Citrus Sinensis ID: 018538

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----
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
ccccccccccccccEEccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHHcEEEEEEEcccccccccHHHHHHHHcccccHHHHcccccccccEEEccccEEEccccEEEEcccEEEEEcccccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHHcccccccccccccccccccEEEEEEcHHHHHHHHHHHHcccccEEEEEEEEccccccEEEEEccccccccEEEccccccccEEEEEEEEEcccccccc
cccccHHHHHcccccccccHHHHHHHHHHcccHHcccccccccEEEEEccccccEEcccccccccHHHHHHHHccccccccccccHccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHHccEEEEEccccccccccHHHEEEEcccccHHHHHHHHccccccHHHHccccEEcccccccccccEEEEEcccccccccEEcccccEEEEEcccEEEEEcccccccccccccHHHHHHHHHHHHcccccccccccEccccccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccccccccEEEccccccccHHHHEEEEEcHHHHHHc
MSSVSFSSIftnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFsssnrnfvceswkrhvfthtdTAAIaaattpssygypeyhrllpcpsqncpprvehlvvseggpVLEYICRelnlpplfvaDLIHFGAVYYAlvcpkppltatpeqmrvfkevtdpsvlskrssikgkTVREAQKTFRITHVDQIVEAGtylrvhvhpkrfprcydidwnsrIIAVTEshvvldkpagtsvggttdniEESCATFASRalglttplrtthqidnctegCVVLARTQEYCSIFHRKIREKKVKKLYLALttaplpvgimthymrpiniaprlvsegKTIFGLALMIREMVWKFEACIL
MSSVSFSSIFtnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEqmrvfkevtdpsvlskrssikgktvreaqktfrithvdqiVEAGtylrvhvhpkrfPRCYDIDWNSRIIAVTeshvvldkpagtsvggttdNIEESCATFASRALGlttplrtthqidnCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTtaplpvgimTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFthtdtaaiaaattPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
***************SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLT*******************************AQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACI*
******S*IFTNNGRSLGAPVSLLRTLASTHASCHRNIY***********************VFT***************YGYPEYHRLLPCP**************EGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVL****************TFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMR**************IFGLALMIREMVWKFEACIL
********IFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
*****FSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMVWKFEACIL
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 ?
Query354 2.2.26 [Sep-21-2011]
Q9SVS0 472 RNA pseudourine synthase yes no 0.937 0.703 0.640 1e-119
A3BN26 477 RNA pseudourine synthase yes no 0.717 0.532 0.716 1e-102
P57430314 Ribosomal large subunit p yes no 0.290 0.328 0.278 4e-06
Q8K9J8314 Ribosomal large subunit p yes no 0.242 0.273 0.310 2e-05
Q28C59 324 RNA pseudouridylate synth yes no 0.262 0.287 0.316 0.0002
Q89AH2315 Ribosomal large subunit p yes no 0.259 0.292 0.291 0.0003
>sp|Q9SVS0|PUS6_ARATH RNA pseudourine synthase 6, chloroplastic OS=Arabidopsis thaliana GN=At4g21770 PE=2 SV=1 Back     alignment and function desciption
 Score =  429 bits (1104), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 219/342 (64%), Positives = 266/342 (77%), Gaps = 10/342 (2%)

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 LTTAPLPVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMV 346
           L  APLP+GI++HYMRP N+APRLV+E  +I G  L   E++
Sbjct: 296 LAAAPLPIGIISHYMRPKNMAPRLVAE-DSIQGWHLCQLEVL 336

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|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|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

