Citrus Sinensis ID: 011530

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480---

MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNVGSGV

cccccccccccccccccccHHHHHHHHHHccccccccccccccEEccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccEEEEEccccccccEEEcccccccHHHHHHHHHcccEEEEEccccccccccHHHHHHHHcccccccccHHHHHccccEEEcccccEEcccccEEccccEEEEEcccccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHHccccccccccccccccccEEEEEEEcHHHHHHHHHHHHccccccEEEEEEEEccccccEEEEcccccccccccccccEEEEEEEEccccccccccccccEEEEEEccccccccEEEEEEEccccHHHHHHHHHHHcccccccccccccHHHccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccEEEEcccccccccccccccc

cccccHHHHHcccccccccHHHHHHHHHHcccHHccccccccccEEEEEcccccccccccccEccHHHHHHHcccccccccccccHccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHcccEEEEEccccccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHccEEEEEcccccEEEEcccEEEEEEcccccccccccccccEEEEEcccEEEEEcccccccccccccccHHHHHHHHHHcccccccccccHccccccEEEEEEccHHHHHHHHHHHHHccEEEEEEEEEEccccccEEEEEccccEEcccEEEccccccEEEEEccccccccccccccEEEEEEccccccccEEEEEccccccccHHHHHHHHHcccccccccccccccHccccccccccccccccccHHHHHHHHHHHHHHccccccccEEccccccEEEcccccEEEEccccEEEEEEcccccc

MSSVSFSSIftnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFsssnrnfvceswkrhvfthtdTAAIaaattpssygypeyhrllpcpsqncpprvehlvvseggpVLEYICRelnlpplfvaDLIHFGAVYYAlvcpkppltatpeqmrvfkevtdpsvlskrssikgkTVREAQKTFRITHVDQIVEAGtylrvhvhpkrfprcydidwnsrIIAVTEshvvldkpagtsvggttdniEESCATFASRalglttplrtthqidnctegCVVLARTQEYCSIFHRKIREKKVKKLYLALttaplpvgimthymrpiniaprlvsegWYLCQLEvmeckkvpwpdatvgkaysiedcgwpsrdyaYECKIKLLTGRTHQVRAQLAAcgapivgdsmympAAIAqlsspglnpfgkcqkeyasdddkEMAVIEWISqhgmepsvaIGLQAchiswddgeccyearspwwrckcnvgsgv

MSSVSFSSIFtnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEqmrvfkevtdpsvlskrssikgktvreaqktfrithvdqiVEAGtylrvhvhpkrfPRCYDIDWNSRIIAVTeshvvldkpagtsvggttdNIEESCATFASRALGlttplrtthqidnCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEarspwwrckcnvgsgv

MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFthtdtaaiaaattPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNVGSGV

***************SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLT*******************************AQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEY*****KEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNV****

******S*IFTNNGRSLGAPVSLLRTLASTHA***********************CESWKRHVFTHTDT***********YGYPEYHRLLPCPSQ************EGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTD*********************FRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLV**********VM****VP***ATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI*****P****FGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNV****

********IFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNVGSGV

*****FSSIFTNNGRSLGAPVSLLRTLASTHASCH*NIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWRCKCNVGS**

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		483	2.2.26 [Sep-21-2011]
Q9SVS0		472	RNA pseudourine synthase	yes	no	0.954	0.976	0.656	0.0
A3BN26		477	RNA pseudourine synthase	yes	no	0.821	0.832	0.657	1e-155
P57430		314	Ribosomal large subunit p	yes	no	0.349	0.538	0.258	4e-10
Q8K9J8		314	Ribosomal large subunit p	yes	no	0.325	0.5	0.265	8e-09
P59835		320	Ribosomal large subunit p	yes	no	0.343	0.518	0.309	4e-08
Q8PHN2		331	Ribosomal large subunit p	yes	no	0.331	0.483	0.287	1e-07
Q89AH2		315	Ribosomal large subunit p	yes	no	0.343	0.526	0.275	2e-07
Q9CK02		219	Ribosomal large subunit p	yes	no	0.360	0.794	0.248	3e-07
P54604		302	Uncharacterized RNA pseud	yes	no	0.306	0.490	0.247	5e-07
P43930		224	Uncharacterized RNA pseud	yes	no	0.312	0.674	0.264	6e-07

>sp\|Q9SVS0\|PUS6_ARATH RNA pseudourine synthase 6, chloroplastic OS=Arabidopsis thaliana GN=At4g21770 PE=2 SV=1	Back alignment and function desciption

 Score =  642 bits (1656), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/477 (65%), Positives = 377/477 (79%), Gaps = 16/477 (3%)

Query: 7   SSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNV-VLSFSSSNRNFVCESWKRHVFT 65
           S   T   R+L APVSLLRTLAST  +    +++SN     F SS + F C S       
Sbjct: 3   SPALTGGYRNLTAPVSLLRTLASTRVTT--PLFRSNKHSPRFISSPKRFTCLS-----LL 55

Query: 66  HTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVL-EYICRELNLPP 124
            TD+      ++ S+ GY EY+RL+PCP+ N PPR+EH+VV E   ++ E+I ++L+LPP
Sbjct: 56  KTDSQNQTTLSSSSNSGYHEYNRLMPCPAYNLPPRIEHMVVLEDDVLVSEFISKQLDLPP 115

Query: 125 LFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTF 184
           L+VADLI FGAV+YALVCPKPP TATPE++ +F+EVT PSVL KRSSIKGKTVREAQKTF
Sbjct: 116 LYVADLIRFGAVHYALVCPKPPPTATPEEIILFEEVTSPSVLKKRSSIKGKTVREAQKTF 175

Query: 185 RITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDN 244
           R+TH +Q  EAGTYLRVHVHPKR PRCY+IDW SRI+AVT+S+V+LDKPAGT+VGGTTDN
Sbjct: 176 RVTHTNQYAEAGTYLRVHVHPKRSPRCYEIDWKSRIVAVTDSYVILDKPAGTTVGGTTDN 235

