQIMS 85
            +R  ++ Y A V G P  ++G++  PL          KV  + GK              
Sbjct: 86  REREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGK-------------- 131

Query: 86  AQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
              A T Y+V++ +      + L P+TGR HQLRVH    LG PI+GD  Y 
Sbjct: 132 --PAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLA-LGHPILGDRFYA 180

PyMOL of 2i82

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Length = 228	Back alignment and structure

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		236
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	100.0
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	100.0
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	100.0
2oml_A		189	Ribosomal large subunit pseudouridine synthase E;	99.97
2olw_A		217	Ribosomal large subunit pseudouridine synthase E;	99.96
1ksk_A		234	Ribosomal small subunit pseudouridine synthase A;	99.94
1vio_A		243	Ribosomal small subunit pseudouridine synthase A;	99.93
2gml_A		237	Ribosomal large subunit pseudouridine synthase F;	99.89
3dh3_A		290	Ribosomal large subunit pseudouridine synthase F;	99.85

>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

Probab=100.00  E-value=1.4e-44  Score=305.73  Aligned_cols=177  Identities=24%  Similarity=0.351  Sum_probs=143.0

Q ss_pred             cccccccCCCCcceeeeeecccchh----hhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613            7 ASHVYEKCIAVSSGIITVERVMYKD----NDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ   82 (236)
Q Consensus         7 ~~~~vhRLD~~TSGllLlak~~~~~----~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~   82 (236)
                      .+++|||||++||||||||||....    .+|+++.|+|+|+|+|.|.+++++++|+.||.+.....+. .++.+ .   
T Consensus        45 ~~~~VhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~g~-~~~~~-~---  119 (228)
T 1v9k_A           45 FLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE-RIVRV-S---  119 (228)
T ss_dssp             CCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSC-EEEEE-C---
T ss_pred             ccceEecCCCCCeEEEEEEeCHHHHHHHHHHHHhCCeeEEEEEEEecccCCCCCEEeCceeccCCCCCc-eEEEE-C---
Confidence            4678999999999999999995432    3578899999999999999988889999999876433321 22333 2   


Q ss_pred             cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccccc
Q 026613           83 IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPK  162 (236)
Q Consensus        83 ~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~  162 (236)
                       .+++.|.|.|++++.. .++++++|+|.|||+||||+||++ +||||+||.+||....+.               .+..
T Consensus       120 -~~gk~a~t~~~vl~~~-~~~slv~~~l~TGR~HQIR~hla~-lG~PI~gD~~YG~~~~~~---------------~~~~  181 (228)
T 1v9k_A          120 -QEGKPSETRFKVEERY-AFATLVRCSPVTGRTHQIRVHTQY-AGHPIAFDDRYGDREFDR---------------QLTE  181 (228)
T ss_dssp             -TTSBCCCEEEEEEEEC-SSEEEEEEEESSCCTTHHHHHHHH-TTCCBTTCTTTSCHHHHH---------------HHHH
T ss_pred             -CCCcEEEEEEEEEEEc-CCeEEEEEEECCCCchHHHHHHHH-CCCcEecCcccCCccccc---------------hhhc
Confidence             2479999999999997 779999999999999999999997 999999999999742100               0000


Q ss_pred             ccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHhc
Q 026613          163 EKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  235 (236)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l~  235 (236)
                            .        .....|++|||++|.|+||               .+++.++|+||+|++|..+++.|+
T Consensus       182 ------~--------~~~~~r~~LHa~~l~f~hP---------------~t~~~~~~~aplp~~~~~~l~~l~  225 (228)
T 1v9k_A          182 ------A--------GTGLNRLFLHAAALKFTHP---------------GTGEVMRIEAPMDEGLKRCLQKMR  225 (228)
T ss_dssp             ------T--------TCCCCSCCEEEEEEEEECT---------------TTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             ------c--------cCCCCChhhccceeEeeCC---------------CCCCEEEEEeCCcHHHHHHHHHhh
Confidence                  0        0014689999999999998               589999999999999999998875

PyMOL of 1v9k

>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

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}	Back alignment and structure

>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}	Back alignment and structure

>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}	Back alignment and structure

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*	Back alignment and structure

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5	Back alignment and structure

>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}	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

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		236
d1v9ka_		227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	7e-08
d1v9fa_		250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	5e-05