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 ?
Query354
224076324 470 predicted protein [Populus trichocarpa] 0.901 0.678 0.719 1e-133
225444351 472 PREDICTED: RNA pseudourine synthase 6, c 0.867 0.650 0.731 1e-132
255554955 476 ribosomal pseudouridine synthase, putati 0.912 0.678 0.714 1e-132
449467613 475 PREDICTED: RNA pseudourine synthase 6, c 0.895 0.667 0.695 1e-126
449488468 475 PREDICTED: LOW QUALITY PROTEIN: RNA pseu 0.895 0.667 0.695 1e-126
356546416 473 PREDICTED: RNA pseudourine synthase 6, c 0.875 0.655 0.669 1e-123
449454720 475 PREDICTED: RNA pseudourine synthase 6, c 0.915 0.682 0.655 1e-122
449488373 475 PREDICTED: RNA pseudourine synthase 6, c 0.915 0.682 0.655 1e-122
356557901 473 PREDICTED: RNA pseudourine synthase 6, c 0.898 0.672 0.682 1e-121
297799888 476 pseudouridine synthase family protein [A 0.943 0.701 0.642 1e-118
>gi|224076324|ref|XP_002304926.1| predicted protein [Populus trichocarpa] gi|222847890|gb|EEE85437.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  479 bits (1234), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 238/331 (71%), Positives = 274/331 (82%), Gaps = 12/331 (3%)

Query: 1   MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWK 60
           M+S++ +SIF+ + RS  APV+LLRTLA T A    ++ K  +V   S S +   CES K
Sbjct: 1   MASLNLASIFSYSYRSFSAPVTLLRTLAFTRA---YSLNKKALVWC-SLSKKKLSCESLK 56

Query: 61  RHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICREL 120
           + +   T T+++         GYPEY RLLPCPS N PPR+EHLVVSE GPVL+YIC+ L
Sbjct: 57  QDIACTTATSSVN--------GYPEYTRLLPCPSHNSPPRIEHLVVSEEGPVLDYICKAL 108

Query: 121 NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREA 180
           +LPPLFVADLIHFGAV+YALVCP+PP TATPEQ+RVF+EVT PSVL KR+SIKGKTVREA
Sbjct: 109 DLPPLFVADLIHFGAVHYALVCPQPPRTATPEQIRVFEEVTAPSVLKKRASIKGKTVREA 168

Query: 181 QKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGG 240
           QKTFRITHVDQ +EAG YLRVHVHPKRFPRCYDIDW SRII VTES VVLDKPAGTSVGG
Sbjct: 169 QKTFRITHVDQFLEAGMYLRVHVHPKRFPRCYDIDWKSRIIHVTESFVVLDKPAGTSVGG 228

Query: 241 TTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKK 300
           TTDNIEESCATFA+RALGLT PLRTTHQIDNCTEGCVVLART+E CS+FH KIREK VKK
Sbjct: 229 TTDNIEESCATFATRALGLTAPLRTTHQIDNCTEGCVVLARTREDCSVFHGKIREKTVKK 288

Query: 301 LYLALTTAPLPVGIMTHYMRPINIAPRLVSE 331
           LY+AL  +P+P+G++ HYMRPIN+APRLVSE
Sbjct: 289 LYIALAASPVPIGVVNHYMRPINMAPRLVSE 319

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|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
>gi|449467613|ref|XP_004151517.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus] 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|356546416|ref|XP_003541622.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max] 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|356557901|ref|XP_003547248.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|297799888|ref|XP_002867828.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297313664|gb|EFH44087.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] 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 ?
Query354
TAIR|locus:2119073 472 AT4G21770 [Arabidopsis thalian 0.898 0.673 0.651 3.8e-110
DICTYBASE|DDB_G0277359 386 DDB_G0277359 "Pseudouridylate 0.418 0.383 0.266 2.8e-05
TIGR_CMR|APH_0549297 APH_0549 "ribosomal large subu 0.463 0.552 0.244 0.00013
TIGR_CMR|GSU_0671296 GSU_0671 "ribosomal large subu 0.237 0.283 0.310 0.00032
CGD|CAL0004292 402 orf19.2788 [Candida albicans ( 0.302 0.266 0.315 0.00084
UNIPROTKB|Q59PV5 402 CaO19.2788 "Putative uncharact 0.302 0.266 0.315 0.00084
GENEDB_PFALCIPARUM|PFE1080w 487 PFE1080w "ribosomal large subu 0.290 0.211 0.301 0.00088
UNIPROTKB|Q8I3P7 487 PFE1080w "Ribosomal large subu 0.290 0.211 0.301 0.00088
TAIR|locus:2119073 AT4G21770 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1088 (388.1 bits), Expect = 3.8e-110, P = 3.8e-110
 Identities = 213/327 (65%), Positives = 255/327 (77%)