Query: 245 IEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304
           IEESCATFASRAL L  PL+TTHQIDNCTEGCVV ART+EYCS+FH KIR K+VKKLY A
Sbjct: 236 IEESCATFASRALDLPEPLKTTHQIDNCTEGCVVFARTKEYCSVFHTKIRNKEVKKLYRA 295

Query: 305 LTTAPLPVGIMTHYMRPINIAPRLVSE----GWYLCQLEVMECKKVPWPDATVGKAYSIE 360
           L  APLP+GI++HYMRP N+APRLV+E    GW+LCQLEV+ECKK+PWPDA   K + IE
Sbjct: 296 LAAAPLPIGIISHYMRPKNMAPRLVAEDSIQGWHLCQLEVLECKKIPWPDAATEKKHDIE 355

Query: 361 DCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGK 420
           DCGW S+++AYEC I LLTG+THQ+RAQLAACGAP+VGDSMYMPAAIA++ +P  NP+GK
Sbjct: 356 DCGWTSKEFAYECTINLLTGKTHQIRAQLAACGAPLVGDSMYMPAAIAEMGNPDTNPYGK 415

Query: 421 CQKEYASDDD-KEMAVIEWISQHGMEPSVAIGLQACHISW--DDGECCYEARSPWWR 474
            +K Y  +++ KE AV EWI +HG EP V IGLQAC ISW  DDGE  YEA +PWWR
Sbjct: 416 AKKHYTMEENQKETAVAEWIDRHGKEPRVGIGLQACQISWDDDDGEHFYEAGTPWWR 472

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

>sp\|A3BN26\|PUS6_ORYSJ RNA pseudourine synthase 6, chloroplastic OS=Oryza sativa subsp. japonica GN=Os07g0660400 PE=2 SV=1	Back alignment and function description

>sp\|P57430\|RLUC_BUCAI Ribosomal large subunit pseudouridine synthase C OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=rluC PE=3 SV=1	Back alignment and function description

>sp\|Q8K9J8\|RLUC_BUCAP Ribosomal large subunit pseudouridine synthase C OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN=rluC PE=3 SV=1	Back alignment and function description

>sp\|P59835\|RLUC_HAEDU Ribosomal large subunit pseudouridine synthase C OS=Haemophilus ducreyi (strain 35000HP / ATCC 700724) GN=rluC PE=3 SV=1	Back alignment and function description

>sp\|Q8PHN2\|RLUD_XANAC Ribosomal large subunit pseudouridine synthase D OS=Xanthomonas axonopodis pv. citri (strain 306) GN=rluD PE=3 SV=1	Back alignment and function description

>sp\|Q89AH2\|RLUC_BUCBP Ribosomal large subunit pseudouridine synthase C OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rluC PE=3 SV=1	Back alignment and function description

>sp\|Q9CK02\|RLUA_PASMU Ribosomal large subunit pseudouridine synthase A OS=Pasteurella multocida (strain Pm70) GN=rluA PE=3 SV=1	Back alignment and function description

>sp\|P54604\|YHCT_BACSU Uncharacterized RNA pseudouridine synthase YhcT OS=Bacillus subtilis (strain 168) GN=yhcT PE=3 SV=2	Back alignment and function description

>sp\|P43930\|Y042_HAEIN Uncharacterized RNA pseudouridine synthase HI_0042 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=HI_0042 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
Query		483
255554955		476	ribosomal pseudouridine synthase, putati	0.968	0.983	0.707	0.0
224076324		470	predicted protein [Populus trichocarpa]	0.960	0.987	0.712	0.0
225444351		472	PREDICTED: RNA pseudourine synthase 6, c	0.929	0.951	0.721	0.0
449467613		475	PREDICTED: RNA pseudourine synthase 6, c	0.956	0.972	0.679	0.0
356546416		473	PREDICTED: RNA pseudourine synthase 6, c	0.939	0.959	0.669	0.0
356557901		473	PREDICTED: RNA pseudourine synthase 6, c	0.956	0.976	0.686	0.0
449488468		475	PREDICTED: LOW QUALITY PROTEIN: RNA pseu	0.956	0.972	0.677	0.0
449454720		475	PREDICTED: RNA pseudourine synthase 6, c	0.933	0.949	0.682	0.0
449488373		475	PREDICTED: RNA pseudourine synthase 6, c	0.933	0.949	0.680	0.0
255554953		395	ribosomal pseudouridine synthase, putati	0.805	0.984	0.755	0.0

>gi\|255554955\|ref\|XP_002518515.1\| ribosomal pseudouridine synthase, putative [Ricinus communis] gi\|223542360\|gb\|EEF43902.1\| ribosomal pseudouridine synthase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  712 bits (1838), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/482 (70%), Positives = 404/482 (83%), Gaps = 14/482 (2%)

Query: 1   MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHA-SCHRNIYKSNVV-LSFSSSNRNFVCES 58
           MSS+S +SIF    RS   PV++LRTLASTHA S HR+  K+ +   S +S  R F CES
Sbjct: 1   MSSLSLASIFAGGYRSFVTPVTVLRTLASTHAYSFHRHHPKNALARFSLNSHERKFCCES 60

Query: 59  WKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICR 118
            K  V   T+T+ +         G  +Y RLLPCPS N PPR+EHLVV E GPVL+YIC+
Sbjct: 61  SKPEVAYTTNTSCVN--------GNSDYDRLLPCPSYNRPPRIEHLVVLEEGPVLDYICK 112

Query: 119 ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVR 178
            L+LPPLFVADLI FGAV+YALVCP+PP TATPEQ+R+F++ T PSVL KRSSIKGKTVR
Sbjct: 113 ALDLPPLFVADLIDFGAVHYALVCPRPPTTATPEQIRLFEKFTAPSVLKKRSSIKGKTVR 172