>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 = 49.2 bits (116), Expect = 7e-08
 Identities = 43/200 (21%), Positives = 76/200 (38%), Gaps = 52/200 (26%)

Query: 35  EKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQ 94
            ++ +Q+ Y ALV G  +     + APL K ++ +G+  RI  V+ +     + + TR++
Sbjct: 76  REKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE--RIVRVSQE----GKPSETRFK 129

Query: 95  VIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSK 154
           V +      T ++ SP+TGR HQ+RVH     G PI  D +YG +   +      + L  
Sbjct: 130 VEE-RYAFATLVRCSPVTGRTHQIRVHTQYA-GHPIAFDDRYGDREFDRQLTEAGTGL-- 185

Query: 155 DSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKL 214
                                       RL LH   +                       
Sbjct: 186 ---------------------------NRLFLHAAALKFT---------------HPGTG 203

Query: 215 ETLKLVAPLPSHMQRSWDVL 234
           E +++ AP+   ++R    +
Sbjct: 204 EVMRIEAPMDEGLKRCLQKM 223

PyMOL of d1v9ka_

>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
Query		236
d1v9ka_		227	Ribosomal large subunit pseudouridine synthase C,	100.0
d1v9fa_		250	Ribosomal large subunit pseudouridine synthase D,	100.0
d1vioa1		174	Ribosomal small subunit pseudouridine 516 synthase	99.81
d1kska4		172	Ribosomal small subunit pseudouridine 516 synthase	99.74

>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=2.5e-47  Score=320.35  Aligned_cols=178  Identities=25%  Similarity=0.369  Sum_probs=145.6

Q ss_pred             ccccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCC
Q 026613            6 TASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND   81 (236)
Q Consensus         6 ~~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~   81 (236)
                      ...++|||||++||||||||||...    +.+|+++.+.|+|+|+|.|.++...++++.|+.......+  .++....  
T Consensus        43 ~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~a~~~G~~~~~~~~~~~~~~~~~~~~~--~~~~~~~--  118 (227)
T d1v9ka_          43 RFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSG--ERIVRVS--  118 (227)
T ss_dssp             SCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTS--CEEEEEC--
T ss_pred             cccceeeeccceeeeeeeeecchHHHHHHHHHHhcccccceecccccCccccccCccccccccccccce--eeeeecC--
Confidence            3467999999999999999999543    3368999999999999999999888999999877543222  1222222  


Q ss_pred             ccccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCcccc
Q 026613           82 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIP  161 (236)
Q Consensus        82 ~~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~  161 (236)
                        .+++.+.|.|++++.. .+++|++|+|.||||||||+|||+ +||||+||.+||....+.               .+.
T Consensus       119 --~~gk~a~t~~~~l~~~-~~~slv~~~~~TGRtHQIRvHla~-lG~PIvGD~~Yg~~~~~~---------------~~~  179 (227)
T d1v9ka_         119 --QEGKPSETRFKVEERY-AFATLVRCSPVTGRTHQIRVHTQY-AGHPIAFDDRYGDREFDR---------------QLT  179 (227)
T ss_dssp             --TTSBCCCEEEEEEEEC-SSEEEEEEEESSCCTTHHHHHHHH-TTCCBTTCTTTSCHHHHH---------------HHH
T ss_pred             --CCCcccceeehhhhhc-CCcEEEEEEeccCchHHHHHHHhh-cCceeccCcccccccccc---------------cch
Confidence              2489999999999998 899999999999999999999997 999999999999764211               000


Q ss_pred             cccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHhc
Q 026613          162 KEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  235 (236)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l~  235 (236)
                      .              .....+|++|||++|+|+||               .+++.++|+||+|++|.++|+.|+
T Consensus       180 ~--------------~~~~~~rl~LHa~~L~f~hP---------------~t~~~~~~~aplP~~f~~~l~~Lk  224 (227)
T d1v9ka_         180 E--------------AGTGLNRLFLHAAALKFTHP---------------GTGEVMRIEAPMDEGLKRCLQKMR  224 (227)
T ss_dssp             H--------------TTCCCCSCCEEEEEEEEECT---------------TTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             h--------------cccCcchHHHHccccEeECC---------------CCCCEEEEEecCcHHHHHHHHHHH
Confidence            0              00115689999999999998               689999999999999999999986

PyMOL of d1v9ka_

>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