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 331
             L  APLP+GI++HYMRP N+APRLV+E
Sbjct:   296 LAAAPLPIGIISHYMRPKNMAPRLVAE 322
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|APH_0549 APH_0549 "ribosomal large subunit pseudouridine synthase C" [Anaplasma phagocytophilum HZ (taxid:212042)] 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
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
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

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) ?
Q9SVS0PUS6_ARATH5, ., 4, ., 9, 9, ., -0.64030.93780.7033yesno
A3BN26PUS6_ORYSJ5, ., 4, ., 9, 9, ., -0.71650.71750.5324yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer5.4.990.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query354
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 4e-18
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 2e-14
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 8e-08
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 1e-07
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 8e-05
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 2e-04
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 0.001
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase Back     alignment and domain information 
 Score = 79.8 bits (197), Expect = 4e-18
 Identities = 28/109 (25%), Positives = 46/109 (42%), Gaps = 1/109 (0%)

Query: 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYC 286
           ++V++KPAG  V  T  +   S       A      L   H++D  T G ++LA+  E  
Sbjct: 1   YIVVNKPAGVPVHPTDPSDLLSLTALLLVAELGKFRLYPVHRLDRNTSGLLLLAKDGEAA 60

Query: 287 SIFHRKIREKKVKKLYLALTTAPLPV-GIMTHYMRPINIAPRLVSEGKT 334
           +  ++   E+KV+K YLAL   P    G +   ++          E   
Sbjct: 61  NKLNKLFPERKVEKEYLALVDGPEEEEGTIKAPIKKDKAVGFRKKEELD 109

Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA. Length = 149
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD 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|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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 354
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
PRK11180 325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 99.95
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 99.92
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 99.92
PRK10475 290 23S rRNA pseudouridine synthase F; Provisional 99.92
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 99.91
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 99.91
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 99.91
PRK11112 257 tRNA pseudouridine synthase C; Provisional 99.91
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 99.9
KOG1919 371 consensus RNA pseudouridylate synthases [RNA proce 99.87
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 99.85
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.82
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 99.82
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 99.8
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 99.76
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 99.74
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.74
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.69
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.62
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.62
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.58
cd02868 226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 99.16
TIGR00093128 pseudouridine synthase. This model identifies pane 99.14
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 98.8
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 98.37
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 98.22
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.63
smart0036360 S4 S4 RNA-binding domain. 97.47
COG1188100 Ribosome-associated heat shock protein implicated 97.41
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 97.33
PRK00989 230 truB tRNA pseudouridine synthase B; Provisional 97.31
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.28
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.23
PRK04099 273 truB tRNA pseudouridine synthase B; Provisional 97.18
PRK00020 244 truB tRNA pseudouridine synthase B; Provisional 97.17
PRK02484 294 truB tRNA pseudouridine synthase B; Provisional 97.04
PRK02193 279 truB tRNA pseudouridine synthase B; Provisional 97.02
PRK14123 305 tRNA pseudouridine synthase B; Provisional 97.0
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 96.98
cd02573 277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 96.96
PRK14124 308 tRNA pseudouridine synthase B; Provisional 96.96
PRK03287 298 truB tRNA pseudouridine synthase B; Provisional 96.95
PRK00130 290 truB tRNA pseudouridine synthase B; Provisional 96.95
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 96.95
PRK02755 295 truB tRNA pseudouridine synthase B; Provisional 96.91
PRK05389 305 truB tRNA pseudouridine synthase B; Provisional 96.91
PRK04270 300 H/ACA RNA-protein complex component Cbf5p; Reviewe 96.89
PRK01528 292 truB tRNA pseudouridine synthase B; Provisional 96.87
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 96.86
PRK01851 303 truB tRNA pseudouridine synthase B; Provisional 96.82
PRK01550 304 truB tRNA pseudouridine synthase B; Provisional 96.82
PRK05033 312 truB tRNA pseudouridine synthase B; Provisional 96.78
PRK14122 312 tRNA pseudouridine synthase B; Provisional 96.72
CHL00113201 rps4 ribosomal protein S4; Reviewed 96.72
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 96.62
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 96.56
TIGR00425 322 CBF5 rRNA pseudouridine synthase, putative. This f 96.43
COG2302257 Uncharacterized conserved protein, contains S4-lik 96.42
PRK05327203 rpsD 30S ribosomal protein S4; Validated 96.41
PRK04642 300 truB tRNA pseudouridine synthase B; Provisional 96.39
cd02867 312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 95.92
COG0130 271 TruB Pseudouridine synthase [Translation, ribosoma 95.9
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 95.41
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 94.58
PRK1150770 ribosome-associated protein; Provisional 93.85
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 90.85
COG250173 S4-like RNA binding protein [Replication, recombin 90.6
PRK04313237 30S ribosomal protein S4e; Validated 89.79
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 88.48
PLN00036261 40S ribosomal protein S4; Provisional 88.33
PTZ00223273 40S ribosomal protein S4; Provisional 87.98
COG4332203 Uncharacterized protein conserved in bacteria [Fun 87.73
PTZ00118262 40S ribosomal protein S4; Provisional 87.45
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 87.27
PF1445181 Ub-Mut7C: Mut7-C ubiquitin 83.26
PLN00189194 40S ribosomal protein S9; Provisional 82.84
PRK0177795 hypothetical protein; Validated 82.75
PF06353142 DUF1062: Protein of unknown function (DUF1062); In 82.4
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=1.4e-35  Score=286.21  Aligned_cols=168  Identities=23%  Similarity=0.300  Sum_probs=146.0

Q ss_pred             cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (354)
Q Consensus       111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~  189 (354)
                      +|++||++ + .+||+.++++|++|.|.                                  |||+.+          ++
T Consensus        14 rld~~L~~-l~~~sr~~~~~~i~~g~v~----------------------------------vNg~~v----------~~   48 (289)
T COG0564          14 RLDKFLAK-LLPISRSRIQKLIRKGRVR----------------------------------VNGKKV----------KP   48 (289)
T ss_pred             CHHHHHHH-ccCcCHHHHHHHHHCCCEE----------------------------------ECCEEc----------cC
Confidence            49999999 6 49999999999999999                                  899874          47


Q ss_pred             ceeecCCcEEEEecCCCCCC-CCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC-CCCceecc
Q 018538          190 DQIVEAGTYLRVHVHPKRFP-RCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTTH  267 (354)
Q Consensus       190 ~~~V~~GD~I~V~~~~~~~~-~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~-~~~~~~VH  267 (354)
                      +++|..||.|++...+.... ...+.+.+++|||||++++|||||+||+|||++++..+|+++.++.+... ...+++||
T Consensus        49 ~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vH  128 (289)
T COG0564          49 SYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVH  128 (289)
T ss_pred             CeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeec
Confidence            88999999999987653321 22235556899999999999999999999999998899999998887643 35799999


Q ss_pred             CCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC--cceEEccccccC
Q 018538          268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPIN  323 (354)
Q Consensus       268 RLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~--~G~I~~~L~pi~  323 (354)
                      ||||+||||||||||..++..|+++|+++.++|+|+|+|.|.++  +|+|+.++....
T Consensus       129 RLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~  186 (289)
T COG0564         129 RLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDP  186 (289)
T ss_pred             cCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCC
Confidence            99999999999999999999999999999999999999999987  599996655543