Query: 179 EAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSV 238
           EAQKTFRITHVDQ +EAGTYLRVHVHPKRFPRCYDIDW SRIIAVT+ +VVLDKPAGTSV
Sbjct: 173 EAQKTFRITHVDQYLEAGTYLRVHVHPKRFPRCYDIDWKSRIIAVTDCYVVLDKPAGTSV 232

Query: 239 GGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKV 298
           GGT DNIEESCATFA+RALGLTTPL+TTHQIDNCTEGCVVLAR++EYCS+FH KIREKKV
Sbjct: 233 GGTADNIEESCATFATRALGLTTPLKTTHQIDNCTEGCVVLARSKEYCSVFHGKIREKKV 292

Query: 299 KKLYLALTTAPLPVGIMTHYMRPINIAPRLVSE----GWYLCQLEVMECKKVPWPDATVG 354
           KKLYLAL  +P+PVG++ +YMRP+NIAPRL+SE    GW+LCQLEV+EC+KVPWPDA + 
Sbjct: 293 KKLYLALAASPVPVGVIKNYMRPVNIAPRLLSEEFVNGWHLCQLEVLECRKVPWPDAAIE 352

Query: 355 KAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPG 414
           + YS+EDCGWPS+D+AYECKI LLTGRTHQ+RAQLAA GAP+VGDSMYMPAA+A++++PG
Sbjct: 353 EKYSVEDCGWPSKDFAYECKINLLTGRTHQIRAQLAASGAPLVGDSMYMPAAVAEMANPG 412

Query: 415 LNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACHISWDDGECCYEARSPWWR 474
           LNPFGK +K+Y ++ D+ MAV EW++QHG EP VAIGLQAC ISWD+G+  Y+A SPWWR
Sbjct: 413 LNPFGKHRKQYTNESDESMAVAEWVAQHGKEPKVAIGLQACEISWDEGKHIYKAGSPWWR 472

Query: 475 CK 476
           C+
Sbjct: 473 CR 474

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224076324\|ref\|XP_002304926.1\| predicted protein [Populus trichocarpa] gi\|222847890\|gb\|EEE85437.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225444351\|ref\|XP_002264641.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic [Vitis vinifera] gi\|302144082\|emb\|CBI23187.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449467613\|ref\|XP_004151517.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356546416\|ref\|XP_003541622.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|356557901\|ref\|XP_003547248.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|449488468\|ref\|XP_004158048.1\| PREDICTED: LOW QUALITY PROTEIN: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449454720\|ref\|XP_004145102.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449488373\|ref\|XP_004158017.1\| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255554953\|ref\|XP_002518514.1\| ribosomal pseudouridine synthase, putative [Ricinus communis] gi\|223542359\|gb\|EEF43901.1\| ribosomal pseudouridine synthase, putative [Ricinus communis]	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		483
TAIR\|locus:2119073		472	AT4G21770 [Arabidopsis thalian	0.954	0.976	0.651	5.8e-169
DICTYBASE\|DDB_G0277359		386	DDB_G0277359 "Pseudouridylate	0.306	0.383	0.266	1.2e-10
TIGR_CMR\|SPO_0516		347	SPO_0516 "ribosomal large subu	0.347	0.484	0.307	5.9e-10
CGD\|CAL0004292		402	orf19.2788 [Candida albicans (	0.366	0.440	0.306	1.9e-08
UNIPROTKB\|Q59PV5		402	CaO19.2788 "Putative uncharact	0.366	0.440	0.306	1.9e-08
TIGR_CMR\|GSU_0671		296	GSU_0671 "ribosomal large subu	0.173	0.283	0.310	1.6e-07
TIGR_CMR\|APH_0549		297	APH_0549 "ribosomal large subu	0.275	0.447	0.255	6.2e-07
GENEDB_PFALCIPARUM\|PFE1080w		487	PFE1080w "ribosomal large subu	0.213	0.211	0.301	8.2e-07
UNIPROTKB\|Q8I3P7		487	PFE1080w "Ribosomal large subu	0.213	0.211	0.301	8.2e-07
TIGR_CMR\|CHY_1119		301	CHY_1119 "ribosomal large subu	0.060	0.096	0.620	1.4e-06

TAIR\|locus:2119073 AT4G21770 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1643 (583.4 bits), Expect = 5.8e-169, P = 5.8e-169
 Identities = 311/477 (65%), Positives = 373/477 (78%)

Query:     7 SSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLS-FSSSNRNFVCESWKRHVFX 65
             S   T   R+L APVSLLRTLAST  +    +++SN     F SS + F C S  +    
Sbjct:     3 SPALTGGYRNLTAPVSLLRTLASTRVTTP--LFRSNKHSPRFISSPKRFTCLSLLK---- 56

Query:    66 XXXXXXXXXXXXPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVL-EYICRELNLPP 124
                          S+ GY EY+RL+PCP+ N PPR+EH+VV E   ++ E+I ++L+LPP
Sbjct:    57 -TDSQNQTTLSSSSNSGYHEYNRLMPCPAYNLPPRIEHMVVLEDDVLVSEFISKQLDLPP 115

Query:   125 LFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTF 184
             L+VADLI FGAV+YALVCPKPP TATPE++ +F+EVT PSVL KRSSIKGKTVREAQKTF
Sbjct:   116 LYVADLIRFGAVHYALVCPKPPPTATPEEIILFEEVTSPSVLKKRSSIKGKTVREAQKTF 175

Query:   185 RITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDN 244
             R+TH +Q  EAGTYLRVHVHPKR PRCY+IDW SRI+AVT+S+V+LDKPAGT+VGGTTDN
Sbjct:   176 RVTHTNQYAEAGTYLRVHVHPKRSPRCYEIDWKSRIVAVTDSYVILDKPAGTTVGGTTDN 235

Query:   245 IEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304
             IEESCATFASRAL L  PL+TTHQIDNCTEGCVV ART+EYCS+FH KIR K+VKKLY A
Sbjct:   236 IEESCATFASRALDLPEPLKTTHQIDNCTEGCVVFARTKEYCSVFHTKIRNKEVKKLYRA 295

Query:   305 LTTAPLPVGIMTHYMRPINIAPRLVSE----GWYLCQLEVMECKKVPWPDATVGKAYSIE 360
             L  APLP+GI++HYMRP N+APRLV+E    GW+LCQLEV+ECKK+PWPDA   K + IE
Sbjct:   296 LAAAPLPIGIISHYMRPKNMAPRLVAEDSIQGWHLCQLEVLECKKIPWPDAATEKKHDIE 355

Query:   361 DCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGK 420
             DCGW S+++AYEC I LLTG+THQ+RAQLAACGAP+VGDSMYMPAAIA++ +P  NP+GK
Sbjct:   356 DCGWTSKEFAYECTINLLTGKTHQIRAQLAACGAPLVGDSMYMPAAIAEMGNPDTNPYGK 415

Query:   421 CQKEYASDDD-KEMAVIEWISQHGMEPSVAIGLQACHISWDD--GECCYEARSPWWR 474
              +K Y  +++ KE AV EWI +HG EP V IGLQAC ISWDD  GE  YEA +PWWR
Sbjct:   416 AKKHYTMEENQKETAVAEWIDRHGKEPRVGIGLQACQISWDDDDGEHFYEAGTPWWR 472

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

DICTYBASE\|DDB_G0277359 DDB_G0277359 "Pseudouridylate synthase PUS5" [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

CGD\|CAL0004292 orf19.2788 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|Q59PV5 CaO19.2788 "Putative uncharacterized protein" [Candida albicans SC5314 (taxid:237561)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_0671 GSU_0671 "ribosomal large subunit pseudouridine synthase C" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|APH_0549 APH_0549 "ribosomal large subunit pseudouridine synthase C" [Anaplasma phagocytophilum HZ (taxid:212042)]	Back alignment and assigned GO terms

GENEDB_PFALCIPARUM\|PFE1080w PFE1080w "ribosomal large subunit pseudouridylate synthase, putative" [Plasmodium falciparum (taxid:5833)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8I3P7 PFE1080w "Ribosomal large subunit pseudouridylate synthase, putative" [Plasmodium falciparum 3D7 (taxid:36329)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_1119 CHY_1119 "ribosomal large subunit pseudouridine synthase, RluA family" [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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SVS0	PUS6_ARATH	5, ., 4, ., 9, 9, ., -	0.6561	0.9544	0.9766	yes	no
A3BN26	PUS6_ORYSJ	5, ., 4, ., 9, 9, ., -	0.6575	0.8219	0.8322	yes	no

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	0.691

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
Query		483
cd02869		185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	2e-29
pfam00849		149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	6e-27
COG0564		289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	3e-19
cd02557		213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	1e-14
TIGR00005		299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	3e-12
TIGR01621		217	TIGR01621, RluA-like, pseudouridine synthase Rlu f	3e-09
PRK11025		317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	2e-08
cd02558		246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	6e-08
PRK10158		219	PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy	1e-05
cd02550		154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	0.002
cd02563		223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	0.003

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

 Score =  113 bits (284), Expect = 2e-29
 Identities = 50/198 (25%), Positives = 81/198 (40%), Gaps = 33/198 (16%)

Query: 228 VVLDKPAGTSVGGTTDNIEESCATF---ASRALGLTTPLRTTHQIDNCTEGCVVLARTQE 284
           +V++KPAG  V     ++  +           LG        H++D  T G +++A+ ++
Sbjct: 2   LVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKK 61

Query: 285 YCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYM-----RPINIAPRLVSEGWYLC--Q 337
             +   ++ +E+KVKK YLAL     P    T        +    A  +VSE        
Sbjct: 62  AAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAITH 121

Query: 338 LEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIV 397
            +V+E     + + T+                    +++L TGRTHQ+R  LA+ G PIV
Sbjct: 122 YKVLE----RFGNVTL-------------------VELQLETGRTHQIRVHLASIGHPIV 158

Query: 398 GDSMYMPAAIAQLSSPGL 415
           GD  Y   A        L
Sbjct: 159 GDPKYGGKASDSPGLKRL 176

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\|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase	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\|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2	Back alignment and domain information

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

>gnl\|CDD\|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621	Back alignment and domain information

>gnl\|CDD\|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; 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\|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional	Back alignment and domain information

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		483
COG0564		289	RluA Pseudouridylate synthases, 23S RNA-specific [	100.0
PRK11180		325	rluD 23S rRNA pseudouridine synthase D; Provisiona	100.0
PRK11025		317	23S rRNA pseudouridylate synthase C; Provisional	100.0
TIGR00005		299	rluA_subfam pseudouridine synthase, RluA family. m	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
TIGR01621		217	RluA-like pseudouridine synthase Rlu family protei	100.0
KOG1919		371	consensus RNA pseudouridylate synthases [RNA proce	100.0
cd02563		223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	100.0
PRK11112		257	tRNA pseudouridine synthase C; Provisional	100.0
PRK10158		219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	100.0
PRK10839		232	16S rRNA pseudouridylate synthase A; Provisional	100.0
cd02869		185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	100.0
PRK10700		289	23S rRNA pseudouridylate synthase B; Provisional	100.0
PRK10475		290	23S rRNA pseudouridine synthase F; Provisional	100.0
cd02550		154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.98
COG1187		248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.97
cd02556		167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.97
cd02870		146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.96
cd02553		167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.96
PF00849		164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.96
cd02566		168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.95
PRK11394		217	23S rRNA pseudouridine synthase E; Provisional	99.94
cd02555		177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.94
TIGR00093		128	pseudouridine synthase. This model identifies pane	99.91
cd02554		164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.9
cd02868		226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	99.11
cd00165		70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	98.71
TIGR02988		59	YaaA_near_RecF S4 domain protein YaaA. This small	98.23
PF01479		48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.2
cd02572		182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	97.58
smart00363		60	S4 S4 RNA-binding domain.	97.34
PRK00989		230	truB tRNA pseudouridine synthase B; Provisional	97.25
PLN00051		267	RNA-binding S4 domain-containing protein; Provisio	97.22
TIGR00431		209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	97.17
cd00506		210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	97.16
PRK04099		273	truB tRNA pseudouridine synthase B; Provisional	97.15
COG1188		100	Ribosome-associated heat shock protein implicated	97.1
PRK00020		244	truB tRNA pseudouridine synthase B; Provisional	97.08
TIGR03069		257	PS_II_S4 photosystem II S4 domain protein. Members	97.05
PRK02484		294	truB tRNA pseudouridine synthase B; Provisional	96.98
cd01291		87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	96.97
PRK14124		308	tRNA pseudouridine synthase B; Provisional	96.95
PRK14123		305	tRNA pseudouridine synthase B; Provisional	96.95
PRK02193		279	truB tRNA pseudouridine synthase B; Provisional	96.93
PRK03287		298	truB tRNA pseudouridine synthase B; Provisional	96.91
PRK14846		345	truB tRNA pseudouridine synthase B; Provisional	96.9
PRK00130		290	truB tRNA pseudouridine synthase B; Provisional	96.88
PRK02755		295	truB tRNA pseudouridine synthase B; Provisional	96.88
TIGR01017		200	rpsD_bact ribosomal protein S4, bacterial/organell	96.85
PRK05389		305	truB tRNA pseudouridine synthase B; Provisional	96.82
COG2302		257	Uncharacterized conserved protein, contains S4-lik	96.8
cd02573		277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	96.8
PRK01528		292	truB tRNA pseudouridine synthase B; Provisional	96.8
PRK04270		300	H/ACA RNA-protein complex component Cbf5p; Reviewe	96.78
PRK01550		304	truB tRNA pseudouridine synthase B; Provisional	96.75
PRK01851		303	truB tRNA pseudouridine synthase B; Provisional	96.74
PRK05033		312	truB tRNA pseudouridine synthase B; Provisional	96.71
CHL00113		201	rps4 ribosomal protein S4; Reviewed	96.71
PRK14122		312	tRNA pseudouridine synthase B; Provisional	96.5
TIGR00478		228	tly hemolysin TlyA family protein. Hemolysins are	96.41
PRK04642		300	truB tRNA pseudouridine synthase B; Provisional	96.38
TIGR00425		322	CBF5 rRNA pseudouridine synthase, putative. This f	96.38
PRK05327		203	rpsD 30S ribosomal protein S4; Validated	96.3
PRK10348		133	ribosome-associated heat shock protein Hsp15; Prov	96.15
COG0130		271	TruB Pseudouridine synthase [Translation, ribosoma	95.95
COG0522		205	RpsD Ribosomal protein S4 and related proteins [Tr	95.92
cd02867		312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	95.9
COG1189		245	Predicted rRNA methylase [Translation, ribosomal s	94.35
PRK11507		70	ribosome-associated protein; Provisional	93.21
PRK04051		177	rps4p 30S ribosomal protein S4P; Validated	91.91
PRK04313		237	30S ribosomal protein S4e; Validated	89.17
COG2501		73	S4-like RNA binding protein [Replication, recombin	88.24
PLN00189		194	40S ribosomal protein S9; Provisional	87.45
PF13275		65	S4_2: S4 domain; PDB: 1P9K_A.	86.89
PTZ00223		273	40S ribosomal protein S4; Provisional	86.06
PLN00036		261	40S ribosomal protein S4; Provisional	86.02
TIGR01018		162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	85.58
PTZ00118		262	40S ribosomal protein S4; Provisional	84.91
PRK01777		95	hypothetical protein; Validated	82.14
KOG2559		318	consensus Predicted pseudouridine synthase [Transl	81.54
PTZ00155		181	40S ribosomal protein S9; Provisional	80.83

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

Probab=100.00  E-value=1.6e-53  Score=427.39  Aligned_cols=261  Identities=24%  Similarity=0.299  Sum_probs=209.9

Q ss_pred             CCCcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530          108 EGGPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI  186 (483)
Q Consensus       108 ~~~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~  186 (483)
                      ++.||++||++ +. +||+++.++|++|+|                                  .|||++++        
T Consensus        11 ~g~rld~~L~~-l~~~sr~~~~~~i~~g~v----------------------------------~vNg~~v~--------   47 (289)
T COG0564          11 AGQRLDKFLAK-LLPISRSRIQKLIRKGRV----------------------------------RVNGKKVK--------   47 (289)
T ss_pred             cCCCHHHHHHH-ccCcCHHHHHHHHHCCCE----------------------------------EECCEEcc--------
Confidence            34577799999 54 999999999999999                                  68999885        


Q ss_pred             cCCCceecCCCEEEEecCCCCC-CcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccC-CCCCc
Q 011530          187 THVDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLR  264 (483)
Q Consensus       187 ~~~~~~v~~GD~I~v~~~~~~~-p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~-~~~l~  264 (483)
                        ++++|..||+|.+....... ....+.+.++.|||||++++|||||+||+|||+..+...++...+....+. ...++
T Consensus        48 --~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~  125 (289)
T COG0564          48 --PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPG  125 (289)
T ss_pred             --CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCcee
Confidence              78999999999999876443 222233445889999999999999999999999888888888877655432 34678


Q ss_pred             cccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEee
Q 011530          265 TTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVME  342 (483)
Q Consensus       265 ~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~  342 (483)
                      +||||||+||||||||||..+++.|+++|+++.+.|+|+|+|.|.++  .|.|+.++.......         ..+.+..
T Consensus       126 ~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~---------~~~~v~~  196 (289)
T COG0564         126 IVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNR---------KKMAVVK  196 (289)
T ss_pred             eeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCC---------ceEEEec
Confidence            99999999999999999999999999999999999999999999886  478887654322111         1122222


Q ss_pred             cccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChh---h---hhhc-----C
Q 011530          343 CKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPA---A---IAQL-----S  411 (483)
Q Consensus       343 ~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~---~---~~~~-----~  411 (483)
                      ..   . .+.+.|.|++++..   ....++++|+|+||||||||+||++|||||+||++||+.   .   ..++     .
T Consensus       197 ~~---~-gk~A~T~~~~l~~~---~~~~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~  269 (289)
T COG0564         197 EG---S-GKPAITHYEVLERF---GDNYTLVELKPETGRTHQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHAYK  269 (289)
T ss_pred             cC---C-CCceEEEEEehhcc---CCceEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcccCCchhhcccCcchhhhhhce
Confidence            11   1 34567999999852   222689999999999999999999999999999999974   1   2233     3


Q ss_pred             CCCCCCCCCceeeEecCh
Q 011530          412 SPGLNPFGKCQKEYASDD  429 (483)
Q Consensus       412 l~f~hP~t~~~~~f~~~~  429 (483)
                      +.|.||.+++.+.|++|.
T Consensus       270 l~f~hp~t~~~~~~~a~~  287 (289)
T COG0564         270 LSFTHPLTGEELEFEAPL  287 (289)
T ss_pred             eEccCCCCCCEEEEecCC
Confidence            789999999999999863

>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

>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

>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

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

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; 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

>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

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA	Back alignment and domain information

>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

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA	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

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like	Back alignment and domain information

>smart00363 S4 S4 RNA-binding domain	Back alignment and domain information

>PRK00989 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PLN00051 RNA-binding S4 domain-containing protein; Provisional	Back alignment and domain information

>TIGR00431 TruB tRNA pseudouridine 55 synthase	Back alignment and domain information

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family	Back alignment and domain information

>PRK04099 truB tRNA pseudouridine synthase B; Provisional	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

>PRK00020 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR03069 PS_II_S4 photosystem II S4 domain protein	Back alignment and domain information

>PRK02484 truB tRNA pseudouridine synthase B; 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

>PRK14124 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14123 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02193 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK03287 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14846 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK00130 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02755 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type	Back alignment and domain information

>PRK05389 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]	Back alignment and domain information

>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like	Back alignment and domain information

>PRK01528 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

>PRK01550 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01851 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05033 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>CHL00113 rps4 ribosomal protein S4; Reviewed	Back alignment and domain information

>PRK14122 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR00478 tly hemolysin TlyA family protein	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

>PRK05327 rpsD 30S ribosomal protein S4; Validated	Back alignment and domain information

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional	Back alignment and domain information

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG0522 RpsD Ribosomal protein S4 and related proteins [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

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK11507 ribosome-associated protein; Provisional	Back alignment and domain information

>PRK04051 rps4p 30S ribosomal protein S4P; Validated	Back alignment and domain information

>PRK04313 30S ribosomal protein S4e; Validated	Back alignment and domain information

>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

>PF13275 S4_2: S4 domain; PDB: 1P9K_A	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

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)	Back alignment and domain information

>PTZ00118 40S ribosomal protein S4; Provisional	Back alignment and domain information

>PRK01777 hypothetical protein; Validated	Back alignment and domain information

>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PTZ00155 40S ribosomal protein S9; 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
Query		483
2i82_A		217	Crystal Structure Of Pseudouridine Synthase Rlua: I		2e-06
1xpi_A		231	Crystal Structure Of The Catalytic Domain Of E. Col		2e-06
1v9k_A		228	The Crystal Structure Of The Catalytic Domain Of Ps		3e-06

>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust. Identities = 53/196 (27%), Positives = 84/196 (42%), Gaps = 42/196 (21%) Query: 220 IIAVTESHV-VLDKPAGT-SVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCV 277 +I + H+ V++KP+G SV G + ++S T R + H++D T G + Sbjct: 13 VILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQA---ESVHRLDXATSGVI 69 Query: 278 VLARTQEYCSIFHRKIREKKVKKLYLALTTA-PLPVGIMTHYMRPINIAPRLVSEGWYLC 336 V+A T+ R+ RE++ KK Y+A P P +EG L Sbjct: 70 VVALTKAAERELKRQFREREPKKQYVARVWGHPSP------------------AEG--LV 109 Query: 337 QLEVMECKKVPWPDATVGKAYSIEDCGWPSR----------DYAYECKIKLLTGRTHQVR 386 L ++ C WP+ K + G P++ D +K +TGR+HQ+R Sbjct: 110 DLPLI-CD---WPNRPKQKV--CYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLR 163 Query: 387 AQLAACGAPIVGDSMY 402 A G PI+GD Y Sbjct: 164 VHXLALGHPILGDRFY 179

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		483
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	4e-12
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	3e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	6e-06

>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 = 64.4 bits (158), Expect = 4e-12
 Identities = 44/202 (21%), Positives = 73/202 (36%), Gaps = 56/202 (27%)

Query: 228 VVLDKPAGTSV-------GGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLA 280
           +VL+KP+GT+V        G  + +        +R L L       H++D  T G +++A
Sbjct: 12  LVLNKPSGTAVHGGSGLSFGVIEGLRALR--PEARFLELV------HRLDRDTSGVLLVA 63

Query: 281 RTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAP--RLVSEGWYLCQL 338
           + +      H ++REK ++K YLAL       G    +++ +  AP  +           
Sbjct: 64  KKRSALRSLHEQLREKGMQKDYLALV-----RGQWQSHVKSVQ-APLLK----------- 106

Query: 339 EVMECKKVPWPDATVGKAYSIEDCGWPS----------RDYAY-ECKIKLLTGRTHQVRA 387
                        +  +   +   G PS                 C    +TGRTHQ+R 
Sbjct: 107 ---------NILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCS--PVTGRTHQIRV 155

Query: 388 QLAACGAPIVGDSMYMPAAIAQ 409
                G PI  D  Y      +
Sbjct: 156 HTQYAGHPIAFDDRYGDREFDR 177

PyMOL of 1v9k

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

>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		483
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	100.0
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	100.0
1ksk_A		234	Ribosomal small subunit pseudouridine synthase A;	100.0
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	100.0
1vio_A		243	Ribosomal small subunit pseudouridine synthase A;	100.0
3dh3_A		290	Ribosomal large subunit pseudouridine synthase F;	100.0
2oml_A		189	Ribosomal large subunit pseudouridine synthase E;	100.0
2olw_A		217	Ribosomal large subunit pseudouridine synthase E;	100.0
2gml_A		237	Ribosomal large subunit pseudouridine synthase F;	99.96
2k6p_A		92	Uncharacterized protein HP_1423; alpha-L motif, RN	98.1
1p9k_A		79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.68
1dm9_A		133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	97.62
2vqe_D		209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	97.6
1c05_A		159	Ribosomal protein S4 delta 41; two subdomains, uni	97.26
2cqj_A		71	BRMS2, U3 small nucleolar ribonucleoprotein protei	97.13
3r8n_D		205	30S ribosomal protein S4; protein biosynthesis, RN	96.83
3hp7_A		291	Hemolysin, putative; structural genomics, APC64019	96.81
3bbn_D		201	Ribosomal protein S4; small ribosomal subunit, spi	96.8
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	96.66
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	96.55
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	96.52
1sgv_A		316	TRNA pseudouridine synthase B; hinged motion, tRNA	96.43
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	96.39
3j20_D		180	30S ribosomal protein S4P; archaea, archaeal, KINK	96.3
3u28_A		400	H/ACA ribonucleoprotein complex subunit 4; pseudou	96.15
2xzm_D		181	Ribosomal protein S4 containing protein; ribosome,	96.04
3u5c_J		197	40S ribosomal protein S9-A; translation, ribosome,	94.97
3j20_E		243	30S ribosomal protein S4E; archaea, archaeal, KINK	94.57
3kbg_A		213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	92.95
3iz6_C		195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	90.75

>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=1.4e-50  Score=412.29  Aligned_cols=257  Identities=17%  Similarity=0.213  Sum_probs=157.4

Q ss_pred             CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (483)
Q Consensus       110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~  188 (483)
                      .||++||++.+ .+||+.++++|+.|.|                                  .|||+.+.         +
T Consensus        17 ~RLd~~L~~~~~~~SR~~~~~lI~~G~V----------------------------------~VNG~~v~---------~   53 (325)
T 1v9f_A           17 QRLDQALAEMFPDYSRSRIKEWILDQRV----------------------------------LVNGKVCD---------K   53 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chHHHHHHhhccccCHHHHHHHHHCCCE----------------------------------EECCEEcc---------C
Confidence            45559999998 7999999999999999                                  58998744         4


Q ss_pred             CCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhcc---CCCCCcc
Q 011530          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALG---LTTPLRT  265 (483)
Q Consensus       189 ~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~---~~~~l~~  265 (483)
                      +++.|++||.|.+...+.+.......+.++.|+|||++|+|||||+||+||+.......++.+.+...+.   ....+++
T Consensus        54 ~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~  133 (325)
T 1v9f_A           54 PKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI  133 (325)
T ss_dssp             ----------------------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGB
T ss_pred             CCCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceee
Confidence            8899999999999875533221112234578999999999999999999999887767788777754332   1235789


Q ss_pred             ccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC-ccceeecccccccCCccccCCeeeeeEEEeecc
Q 011530          266 THQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECK  344 (483)
Q Consensus       266 VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~  344 (483)
                      |||||++||||||||||+++++.|+++|++++++|+|+|+|.|.++ +|.|+.++.......      .+   +.+.   
T Consensus       134 vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~g~i~~~i~~~~~~~------~~---~~v~---  201 (325)
T 1v9f_A          134 VHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKR------TH---MAVH---  201 (325)
T ss_dssp             CCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEEECSSCT------TC---EEEC---
T ss_pred             ecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCCCCEEeeeeeECCCCC------EE---EEEC---
Confidence            9999999999999999999999999999999999999999999887 488887664321110      01   1121   


Q ss_pred             cCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhh----------------hh
Q 011530          345 KVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAA----------------IA  408 (483)
Q Consensus       345 ~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~----------------~~  408 (483)
                        . +.+.+.|.|++++.    ....++++|+|.||||||||+||+++||||+||.+||+..                ..
T Consensus       202 --~-~gk~a~t~~~vl~~----~~~~slv~~~l~TGR~HQIRvhla~lG~PI~GD~~Yg~~~~~~~~~~~~~~~~~~~~~  274 (325)
T 1v9f_A          202 --P-MGKPAVTHYRIMEH----FRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFD  274 (325)
T ss_dssp             --T-TSBCCEEEEEEEEE----CSSEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCC
T ss_pred             --C-CCeeEEEEEEEeEE----cCCeEEEEEEECCCCcHHHHHHHHhCCCceeCChhhCCccccccccchhhhhhccCCc
Confidence              1 12345689999985    3468999999999999999999999999999999999641                12


Q ss_pred             hcC-----CCCCCCCCCceeeEecC
Q 011530          409 QLS-----SPGLNPFGKCQKEYASD  428 (483)
Q Consensus       409 ~~~-----l~f~hP~t~~~~~f~~~  428 (483)
                      +++     +.|.||++++.+.|++|
T Consensus       275 r~~LHA~~L~f~hP~~~~~~~~~ap  299 (325)
T 1v9f_A          275 RQALHATMLRLYHPISGIEMEWHAP  299 (325)
T ss_dssp             SCSEEEEEEEEECTTTCCEEEEECC
T ss_pred             ChhhheeeeEeeCCCCCCEEEEEec
Confidence            333     68999999999999986