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; 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
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family Back     alignment and domain information
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>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
>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
>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
>TIGR00093 pseudouridine synthase 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
>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
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 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
>PRK01528 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
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>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
>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
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; 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
>PF14451 Ub-Mut7C: Mut7-C ubiquitin Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PRK01777 hypothetical protein; Validated Back     alignment and domain information
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function 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 ?
Query354
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 6e-04
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 9e-04
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 Back     alignment and structure 
Iteration: 1

 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 220 IIAVTESHV-VLDKPAGTSVGGTTD---NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           +I   + H+ VL+KP+GT+V G +     + E        A      L   H++D  T G
Sbjct: 6   VILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA----RFLELVHRLDRDTSG 61
Query: 276 CVVLARTQEYCSIFHRKIREKKVKKLYLAL 305
            +++A+ +      H ++REK ++K YLAL
Sbjct: 62  VLLVAKKRSALRSLHEQLREKGMQKDYLAL 91
>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 ?
Query354
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-07
>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
 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 59/341 (17%), Positives = 92/341 (26%), Gaps = 98/341 (28%)

Query: 39  YKSNVVLSFSSS----NRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPS 94
            +  +V  F       N  F+           T+    +  T      Y E    L    
Sbjct: 74  KQEEMVQKFVEEVLRINYKFLMSPI------KTEQRQPSMMTRM----YIEQRDRL---- 119

Query: 95  QNCPPRVEHLVVSEGGPVLEYICRE--LNL-PPLFVADLIH----FG-AVYYALVCPKPP 146
            N         VS   P L+   R+  L L P   V  LI      G       VC    
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKL--RQALLELRPAKNV--LIDGVLGSGKTWVALDVCLSYK 175

Query: 147 LTATPEQMRVF-----KEVTDPSVLSKRSS----IKGKTVREAQKTFRITHVDQIVEAGT 197
           +    +  ++F        +  +VL         I       +  +  I    +I     
Sbjct: 176 VQCKMD-FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL--RIHSIQA 232

Query: 198 YLRVHVHPKRFPRCYDI-D--WNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFAS 254
            LR  +  K +  C  +     N++           +                     + 
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWN------AFN--------------------LSC 266

Query: 255 RALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRK-IREKKVKKL---YLALTTAPL 310
           + L LTT  R     D      +  A T       H   +   +VK L   YL      L
Sbjct: 267 KIL-LTT--RFKQVTDF-----LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318

Query: 311 PVGIMTHYMRPINIAPRLVSEGKTIFGLALMIREMV--WKF 349
           P  ++T         PR +S       +A  IR+ +  W  
Sbjct: 319 PREVLT-------TNPRRLS------IIAESIRDGLATWDN 346

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query354
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 99.96
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 99.95
3dh3_A 290 Ribosomal large subunit pseudouridine synthase F; 99.94
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 99.92
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 99.9
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 99.86
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 99.85
2gml_A 237 Ribosomal large subunit pseudouridine synthase F; 99.69
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.2
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 97.63
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 97.57
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 97.26
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 97.09
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 96.86
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 96.69
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 96.66
1k8w_A 327 TRNA pseudouridine synthase B; protein-RNA complex 96.64
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 96.62
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 96.61
1r3e_A 309 TRNA pseudouridine synthase B; RNA modification, p 96.55
1sgv_A 316 TRNA pseudouridine synthase B; hinged motion, tRNA 96.41
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 96.35
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 96.09
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 95.63
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 95.06
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 94.31
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 93.27
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 91.62
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 83.68
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 83.09
>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=7.1e-34  Score=276.28  Aligned_cols=170  Identities=14%  Similarity=0.164  Sum_probs=97.5