PyMOL of 1v9f

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

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

>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

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

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}	Back alignment and structure

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

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

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

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}	Back alignment and structure

>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

>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

>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

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}	Back alignment and structure

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}	Back alignment and structure

>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

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A	Back alignment and structure

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A	Back alignment and structure

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>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

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A	Back alignment and structure

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D	Back alignment and structure

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*	Back alignment and structure

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>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

>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

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		483
d1v9ka_		227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-06
d1v9fa_		250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-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 = 46.5 bits (109), Expect = 2e-06
 Identities = 34/193 (17%), Positives = 62/193 (32%), Gaps = 16/193 (8%)

Query: 228 VVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCS 287
           +VL+KP+GT+V G +                    L   H++D  T G +++A+ +    
Sbjct: 11  LVLNKPSGTAVHGGSGL-SFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALR 69

Query: 288 IFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVP 347
             H ++REK +                  +           V          +++  +  
Sbjct: 70  SLHEQLREKGM---------------QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERI 114

Query: 348 WPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI 407
              +  GK             +A   +   +TGRTHQ+R      G PI  D  Y     
Sbjct: 115 VRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREF 174

Query: 408 AQLSSPGLNPFGK 420
            +  +       +
Sbjct: 175 DRQLTEAGTGLNR 187

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		483
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	99.93
d1kska4		172	Ribosomal small subunit pseudouridine 516 synthase	99.89
d1kska3		59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.6
d1vioa2		58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.56
d1p9ka_		79	Hypothetical protein YbcJ {Escherichia coli [TaxId	97.81
d1dm9a_		104	Heat shock protein 15 kD {Escherichia coli [TaxId:	97.58
d1k8wa5		242	Pseudouridine synthase II TruB {Escherichia coli [	96.87
d1r3ea2		228	Pseudouridine synthase II TruB {Thermotoga maritim	96.76
d2ey4a2		245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	96.66
d1sgva2		233	Pseudouridine synthase II TruB {Mycobacterium tube	96.59
d1c06a_		159	Ribosomal protein S4 {Bacillus stearothermophilus	96.57
d2apoa2		230	Pseudouridine synthase II TruB {Archaeon Methanoco	96.44
d2gy9d1		204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	96.04
d2uubd1		208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	95.94
d1h3fa2		81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	95.3
d1jh3a_		99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	94.1

>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=9.8e-45  Score=349.18  Aligned_cols=209  Identities=22%  Similarity=0.227  Sum_probs=157.1

Q ss_pred             eEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCc
Q 011530          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKV  298 (483)
Q Consensus       219 ~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v  298 (483)
                      .|||||++|||||||+||+||++..... ++...+.........+++|||||++||||||||||+++++.|+++|+++.+
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~-~~~~~l~~~~~~~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v   80 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSF-GVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM   80 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBC-CHHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCS
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcc-hHHHHHHHhCCCCcccceeeeccceeeeeeeeecchHHHHHHHHHHhcccc
Confidence            5999999999999999999999776544 445555544444556789999999999999999999999999999999999


Q ss_pred             ceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEE
Q 011530          299 KKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIK  376 (483)
Q Consensus       299 ~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~  376 (483)
                      .|+|+|+|.|.++  .+.++.++.......     +..  .+.+.      ...+.+.|.|++++.    ....++++|+
T Consensus        81 ~K~Y~a~~~G~~~~~~~~~~~~~~~~~~~~-----~~~--~~~~~------~~gk~a~t~~~~l~~----~~~~slv~~~  143 (227)
T d1v9ka_          81 QKDYLALVRGQWQSHVKSVQAPLLKNILQS-----GER--IVRVS------QEGKPSETRFKVEER----YAFATLVRCS  143 (227)
T ss_dssp             EEEEEEEEESCCCTTCCEECCCEEEEECTT-----SCE--EEEEC------TTSBCCCEEEEEEEE----CSSEEEEEEE
T ss_pred             cceecccccCccccccCccccccccccccc-----eee--eeecC------CCCcccceeehhhhh----cCCcEEEEEE
Confidence            9999999999886  445554332211110     110  01111      123445789999985    4578999999


Q ss_pred             EcCCcchHHHHHHHHcCCCeeecCCCChhhhhhcCCCCCCCCCCceeeEecChhhHHHHHHHHHhcCCCCCcceeEEEEE
Q 011530          377 LLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQACH  456 (483)
Q Consensus       377 l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~l~f~hP~t~~~~~f~~~~~~~~~~~~~l~~h~~e~~~~I~LhA~~  456 (483)
                      |.||||||||+||+++||||+||.+||+...++                        .+.+     .......++|||++
T Consensus       144 ~~TGRtHQIRvHla~lG~PIvGD~~Yg~~~~~~------------------------~~~~-----~~~~~~rl~LHa~~  194 (227)
T d1v9ka_         144 PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDR------------------------QLTE-----AGTGLNRLFLHAAA  194 (227)
T ss_dssp             ESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHHH------------------------HHHH-----TTCCCCSCCEEEEE
T ss_pred             eccCchHHHHHHHhhcCceeccCcccccccccc------------------------cchh-----cccCcchHHHHccc
Confidence            999999999999999999999999999654311                        0000     11222368999999


Q ss_pred             eeec----CcceEEEeCCCccc
Q 011530          457 ISWD----DGECCYEARSPWWR  474 (483)
Q Consensus       457 ~~~~----g~~~~f~a~~P~W~  474 (483)
                      ++|.    |+...|+|++|.+.
T Consensus       195 L~f~hP~t~~~~~~~aplP~~f  216 (227)
T d1v9ka_         195 LKFTHPGTGEVMRIEAPMDEGL  216 (227)
T ss_dssp             EEEECTTTCCEEEEECCCCHHH
T ss_pred             cEeECCCCCCEEEEEecCcHHH
Confidence            9993    67778999999654

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

>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

>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

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}	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