Q ss_pred             cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (354)
Q Consensus       111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~  189 (354)
                      +|++||++.+ .+||+.++++|+.|.|+                                  |||+.+         +++
T Consensus        18 RLd~~L~~~~~~~SR~~~~~lI~~G~V~----------------------------------VNG~~v---------~~~   54 (325)
T 1v9f_A           18 RLDQALAEMFPDYSRSRIKEWILDQRVL----------------------------------VNGKVC---------DKP   54 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHhhccccCHHHHHHHHHCCCEE----------------------------------ECCEEc---------cCC
Confidence            3999999988 89999999999999999                                  889863         467


Q ss_pred             ceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC---CCCceec
Q 018538          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTT  266 (354)
Q Consensus       190 ~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~---~~~~~~V  266 (354)
                      +++|.+||.|.|..++.......+...+++|+|||++|+|+|||+||+||++.++...|+.+.+..++..   ...+++|
T Consensus        55 ~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~v  134 (325)
T 1v9f_A           55 KEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIV  134 (325)
T ss_dssp             ---------------------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBC
T ss_pred             CCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceeee
Confidence            8899999999998654322111234456899999999999999999999998877677898888766531   2358999


Q ss_pred             cCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC-cceEEccccccC
Q 018538          267 HQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP-VGIMTHYMRPIN  323 (354)
Q Consensus       267 HRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~-~G~I~~~L~pi~  323 (354)
                      ||||++||||||||||+++++.|+++|++++|+|+|+|+|.|.++ +|+|+.+|.+..
T Consensus       135 hRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~g~i~~~i~~~~  192 (325)
T 1v9f_A          135 HRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHP  192 (325)
T ss_dssp             CCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEEECS
T ss_pred             cCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCCCCEEeeeeeECC
Confidence            999999999999999999999999999999999999999999988 799997776543
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6 Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>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
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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
>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
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>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
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query354
d1v9fa_ 250 Ribosomal large subunit pseudouridine synthase D, 99.93
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 99.92
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 99.63
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 99.51
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 98.43
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 98.4
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 97.66
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 97.43
d1k8wa5 242 Pseudouridine synthase II TruB {Escherichia coli [ 96.94
d1r3ea2 228 Pseudouridine synthase II TruB {Thermotoga maritim 96.85
d1sgva2 233 Pseudouridine synthase II TruB {Mycobacterium tube 96.71
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 96.67
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 96.47
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 96.13
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 95.7
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 95.45
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 94.29
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 92.93
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {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 D, RluD
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=3e-26  Score=213.14  Aligned_cols=112  Identities=15%  Similarity=0.182  Sum_probs=97.6

Q ss_pred             CCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC---CCCceeccCCCCCCceEEEeeCCHHHHHHHH
Q 018538          214 IDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTTHQIDNCTEGCVVLARTQEYCSIFH  290 (354)
Q Consensus       214 ~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~---~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~  290 (354)
                      ++.+++|||||++|||||||+||+|||+.++..+++.+.+..++..   ...+++|||||++||||||||||.++++.|+
T Consensus         4 ~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~~a~~~l~   83 (250)
T d1v9fa_           4 QDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLV   83 (250)
T ss_dssp             CCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHH
T ss_pred             CCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhccCCCceeEEeecCCCCcceEEEecccHHHHhhh
Confidence            4567899999999999999999999999887788898888776632   2357899999999999999999999999999


Q ss_pred             HhHhcCccceEEEEEEeccCC-cceEEccccccCCC
Q 018538          291 RKIREKKVKKLYLALTTAPLP-VGIMTHYMRPINIA  325 (354)
Q Consensus       291 ~~f~~~~V~K~YlAlV~G~l~-~G~I~~~L~pi~r~  325 (354)
                      ++|+++.|.|+|+|++.|.++ ++.++.++......
T Consensus        84 ~~f~~~~v~K~Y~a~~~g~~~~~~~~~~~~~~~~~~  119 (250)
T d1v9fa_          84 ESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTK  119 (250)
T ss_dssp             HHHHTTCSEEEEEEEEESCCCCCEEEECCEEECSSC
T ss_pred             hhhccceEeEEeeeeeccccccccccccccccCCcc
Confidence            999999999999999999998 77888666554443
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure