Citrus Sinensis ID: 023331

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Local Sequence Feature Prediction

Residue Number Marker
--------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----
Protein Sequence
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHccEEEEEcccccccccccHHHHHHHHHcccccHHcccccccccccEEccccEEEcccccEEccccEEEEEcccccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHHccccccccccccccccccEEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHcccccccccHHHHHHHHHHcccHHcccccccccEEEEEccccccEEcccccccccHHHHHHHHccccccccccccHccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHcccEEEEEccccccccccHHHHHHHHccccHHHHHHHHccccccHHHHccccEEcccccccccccEEEEEccccccccEEEEccccEEEEEcccEEEEEcccccccccccccHHHHHHHHHHHHHcccccccccEEccccccEEEEEEEccc
Coil and Loop (DISEMBL)
MSSVSFSSIftnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFsssnrnfvceswkrhvfthtdTAAIaaattpssygypeyhrllpcpsqncpprvehlvvseggpVLEYICRelnlpplfvaDLIHFGAVYYAlvcpkppltatpeqmrvfkevtdpsvlskrssikgkTVREAQKTFRITHVDQIVEAGtylrvhvhpkrfprcydidwnsrIIAVTEshvvldkpagtsvggttdniEESCATFASRalglttplrtthqidnctegwyCYFTTLA
Flexible Loop (DISEMBL)
MSSVSFSSIFtnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEqmrvfkevtdpsvlskrssikgktvreaqktfrithvdqiVEAGtylrvhvhpkrfPRCYDIDWNSRIIAVTeshvvldkpagtsvggttdNIEESCATFASRalglttplrtthqidncteGWYCYFTTLA
Low Complexity Region (SEG)
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFthtdtaaiaaattPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA
Disordered region (IsUnstruct)
***************SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLT*******************************AQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT**
Disordered Region (DISOPRED)
******S*IFTNNGRSLGAPVSLLRTLASTHASC*********************CESWKRHVFTHTDTAA*****TP*SYGYPEYHRLLPCP**************EGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDP**********************ITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL*
Disordered Region (DISEMBL)
********IFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA
Disordered Region (DISPRO)
*****FSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	284	2.2.26 [Sep-21-2011]
Q9SVS0	472	RNA pseudourine synthase	yes	no	0.922	0.555	0.642	1e-92
A3BN26	477	RNA pseudourine synthase	yes	no	0.697	0.415	0.712	5e-77

>sp|Q9SVS0|PUS6_ARATH RNA pseudourine synthase 6, chloroplastic OS=Arabidopsis thaliana GN=At4g21770 PE=2 SV=1

 Score =  339 bits (870), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 174/271 (64%), Positives = 210/271 (77%), Gaps = 9/271 (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 IEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           IEESCATFASRAL L  PL+TTHQIDNCTEG
Sbjct: 236 IEESCATFASRALDLPEPLKTTHQIDNCTEG 266

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

 Score =  287 bits (735), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 141/198 (71%), Positives = 164/198 (82%)

Query: 78  PSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVY 137
           P++  YP Y RLLPCP Q+ PPR+EHLV  E    +++I R L LPPL+VADLI FGAVY
Sbjct: 66  PATAAYPVYGRLLPCPLQDDPPRIEHLVAREDEVAVDFISRSLTLPPLYVADLIKFGAVY 125

Query: 138 YALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGT 197
           YALV P+PP  A PE +R+F+EVT+PSVL +R SIKGKTVREAQKTFR+T  +Q +EAGT
Sbjct: 126 YALVAPQPPPHAAPEHVRIFREVTEPSVLCRRKSIKGKTVREAQKTFRVTDPNQRLEAGT 185

Query: 198 YLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRAL 257
           YLRVHVHPKRFPRCY+IDW SR+IAVT+++VVLDKPA TSVGG TDNIEESC  F SRAL
Sbjct: 186 YLRVHVHPKRFPRCYEIDWKSRVIAVTDNYVVLDKPAATSVGGATDNIEESCVVFTSRAL 245

Query: 258 GLTTPLRTTHQIDNCTEG 275
           GL TPL TTHQIDNC+EG
Sbjct: 246 GLETPLMTTHQIDNCSEG 263

Oryza sativa subsp. japonica (taxid: 39947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	284
224076324	470	predicted protein [Populus trichocarpa]	0.926	0.559	0.716	1e-106
255554955	476	ribosomal pseudouridine synthase, putati	0.940	0.560	0.707	1e-104
225444351	472	PREDICTED: RNA pseudourine synthase 6, c	0.894	0.538	0.732	1e-103
449467613	475	PREDICTED: RNA pseudourine synthase 6, c	0.862	0.515	0.705	3e-97
449488468	475	PREDICTED: LOW QUALITY PROTEIN: RNA pseu	0.862	0.515	0.705	4e-97
356546416	473	PREDICTED: RNA pseudourine synthase 6, c	0.894	0.536	0.639	1e-93
449471733	287	PREDICTED: RNA pseudourine synthase 6, c	0.887	0.878	0.653	4e-93
449488373	475	PREDICTED: RNA pseudourine synthase 6, c	0.887	0.530	0.653	6e-93
449454720	475	PREDICTED: RNA pseudourine synthase 6, c	0.887	0.530	0.653	6e-93
356557901	473	PREDICTED: RNA pseudourine synthase 6, c	0.922	0.553	0.661	2e-92

>gi|224076324|ref|XP_002304926.1| predicted protein [Populus trichocarpa] gi|222847890|gb|EEE85437.1| predicted protein [Populus trichocarpa]

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 197/275 (71%), Positives = 224/275 (81%), Gaps = 12/275 (4%)

Query: 1   MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWK 60
           M+S++ +SIF+ + RS  APV+LLRTLA T A    ++ K  +V   S S +   CES K
Sbjct: 1   MASLNLASIFSYSYRSFSAPVTLLRTLAFTRAY---SLNKKALVWC-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 TTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           TTDNIEESCATFA+RALGLT PLRTTHQIDNCTEG
Sbjct: 229 TTDNIEESCATFATRALGLTAPLRTTHQIDNCTEG 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554955|ref|XP_002518515.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223542360|gb|EEF43902.1| ribosomal pseudouridine synthase, putative [Ricinus communis]

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 196/277 (70%), Positives = 223/277 (80%), Gaps = 10/277 (3%)

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 GGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           GGT DNIEESCATFA+RALGLTTPL+TTHQIDNCTEG
Sbjct: 233 GGTADNIEESCATFATRALGLTTPLKTTHQIDNCTEG 269

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 197/269 (73%), Positives = 218/269 (81%), Gaps = 15/269 (5%)

Query: 7   SSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTH 66
           SS++ +N RS G PV+L RTLAS           SNV   FS  ++  V  S      T 
Sbjct: 16  SSLWNSNCRSFGTPVALARTLAS-----------SNV---FSRRHKRVVWCS-NNPTCTR 60

Query: 67  TDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLF 126
             TA+  +A T S  GYPEYHRLLPCPSQN PPRVEHLVVSEGG VL+YI + L+LPPLF
Sbjct: 61  ELTASSDSANTSSVNGYPEYHRLLPCPSQNGPPRVEHLVVSEGGCVLDYISKALDLPPLF 120

Query: 127 VADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186
           VADLIHFGAVYYALVCP+PP +ATPEQ+R+FKEVT PSVL KR SIKGKT+REAQKTFRI
Sbjct: 121 VADLIHFGAVYYALVCPEPPPSATPEQVRLFKEVTAPSVLRKRPSIKGKTIREAQKTFRI 180

Query: 187 THVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIE 246
           T V++ VEAGTYLRVHVHPKRFPRCY+IDW SRIIAVTES+VVLDKPAGTSVGGTTDNIE
Sbjct: 181 TDVNEFVEAGTYLRVHVHPKRFPRCYEIDWKSRIIAVTESYVVLDKPAGTSVGGTTDNIE 240

Query: 247 ESCATFASRALGLTTPLRTTHQIDNCTEG 275
           ESCATFA+RALGLTTPLRTTHQIDNCTEG
Sbjct: 241 ESCATFATRALGLTTPLRTTHQIDNCTEG 269

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449467613|ref|XP_004151517.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]

 Score =  360 bits (925), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 182/258 (70%), Positives = 206/258 (79%), Gaps = 13/258 (5%)

Query: 22  SLLRTLA----STHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATT 77
           SLLRTLA    S  A+  R+ +      S  S +  F C+S      + TD   +  AT 
Sbjct: 20  SLLRTLARPRASLSAASSRDYFAPR--RSLGSKSSAFPCKS------SITDVT-VKTATN 70

Query: 78  PSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVY 137
            +  GYP+YHRLLPCPS + PPRVEH+VV E GPV+EYIC+ LNLPPL+VADLIHFGAVY
Sbjct: 71  SAENGYPQYHRLLPCPSFSKPPRVEHMVVLEAGPVMEYICKSLNLPPLYVADLIHFGAVY 130

Query: 138 YALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGT 197
           YALVCP+PP TATPEQ+R+FK+ T+PS L  R SIKGKTVREAQKTFRITHVD+ VE GT
Sbjct: 131 YALVCPQPPKTATPEQIRLFKKFTEPSFLKGRKSIKGKTVREAQKTFRITHVDEFVEVGT 190

Query: 198 YLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRAL 257
           YLRVHVHPKRFPRCY+IDW SRIIAVTES+VVLDKPAGTSVGGTTDNIEESCATFA+RAL
Sbjct: 191 YLRVHVHPKRFPRCYEIDWKSRIIAVTESYVVLDKPAGTSVGGTTDNIEESCATFATRAL 250

Query: 258 GLTTPLRTTHQIDNCTEG 275
           GLT+PL TTHQIDNCTEG
Sbjct: 251 GLTSPLWTTHQIDNCTEG 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  360 bits (924), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 182/258 (70%), Positives = 205/258 (79%), Gaps = 13/258 (5%)

Query: 22  SLLRTLA----STHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATT 77
           SLLRTLA    S  A+  R+ +      S  S +  F C+S      + TD   +  AT 
Sbjct: 20  SLLRTLARPRASLSAASSRDYFAPRC--SLGSKSSAFPCKS------SITDVT-VKTATN 70

Query: 78  PSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVY 137
            +  GYP+YHRLLPCPS + PPRVEH+VV E GPV+EYIC+ LNLPPL+VADLIHFGAVY
Sbjct: 71  SAENGYPQYHRLLPCPSFSKPPRVEHMVVLEAGPVMEYICKSLNLPPLYVADLIHFGAVY 130

Query: 138 YALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGT 197
           YALVCP+PP TATPEQ+R+FK  T+PS L  R SIKGKTVREAQKTFRITHVD+ VE GT
Sbjct: 131 YALVCPQPPKTATPEQIRLFKNXTEPSFLKGRKSIKGKTVREAQKTFRITHVDEFVEVGT 190

Query: 198 YLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRAL 257
           YLRVHVHPKRFPRCY+IDW SRIIAVTES+VVLDKPAGTSVGGTTDNIEESCATFA+RAL
Sbjct: 191 YLRVHVHPKRFPRCYEIDWKSRIIAVTESYVVLDKPAGTSVGGTTDNIEESCATFATRAL 250

Query: 258 GLTTPLRTTHQIDNCTEG 275
           GLT+PL TTHQIDNCTEG
Sbjct: 251 GLTSPLWTTHQIDNCTEG 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546416|ref|XP_003541622.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max]

 Score =  348 bits (894), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 179/280 (63%), Positives = 207/280 (73%), Gaps = 26/280 (9%)

Query: 7   SSIFTNNGRSLGAP-----VSLLRTLASTHASCH------RNIYKSNVVLSFSSSNRNFV 55
           S +F    R L  P     + + R   S+H + H      R+ + SN  L+  +      
Sbjct: 5   SMLFAGGCRILAVPAAARAIRIPRAALSSHHNKHAPSWGCRSSHNSNTALAGEAE----- 59

Query: 56  CESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEY 115
                   F+ TD   + A  T SS  +P+Y RLLPCPS   PPR+EHLV+SEGGPVLE 
Sbjct: 60  --------FSTTDAGNLTA--TSSSDSFPKYDRLLPCPSHKNPPRIEHLVISEGGPVLEL 109

Query: 116 ICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGK 175
           IC+ L+LPPL+V+DLI FGAVYYALVCP+PP  AT EQ+RVFKEVT+PSVL KR+SIKGK
Sbjct: 110 ICKALDLPPLYVSDLIQFGAVYYALVCPQPPPNATEEQIRVFKEVTEPSVLRKRASIKGK 169

Query: 176 TVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAG 235
           TVREAQKTFR+THVDQ VE GTYLRVHVHPKRFPR Y+IDW SRIIAV ES+VVLDKPAG
Sbjct: 170 TVREAQKTFRVTHVDQFVEPGTYLRVHVHPKRFPRSYEIDWRSRIIAVAESYVVLDKPAG 229

Query: 236 TSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           TSVGGTTDNIEESCATFA+RALG+TTPL TTHQIDNCTEG
Sbjct: 230 TSVGGTTDNIEESCATFATRALGMTTPLMTTHQIDNCTEG 269

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449471733|ref|XP_004153393.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like, partial [Cucumis sativus]

 Score =  347 bits (889), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 170/260 (65%), Positives = 204/260 (78%), Gaps = 8/260 (3%)

Query: 16  SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAA 75
           SL  P  + RT A+  AS     + +  + SFS +++ F CES      + TD      A
Sbjct: 17  SLNLPREVARTRANLSASISSTCFAA--LRSFSFNSKAFPCES------STTDVNVTQTA 68

Query: 76  TTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGA 135
           T  +  GYP+YHRLLPC S N PPRVEHLVV EGGPV+EYI + L+LPP++VADLIHFGA
Sbjct: 69  TNSAENGYPQYHRLLPCTSFNVPPRVEHLVVLEGGPVMEYISKSLDLPPMYVADLIHFGA 128

Query: 136 VYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEA 195
           VYYALVCP+PP TA+ E++R+FK+ T PS L  R SIKGKT+REAQKTFRITH+D+ VE 
Sbjct: 129 VYYALVCPQPPPTASSEEIRLFKKFTQPSFLIGRKSIKGKTLREAQKTFRITHIDEFVEV 188

Query: 196 GTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASR 255
           GTYLRV+VHPKRFPRCY++DW SRIIAVT+S+VVLDKPAGTSVGGTT+NIEE+C TFA+R
Sbjct: 189 GTYLRVYVHPKRFPRCYEVDWKSRIIAVTDSYVVLDKPAGTSVGGTTNNIEETCVTFATR 248

Query: 256 ALGLTTPLRTTHQIDNCTEG 275
           ALGLT+PL TTHQIDNCTEG
Sbjct: 249 ALGLTSPLWTTHQIDNCTEG 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449488373|ref|XP_004158017.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]

 Score =  346 bits (888), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 170/260 (65%), Positives = 204/260 (78%), Gaps = 8/260 (3%)

Query: 16  SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAA 75
           SL  P  + RT A+  AS     + +  + SFS +++ F CES      + TD      A
Sbjct: 17  SLNLPREVARTRANLSASISSTCFAA--LRSFSFNSKAFPCES------STTDVNVTQTA 68

Query: 76  TTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGA 135
           T  +  GYP+YHRLLPC S N PPRVEHLVV EGGPV+EYI + L+LPP++VADLIHFGA
Sbjct: 69  TNSAENGYPQYHRLLPCTSFNVPPRVEHLVVLEGGPVMEYISKSLDLPPMYVADLIHFGA 128

Query: 136 VYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEA 195
           VYYALVCP+PP TA+ E++R+FK+ T PS L  R SIKGKT+REAQKTFRITH+D+ VE 
Sbjct: 129 VYYALVCPQPPPTASSEEIRLFKKFTQPSFLIGRKSIKGKTLREAQKTFRITHIDEFVEV 188

Query: 196 GTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASR 255
           GTYLRV+VHPKRFPRCY++DW SRIIAVT+S+VVLDKPAGTSVGGTT+NIEE+C TFA+R
Sbjct: 189 GTYLRVYVHPKRFPRCYEVDWKSRIIAVTDSYVVLDKPAGTSVGGTTNNIEETCVTFATR 248

Query: 256 ALGLTTPLRTTHQIDNCTEG 275
           ALGLT+PL TTHQIDNCTEG
Sbjct: 249 ALGLTSPLWTTHQIDNCTEG 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454720|ref|XP_004145102.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Cucumis sativus]

 Score =  346 bits (888), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 170/260 (65%), Positives = 204/260 (78%), Gaps = 8/260 (3%)

Query: 16  SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAA 75
           SL  P  + RT A+  AS     + +  + SFS +++ F CES      + TD      A
Sbjct: 17  SLNLPREVARTRANLSASISSTCFAA--LRSFSFNSKAFPCES------STTDVNVTQTA 68

Query: 76  TTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGA 135
           T  +  GYP+YHRLLPC S N PPRVEHLVV EGGPV+EYI + L+LPP++VADLIHFGA
Sbjct: 69  TNSAENGYPQYHRLLPCTSFNVPPRVEHLVVLEGGPVMEYISKSLDLPPMYVADLIHFGA 128

Query: 136 VYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEA 195
           VYYALVCP+PP TA+ E++R+FK+ T PS L  R SIKGKT+REAQKTFRITH+D+ VE 
Sbjct: 129 VYYALVCPQPPPTASSEEIRLFKKFTQPSFLIGRKSIKGKTLREAQKTFRITHIDEFVEV 188

Query: 196 GTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASR 255
           GTYLRV+VHPKRFPRCY++DW SRIIAVT+S+VVLDKPAGTSVGGTT+NIEE+C TFA+R
Sbjct: 189 GTYLRVYVHPKRFPRCYEVDWKSRIIAVTDSYVVLDKPAGTSVGGTTNNIEETCVTFATR 248

Query: 256 ALGLTTPLRTTHQIDNCTEG 275
           ALGLT+PL TTHQIDNCTEG
Sbjct: 249 ALGLTSPLWTTHQIDNCTEG 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557901|ref|XP_003547248.1| PREDICTED: RNA pseudourine synthase 6, chloroplastic-like [Glycine max]

 Score =  345 bits (884), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 180/272 (66%), Positives = 207/272 (76%), Gaps = 10/272 (3%)

Query: 7   SSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYK---SNVVLSFSSSNRNFVCESWKRHV 63
           S +F+ + RSL  P +  R +  + A+   N  K   S    S  +SN     E+     
Sbjct: 5   SMLFSGSCRSLAMPAAA-RAVRISRAALVNNRNKHPPSWCCRSSHNSNTALAGEA----E 59

Query: 64  FTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLP 123
           F  TD   + A  T SS  + +Y RLLPCPS   PPR+EHLVVSEGGPVLE+IC+ L+LP
Sbjct: 60  FLTTDAGILNA--TSSSDSFRKYDRLLPCPSHKTPPRIEHLVVSEGGPVLEHICKALDLP 117

Query: 124 PLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKT 183
           PL+V+DLI FGAVYYALVCP+PP  AT EQ+RVFKEVT+PSVL KR+SIKGKTVREAQKT
Sbjct: 118 PLYVSDLIQFGAVYYALVCPQPPPNATEEQIRVFKEVTEPSVLRKRASIKGKTVREAQKT 177

Query: 184 FRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTD 243
           FR+THVDQ VE GTYLRVHVHPKR PRCY+IDW SRII V ES+VVLDKPAGTSVGGTTD
Sbjct: 178 FRVTHVDQFVEPGTYLRVHVHPKRSPRCYEIDWRSRIITVAESYVVLDKPAGTSVGGTTD 237

Query: 244 NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           NIEESCATFA+RALG+TTPL TTHQIDNCTEG
Sbjct: 238 NIEESCATFATRALGMTTPLMTTHQIDNCTEG 269

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	284
TAIR|locus:2119073	472	AT4G21770 [Arabidopsis thalian	0.947	0.569	0.622	3.3e-86

TAIR|locus:2119073 AT4G21770 [Arabidopsis thaliana (taxid:3702)]

 Score = 862 (308.5 bits), Expect = 3.3e-86, P = 3.3e-86
 Identities = 173/278 (62%), Positives = 208/278 (74%)

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 IEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282
             IEESCATFASRAL L  PL+TTHQIDNCTEG   +  T
Sbjct:   236 IEESCATFASRALDLPEPLKTTHQIDNCTEGCVVFART 273


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.134   0.420    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      284       271   0.00098  114 3  11 22  0.46    33
                                                     32  0.40    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  615 (65 KB)
  Total size of DFA:  223 KB (2122 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  23.24u 0.11s 23.35t   Elapsed:  00:00:01
  Total cpu time:  23.24u 0.11s 23.35t   Elapsed:  00:00:01
  Start:  Thu May  9 21:13:10 2013   End:  Thu May  9 21:13:11 2013

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

---

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)
A3BN26	PUS6_ORYSJ	5, ., 4, ., 9, 9, ., -	0.7121	0.6971	0.4150	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

No EC number assignment, probably not an enzyme!

---

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	Length	Definition	E-value
Query	284
pfam00849	149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	2e-04

>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 21/49 (42%)

Query: 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           ++V++KPAG  V  T  +   S       A      L   H++D  T G
Sbjct: 1   YIVVNKPAGVPVHPTDPSDLLSLTALLLVAELGKFRLYPVHRLDRNTSG 49

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	284
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	99.96
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	99.93
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	99.92
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	99.92
cd02558	246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	99.86
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	99.83
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	99.77
KOG1919	371	consensus RNA pseudouridylate synthases [RNA proce	99.77
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	99.73
cd02557	213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	99.72
PRK10158	219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	99.7
TIGR01621	217	RluA-like pseudouridine synthase Rlu family protei	99.69
cd02563	223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	99.69
PRK11112	257	tRNA pseudouridine synthase C; Provisional	99.68
cd02550	154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.44
PF00849	164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.4
cd02553	167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.38
cd02556	167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.37
cd02870	146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.37
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.02
PRK11394	217	23S rRNA pseudouridine synthase E; Provisional	99.0
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	98.99
cd02555	177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	98.91
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	98.18
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	97.91
cd02869	185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	97.7
smart00363	60	S4 S4 RNA-binding domain.	97.38
COG1188	100	Ribosome-associated heat shock protein implicated	97.24
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	96.99
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	96.66
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	96.23
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	96.0
CHL00113	201	rps4 ribosomal protein S4; Reviewed	95.89
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	95.89
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	95.75
COG2302	257	Uncharacterized conserved protein, contains S4-lik	95.64
PRK00020	244	truB tRNA pseudouridine synthase B; Provisional	95.55
PRK05033	312	truB tRNA pseudouridine synthase B; Provisional	95.11
PRK05389	305	truB tRNA pseudouridine synthase B; Provisional	95.08
PRK04270	300	H/ACA RNA-protein complex component Cbf5p; Reviewe	94.82
PRK01851	303	truB tRNA pseudouridine synthase B; Provisional	94.33
cd02566	168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	94.07
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	94.0
PRK04642	300	truB tRNA pseudouridine synthase B; Provisional	92.3
TIGR00425	322	CBF5 rRNA pseudouridine synthase, putative. This f	92.28
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	92.26
COG0130	271	TruB Pseudouridine synthase [Translation, ribosoma	90.18
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	88.96
PRK11507	70	ribosome-associated protein; Provisional	88.43
COG2501	73	S4-like RNA binding protein [Replication, recombin	87.35
PF06353	142	DUF1062: Protein of unknown function (DUF1062); In	86.91
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	83.0
cd02554	164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	81.93

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

Probab=99.96  E-value=4.3e-29  Score=233.63  Aligned_cols=129  Identities=17%  Similarity=0.142  Sum_probs=107.9

Q ss_pred             CcHHHHHHHhcC-CCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l~-lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+++.||++ +. +|+++++++++.|.|.+||.                                  .          ..
T Consensus        13 ~rld~~L~~-l~~~sr~~~~~~i~~g~v~vNg~----------------------------------~----------v~   47 (289)
T COG0564          13 QRLDKFLAK-LLPISRSRIQKLIRKGRVRVNGK----------------------------------K----------VK   47 (289)
T ss_pred             CCHHHHHHH-ccCcCHHHHHHHHHCCCEEECCE----------------------------------E----------cc
Confidence            489999998 55 99999999999999999985                                  1          23


Q ss_pred             cCceecCCCEEEEEcCCCCC-CCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC-CCCCccc
Q 023331          189 VDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTT  266 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~-~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~-~~pl~~V  266 (284)
                      .++.|+.||.|++....... ....+.+.+++|||||||++|||||+||+|||+.++..+|+++++..+.+. ...+++|
T Consensus        48 ~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~v  127 (289)
T COG0564          48 PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIV  127 (289)
T ss_pred             CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeee
Confidence            67899999999998754332 223345566899999999999999999999999999999999988766543 3346789


Q ss_pred             cCCCcccceeeeeeeeC
Q 023331          267 HQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       267 HRLDRdTSGLLlfAKT~  283 (284)
                      ||||||||||||||||.
T Consensus       128 HRLDkdTSGlll~AK~~  144 (289)
T COG0564         128 HRLDKDTSGLLLVAKNR  144 (289)
T ss_pred             ccCCCCCceEEEEECCH
Confidence            99999999999999985

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=99.93  E-value=2.2e-25  Score=206.60  Aligned_cols=131  Identities=18%  Similarity=0.131  Sum_probs=104.7

Q ss_pred             CcHHHHHHHhcC-CCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l~-lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+|++||++.+. +|++.++++|+.|.|++||..                                           ++.
T Consensus         6 ~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~-------------------------------------------~~~   42 (299)
T TIGR00005         6 QRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKV-------------------------------------------TAN   42 (299)
T ss_pred             hhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEe-------------------------------------------ccC
Confidence            489999999886 999999999999999999831                                           135


Q ss_pred             cCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC---CCCCcc
Q 023331          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT  265 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~pl~~  265 (284)
                      .++.|+.||.|.|...+...+.....+.+++|+|||++++|||||+||+|||+.++..+|+.+.+..++..   ...+++
T Consensus        43 ~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~  122 (299)
T TIGR00005        43 PKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGI  122 (299)
T ss_pred             cccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCce
Confidence            57799999999997543221222223446789999999999999999999999887778888877655432   134678


Q ss_pred             ccCCCcccceeeeeeeeC
Q 023331          266 THQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       266 VHRLDRdTSGLLlfAKT~  283 (284)
                      |||||++||||||||||.
T Consensus       123 vhRLD~~TSGlll~ak~~  140 (299)
T TIGR00005       123 VHRLDRDTSGLMVVAKTP  140 (299)
T ss_pred             ECCCCCCCceEEEEEcCH
Confidence            999999999999999984

modifies uracil-65 in transfer RNAs to pseudouridine.

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=99.92  E-value=1e-24  Score=205.39  Aligned_cols=129  Identities=17%  Similarity=0.129  Sum_probs=96.4

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+|++||++.+ .+|++.++++|+.|.|++||..                                            ..
T Consensus        20 ~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~--------------------------------------------v~   55 (317)
T PRK11025         20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKR--------------------------------------------IK   55 (317)
T ss_pred             chHHHHHHHhcccCCHHHHHHHHHcCCEEECCEE--------------------------------------------cC
Confidence            48999999877 5899999999999999999851                                            24


Q ss_pred             cCceecCCCEEEEEcCCCCCCCCC--------CCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCC
Q 023331          189 VDQIVEAGTYLRVHVHPKRFPRCY--------DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLT  260 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~~~~~--------~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~  260 (284)
                      +++.|+.||.|++...........        ...++++|||||++++|||||+||+|||+.+... ++.+.+.......
T Consensus        56 ~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~~-~~~~~~~~~~~~~  134 (317)
T PRK11025         56 PEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSF-GVIEGLRALRPEA  134 (317)
T ss_pred             cccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCCc-cHHHHHHHhccCC
Confidence            567999999999863211100000        0124679999999999999999999999876533 4555444332222


Q ss_pred             CCCccccCCCcccceeeeeeeeC
Q 023331          261 TPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       261 ~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ..+++||||||+||||||||||.
T Consensus       135 ~~~~~vhRLD~~TSGlll~Ak~~  157 (317)
T PRK11025        135 RFLELVHRLDRDTSGVLLVAKKR  157 (317)
T ss_pred             CcCceeCCCCCCCceEEEEEcCH
Confidence            33568999999999999999985

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=99.92  E-value=8.5e-25  Score=206.37  Aligned_cols=131  Identities=14%  Similarity=0.085  Sum_probs=103.5

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+|++||++.+ .+|++.++++|+.|.|++||+.                                           +..
T Consensus        18 ~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~-------------------------------------------v~~   54 (325)
T PRK11180         18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------INK   54 (325)
T ss_pred             ccHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccC
Confidence            48999999887 4899999999999999999851                                           124


Q ss_pred             cCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC---CCCCcc
Q 023331          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT  265 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~pl~~  265 (284)
                      +++.|+.||.|++...+.......+.+.+++|||||++++|||||+||+|||+.++..+|+.+.+..++..   ...+++
T Consensus        55 ~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~  134 (325)
T PRK11180         55 PKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI  134 (325)
T ss_pred             CCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccce
Confidence            56788999999998643221112233456899999999999999999999999887778888877655421   123568


Q ss_pred             ccCCCcccceeeeeeeeC
Q 023331          266 THQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       266 VHRLDRdTSGLLlfAKT~  283 (284)
                      |||||++||||||||||.
T Consensus       135 vhRLD~~TSGlll~Ak~~  152 (325)
T PRK11180        135 VHRLDKDTTGLMVVAKTV  152 (325)
T ss_pred             eccCCCCCceeEEEECCH
Confidence            999999999999999984

>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family

Probab=99.86  E-value=7.5e-22  Score=180.18  Aligned_cols=92  Identities=21%  Similarity=0.198  Sum_probs=74.7

Q ss_pred             CcCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCcccc
Q 023331          188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH  267 (284)
Q Consensus       188 ~~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VH  267 (284)
                      .+++.|+.||.|.++......   .+.+++++|||||++++|||||+||+|||+.++..+|+.+.+....+.. .+++||
T Consensus        12 ~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~-~~~~vh   87 (246)
T cd02558          12 DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNP-DLTPAH   87 (246)
T ss_pred             CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCC-cccccc
Confidence            567899999999998532211   1234568999999999999999999999998888888888776655533 456899


Q ss_pred             CCCcccceeeeeeeeC
Q 023331          268 QIDNCTEGWYCYFTTL  283 (284)
Q Consensus       268 RLDRdTSGLLlfAKT~  283 (284)
                      |||++||||||||||.
T Consensus        88 RLD~~TSGlll~Ak~~  103 (246)
T cd02558          88 RLDRLTAGLVLFSKRP  103 (246)
T ss_pred             cCCCCceeEEEEEcCH
Confidence            9999999999999985

This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=99.83  E-value=7.7e-21  Score=171.10  Aligned_cols=114  Identities=11%  Similarity=0.068  Sum_probs=85.2

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCcC
Q 023331          111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD  190 (284)
Q Consensus       111 ~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~~  190 (284)
                      +|+.||++.+.+|++.++++|+.|.|++||..                                           +..++
T Consensus         2 rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~-------------------------------------------~~~~~   38 (232)
T PRK10839          2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEI-------------------------------------------VKNGA   38 (232)
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE-------------------------------------------eccCC
Confidence            68999998888999999999999999999851                                           12456


Q ss_pred             ceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCC
Q 023331          191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID  270 (284)
Q Consensus       191 ~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLD  270 (284)
                      +.|++||.|.+...+..             ..+|++++|||||+||+|||+.. ...|+..++...  ....+++|||||
T Consensus        39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~-~~~tl~~~l~~~--~~~~~~~v~RLD  102 (232)
T PRK10839         39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDP-DHPTVLYFLDEP--VAYKLHAAGRLD  102 (232)
T ss_pred             cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCC-CCCeEEEecccc--cccCceecCCCC
Confidence            79999999987531100             11457999999999999999843 234554332211  122356899999


Q ss_pred             cccceeeeeeeeC
Q 023331          271 NCTEGWYCYFTTL  283 (284)
Q Consensus       271 RdTSGLLlfAKT~  283 (284)
                      +|||||||||||.
T Consensus       103 ~~TSGlll~ak~~  115 (232)
T PRK10839        103 IDTTGLVLMTDDG  115 (232)
T ss_pred             CCceeEEEEecCH
Confidence            9999999999985

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=99.77  E-value=1.4e-18  Score=163.20  Aligned_cols=114  Identities=15%  Similarity=0.127  Sum_probs=88.1

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|++||++....||..+.++|..|.|+|||+.                                            +..
T Consensus         7 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~--------------------------------------------v~~   42 (290)
T PRK10475          7 TRLNKYISESGICSRREADRYIEQGNVFINGKR--------------------------------------------ATI   42 (290)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEE--------------------------------------------ccC
Confidence            489999987645799999999999999999851                                            234


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCC
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRL  269 (284)
                      ++.|.+||.|.|....     ..+      ..+||+++||+|||+|++||+... ...|+.+++...    ..+++||||
T Consensus        43 ~~~V~~gD~V~v~g~~-----i~~------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~VgRL  106 (290)
T PRK10475         43 GDQVKAGDVVKVNGQL-----IEP------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIGRL  106 (290)
T ss_pred             CCCcCCCCEEEECCEE-----ccc------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccccC
Confidence            5678999999886311     000      114899999999999999998765 457777766431    236789999


Q ss_pred             CcccceeeeeeeeC
Q 023331          270 DNCTEGWYCYFTTL  283 (284)
Q Consensus       270 DRdTSGLLlfAKT~  283 (284)
                      |+|||||||||++-
T Consensus       107 DrdTsGLLLlT~dg  120 (290)
T PRK10475        107 DKDSQGLIFLTNHG  120 (290)
T ss_pred             CCCCcceEEEecCH
Confidence            99999999999974

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

Probab=99.77  E-value=1.7e-18  Score=167.46  Aligned_cols=154  Identities=21%  Similarity=0.219  Sum_probs=108.7

Q ss_pred             CCCccccccCCCCCCCCceE---EEeeCC-CC-cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhh
Q 023331           83 YPEYHRLLPCPSQNCPPRVE---HLVVSE-GG-PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRV  156 (284)
Q Consensus        83 ~~~~~~~~~~~~~~~~~rv~---~~vv~~-~g-~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~  156 (284)
                      +.+|.-.+..+.....+.+.   .++... .+ .+.+++..++ ..++.+-...|+.|.|.+||..              
T Consensus        12 ~~~~~~~~~~~~~~v~pyy~~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~--------------   77 (371)
T KOG1919|consen   12 SDEISVYIDGGLRKVAPYYFTYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQ--------------   77 (371)
T ss_pred             ccccceeecCCcceeeeEEEeeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEe--------------
Confidence            34444455555555555422   111111 12 4677776666 6899999999999999999851              


Q ss_pred             hcccCCcccccccccccCcchhhccccccccCcCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCC
Q 023331          157 FKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGT  236 (284)
Q Consensus       157 ~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl  236 (284)
                                                    ...++.++.||.|...++....+   ...++++|+|||++++|||||+||
T Consensus        78 ------------------------------~~v~~i~k~~d~l~~~vhrh~p~---~~~~~~~Iv~ed~~~vVvnKP~gi  124 (371)
T KOG1919|consen   78 ------------------------------VRVSLIVKNGDVLCHTVHRHEPP---VAYLPIRIVFEDKDYVVVNKPHGI  124 (371)
T ss_pred             ------------------------------eeeEEEeccCCEEEEeeccCCCC---ccccccceEEecCCEEEEeCCCCC
Confidence                                          13457889999998776543322   123678999999999999999999


Q ss_pred             ccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeCC
Q 023331          237 SVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA  284 (284)
Q Consensus       237 ~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~~  284 (284)
                      +|||++....+++...+..... ...+++||||||.|||+|+||||.+
T Consensus       125 pVhp~g~~~~n~i~~~l~~~~~-~~~~~~~hRLDr~tSGllvlAkt~~  171 (371)
T KOG1919|consen  125 PVHPTGRYRENTITKILAALHK-VEGLRPCHRLDRLTSGLLVLAKTKE  171 (371)
T ss_pred             ceeccCccccccchHHHHHhcc-ccccccccccCccccceEEEEechh
Confidence            9999888777777665543322 2346789999999999999999963

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=99.73  E-value=1.9e-17  Score=155.07  Aligned_cols=120  Identities=13%  Similarity=0.040  Sum_probs=84.9

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|++||++.-..||..++++|+.|.|+|||+.                                            +.+
T Consensus         3 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNG~~--------------------------------------------~~~   38 (289)
T PRK10700          3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKI--------------------------------------------ATL   38 (289)
T ss_pred             hhHHHHHHHCCCCCHHHHHHHHHcCCEEECCEe--------------------------------------------ccC
Confidence            478999997423899999999999999999851                                            134


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEE-eeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccC
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ  268 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILY-EDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHR  268 (284)
                      .+.|..+|...|.++.+....        ...+ ||++++++|||+|++||++......|+.+++...  ....+++|||
T Consensus        39 g~~V~~~~~d~I~v~g~~~~~--------~~~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~--~~~~~~~VgR  108 (289)
T PRK10700         39 GDRVEVTPGLKIRIDGHLISV--------KESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKL--RGARWIAVGR  108 (289)
T ss_pred             CCEeCCCCCeEEEECCEEeec--------ccccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhh--cCCceeEccC
Confidence            456776644333332211100        0111 6678999999999999998765567888766432  1123568999


Q ss_pred             CCcccceeeeeeeeC
Q 023331          269 IDNCTEGWYCYFTTL  283 (284)
Q Consensus       269 LDRdTSGLLlfAKT~  283 (284)
                      ||+|||||||||++-
T Consensus       109 LD~dTsGLLLlTndg  123 (289)
T PRK10700        109 LDVNTCGLLLFTTDG  123 (289)
T ss_pred             CCCCCceEEEEEcCH
Confidence            999999999999873

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like

Probab=99.72  E-value=1.1e-17  Score=149.53  Aligned_cols=66  Identities=27%  Similarity=0.397  Sum_probs=56.4

Q ss_pred             CcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       217 ~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      +++|||||++++|||||+||+||++......++.+.+....+. ..+++|||||++||||||||||.
T Consensus        15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~-~~~~~vhRLD~~TSGllllak~~   80 (213)
T cd02557          15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGL-TELRPCHRLDRLTSGLLLFAKTS   80 (213)
T ss_pred             CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCC-CCccCccCCCCCCceEEEEECCH
Confidence            5789999999999999999999998776677888877665543 24668999999999999999985

This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional

Probab=99.70  E-value=1.6e-17  Score=149.30  Aligned_cols=63  Identities=22%  Similarity=0.192  Sum_probs=51.3

Q ss_pred             cceEEeeCcEEEEECCCCCccCCCCC-CccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       218 l~ILYEDedLLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||++++|||||+|++|||+.+ ....++.+.+...+  . .+++||||||+||||||||||.
T Consensus        14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~-~~~~vhRLDr~TSGlll~Akt~   77 (219)
T PRK10158         14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--P-QAESVHRLDMATSGVIVVALTK   77 (219)
T ss_pred             CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--C-CCCEECCCCCCCceEEEEECCH
Confidence            68999999999999999999999763 34456666554432  2 3568999999999999999985

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

Probab=99.69  E-value=2.1e-17  Score=148.39  Aligned_cols=63  Identities=19%  Similarity=0.248  Sum_probs=51.2

Q ss_pred             cceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||++++|||||+||+||++.+  ..++.+.+....+. ..+++||||||+||||||||||.
T Consensus         2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~~-~~~~~VhRLDr~TSGlll~Ak~~   64 (217)
T TIGR01621         2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLGV-GQVWLVHRLDKMTSGILLLALNA   64 (217)
T ss_pred             ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcCC-CCccEecCCCCCCceEEEEEcCH
Confidence            47999999999999999999999764  34566655544332 34678999999999999999985

This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.

>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)

Probab=99.69  E-value=3e-17  Score=147.39  Aligned_cols=64  Identities=22%  Similarity=0.279  Sum_probs=48.8

Q ss_pred             cceEEeeCcEEEEECCCCCccCCCCCCccch--HHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEES--CATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~T--L~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||++++|||||+||+|||+.+....+  +...+....+  ..+++|||||++||||||||||.
T Consensus         1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGlll~Ak~~   66 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVLLFALSS   66 (223)
T ss_pred             CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEEEEEECH
Confidence            3699999999999999999999986433332  2222333322  34678999999999999999985

No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.

>PRK11112 tRNA pseudouridine synthase C; Provisional

Probab=99.68  E-value=5.7e-17  Score=148.99  Aligned_cols=64  Identities=23%  Similarity=0.217  Sum_probs=49.0

Q ss_pred             cceEEeeCcEEEEECCCCCccCCCCCCccchH--HHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||++++|||||+||+|||+..+..++.  ...+....+  ..+++||||||+||||||||||.
T Consensus         2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGlll~Ak~~   67 (257)
T PRK11112          2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVLLMALSS   67 (257)
T ss_pred             CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEEEEECCH
Confidence            47999999999999999999999854444432  233322222  24568999999999999999985

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family

Probab=99.44  E-value=5.3e-14  Score=119.32  Aligned_cols=55  Identities=16%  Similarity=0.195  Sum_probs=43.8

Q ss_pred             EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||+|++||++.+....++...+....  ...+++|||||++||||||||||.
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--~~~~~~vhRLD~~TSGlll~ak~~   55 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--GPRVHAAGRLDKDTSGLLLLTNDG   55 (154)
T ss_pred             CEEEECCCCCEEecCCCCCCCcHHHhhhccc--CCceeEeccCCCCCeeEEEEEcCH
Confidence            5899999999999988766677766543221  234678999999999999999985

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.

>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family

Probab=99.40  E-value=1.7e-13  Score=115.22  Aligned_cols=58  Identities=22%  Similarity=0.318  Sum_probs=37.8

Q ss_pred             cEEEEECCCCCccCCCCCCccchHHHHHH---HHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          226 SHVVLDKPAGTSVGGTTDNIEESCATFAS---RALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~---~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      |++|||||+||++|+........+.....   ........+++|||||++||||||||+|.
T Consensus         1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~   61 (164)
T PF00849_consen    1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDK   61 (164)
T ss_dssp             SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSH
T ss_pred             CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCc
Confidence            68999999999999988433333322222   22233456789999999999999999974

This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like

Probab=99.38  E-value=5e-13  Score=115.60  Aligned_cols=55  Identities=16%  Similarity=0.146  Sum_probs=44.3

Q ss_pred             EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||+||+||++. +...++.+.+..+... ..+++|||||++||||||||||.
T Consensus         2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~~-~~~~~vhRLD~~TSGlll~ak~~   56 (167)
T cd02553           2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDRR-RDLFPVGRLDKDTTGLLLLTNDG   56 (167)
T ss_pred             EEEEECCCCCEeCCCC-CCCCcHHHHhhhhccc-CCeEEcccCCCCCEEEEEEEeCH
Confidence            6899999999999764 4568888877655432 24678999999999999999985

This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.

>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like

Probab=99.37  E-value=3.9e-13  Score=116.16  Aligned_cols=55  Identities=13%  Similarity=0.111  Sum_probs=43.5

Q ss_pred             EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|+|||+|++||++......|+.+.+..+.  ...+++|||||+||||||||||+.
T Consensus         2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--~~~~~~V~RLD~~TsGLll~ak~~   56 (167)
T cd02556           2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--IPRWISVGRLDLNTEGLLLFTNDG   56 (167)
T ss_pred             EEEEECCCCcEECccCCCCCccHHHhhhhhc--cCceEEcCcCCCCCeeEEEEECCH
Confidence            7899999999999966555677777664431  223568999999999999999985

This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.

>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA

Probab=99.37  E-value=1.2e-13  Score=116.33  Aligned_cols=54  Identities=17%  Similarity=0.140  Sum_probs=41.9

Q ss_pred             EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||+||++|++......++.+.+..   ....+.+|||||++|||||||||+.
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---~~~~~~~vhRLD~~TsGlll~ak~~   54 (146)
T cd02870           1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---VGERLFPVGRLDYDTEGLLLLTNDG   54 (146)
T ss_pred             CEEEECCCCcEecccCCCCCCEEeeeccc---cCCCEEECCCCCCCCeeEEEEeCCH
Confidence            58999999999999875555666554332   1234678999999999999999985

The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.

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

Probab=99.02  E-value=8e-10  Score=102.40  Aligned_cols=115  Identities=18%  Similarity=0.120  Sum_probs=77.0

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|++||++.---||..+++||..|.|.|||++                                           +...
T Consensus         3 ~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v-------------------------------------------~~~~   39 (248)
T COG1187           3 MRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKV-------------------------------------------ATLG   39 (248)
T ss_pred             cchHHHHHHcCCCCHHHHHHHHHcCCEEECCEE-------------------------------------------eccC
Confidence            478999987555899999999999999999962                                           0122


Q ss_pred             CceecCCC-EEEEEcCCCCCCCCCCCCCCcceEE-eeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCcccc
Q 023331          190 DQIVEAGT-YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH  267 (284)
Q Consensus       190 ~~~L~~GD-~I~V~~~~~~~~~~~~~~~~l~ILY-EDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VH  267 (284)
                      ...+.+++ .|.+.  ..            .+.+ +..-++..|||.|+++.-.......|+..++-........+++|=
T Consensus        40 ~~~v~~~~~~i~v~--g~------------~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvG  105 (248)
T COG1187          40 GVVVDPDDDVVEVD--GK------------RIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG  105 (248)
T ss_pred             CeEeCCCCcEEEEC--CE------------EeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeecc
Confidence            33555553 44442  11            1333 233399999999999987644445555554321111222378899


Q ss_pred             CCCcccceeeeeee
Q 023331          268 QIDNCTEGWYCYFT  281 (284)
Q Consensus       268 RLDRdTSGLLlfAK  281 (284)
                      |||+||+||||+.-
T Consensus       106 RLD~dTeGLLLLTn  119 (248)
T COG1187         106 RLDKDTEGLLLLTN  119 (248)
T ss_pred             ccCCCCeeEEEEeC
Confidence            99999999999863

>PRK11394 23S rRNA pseudouridine synthase E; Provisional

Probab=99.00  E-value=2.5e-10  Score=103.73  Aligned_cols=53  Identities=13%  Similarity=0.149  Sum_probs=41.7

Q ss_pred             cEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      .++++|||+|+++|+.......++.+.+.     ...+++|||||+|||||||||++.
T Consensus        40 ~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----~~~~~~vgRLD~~TsGllLlt~d~   92 (217)
T PRK11394         40 RVILFNKPYDVLPQFTDEAGRKTLKEFIP-----VQGVYAAGRLDRDSEGLLVLTNNG   92 (217)
T ss_pred             EEEEEECCCCCEEeeCCccCCcchHHhcc-----cCCeEEecCCCCCCeeEEEEECCH
Confidence            58999999999999755444566666542     124678999999999999999974

>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

Probab=98.99  E-value=2.3e-09  Score=76.05  Aligned_cols=68  Identities=16%  Similarity=0.132  Sum_probs=54.1

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       111 ~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      +|++||.+.+ ..|++.++++|..|+|++||..                                           ++.+
T Consensus         2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~-------------------------------------------~~~~   38 (70)
T cd00165           2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKV-------------------------------------------VTKP   38 (70)
T ss_pred             cHHHHHHHhccccCHHHHHHHHHcCCEEECCEE-------------------------------------------ccCC
Confidence            5789998774 5899999999999999999851                                           1355


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEE
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD  231 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVN  231 (284)
                      ++.+..||.|.+...+          ++.+|+|||++++|||
T Consensus        39 ~~~v~~~d~i~i~~~~----------~~~~i~~ed~~~lvv~   70 (70)
T cd00165          39 SYKVKPGDVIEVDGKS----------IEEDIVYEDKKLLVVN   70 (70)
T ss_pred             ccCcCCCCEEEEcCCC----------cccceeeccCCEEEeC
Confidence            6788999998886421          1128999999999997

>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family

Probab=98.91  E-value=1e-09  Score=96.41  Aligned_cols=55  Identities=16%  Similarity=0.180  Sum_probs=37.1

Q ss_pred             cEEEEECCCCCccCCCC--------CCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          226 SHVVLDKPAGTSVGGTT--------DNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       226 dLLVVNKPaGl~VHPt~--------~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      -++++|||+|+++....        .....+....+....   ..+++|||||+|||||||||++.
T Consensus         5 ~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~---~~l~~VgRLD~dTsGLLl~t~d~   67 (177)
T cd02555           5 VTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF---ARLAPIGPLDKDASGLLVFSQDG   67 (177)
T ss_pred             EEEEEECCCceEecCCCcccccccccccccchhhhhhhcC---CceeEecCCCCCCeeEEEEECCH
Confidence            36899999999885432        112233333332222   24678999999999999999974

This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=98.18  E-value=4.7e-06  Score=60.58  Aligned_cols=31  Identities=3%  Similarity=-0.212  Sum_probs=28.4

Q ss_pred             CcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~  141 (284)
                      .+|+.||++. ++  ||+.++.+|+.|.|++||.
T Consensus         9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~   41 (59)
T TIGR02988         9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGE   41 (59)
T ss_pred             HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCE
Confidence            5899999987 77  9999999999999999985

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.91  E-value=2.8e-05  Score=53.80  Aligned_cols=31  Identities=19%  Similarity=0.089  Sum_probs=27.2

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      +|+.||.+. +..|+++++++|+.|.|+|||+
T Consensus         2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~   33 (48)
T PF01479_consen    2 RLDKFLSRLGLASSRSEARRLIKQGRVKVNGK   33 (48)
T ss_dssp             BHHHHHHHTTSSSSHHHHHHHHHTTTEEETTE
T ss_pred             CHHHHHHHcCCcCCHHHHHHhcCCCEEEECCE
Confidence            689999854 4578999999999999999985

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family

Probab=97.70  E-value=1.5e-05  Score=68.16  Aligned_cols=23  Identities=17%  Similarity=0.105  Sum_probs=20.3

Q ss_pred             CCCccccCCCcccceeeeeeeeC
Q 023331          261 TPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       261 ~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ..+.+|||||++|||||||||+.
T Consensus        38 ~~~~~v~RLD~~tsGlll~ak~~   60 (185)
T cd02869          38 FRPGLVHRLDKDTSGLLLVAKNK   60 (185)
T ss_pred             CcCceecccCCCCceEEEEEcCH
Confidence            34678999999999999999974

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.

>smart00363 S4 S4 RNA-binding domain

Probab=97.38  E-value=0.00058  Score=46.66  Aligned_cols=31  Identities=19%  Similarity=0.112  Sum_probs=27.0

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      +++.||.+. +..|+..+++++..|.|++||.
T Consensus         2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~   33 (60)
T smart00363        2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGK   33 (60)
T ss_pred             cHHHHHHHcCcccCHHHHHHHHHcCCEEECCE
Confidence            578888876 3689999999999999999985

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]

Probab=97.24  E-value=0.00079  Score=54.94  Aligned_cols=53  Identities=13%  Similarity=0.100  Sum_probs=43.4

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.||.- ++=-+|+.++++++.|.|++||.+                                            ++
T Consensus         9 mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~--------------------------------------------aK   44 (100)
T COG1188           9 MRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQR--------------------------------------------AK   44 (100)
T ss_pred             eehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEE--------------------------------------------cc
Confidence            589999953 344589999999999999999851                                            46


Q ss_pred             cCceecCCCEEEEEcCCC
Q 023331          189 VDQIVEAGTYLRVHVHPK  206 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~  206 (284)
                      +++.|+.||.|+|++...
T Consensus        45 pS~~VK~GD~l~i~~~~~   62 (100)
T COG1188          45 PSKEVKVGDILTIRFGNK   62 (100)
T ss_pred             cccccCCCCEEEEEeCCc
Confidence            778999999999997653

>PLN00051 RNA-binding S4 domain-containing protein; Provisional

Probab=96.99  E-value=0.0014  Score=61.57  Aligned_cols=50  Identities=16%  Similarity=0.131  Sum_probs=44.3

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .|||.+++..+++||++++++|+.|.|.+|+..                                           +.++
T Consensus       192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~-------------------------------------------v~~~  228 (267)
T PLN00051        192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWRE-------------------------------------------VTKN  228 (267)
T ss_pred             ccHHHHHHHHhccCHHHHHHHHHcCcEEECCEE-------------------------------------------cCCC
Confidence            589999999999999999999999999999851                                           2467


Q ss_pred             CceecCCCEEEEE
Q 023331          190 DQIVEAGTYLRVH  202 (284)
Q Consensus       190 ~~~L~~GD~I~V~  202 (284)
                      ++.|++||.|.|.
T Consensus       229 s~~v~~gD~isiR  241 (267)
T PLN00051        229 GTTLKTGDVVSVS  241 (267)
T ss_pred             CCCCCCCCEEEEe
Confidence            7899999999886

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=96.66  E-value=0.0034  Score=58.55  Aligned_cols=32  Identities=13%  Similarity=0.038  Sum_probs=29.8

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.+++..+++||+.+++||+.|.|.+||.
T Consensus       184 ~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~  215 (257)
T TIGR03069       184 LRIDAIASAGFGLSRSKIVDQIKAGRLRLNWK  215 (257)
T ss_pred             ccHHHHHHhhhhhhHHHHHHHHHCCeEEECCE
Confidence            58999998888999999999999999999985

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=96.23  E-value=0.0091  Score=53.79  Aligned_cols=51  Identities=10%  Similarity=0.085  Sum_probs=42.1

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.+|.+.. ..|+..++++|..|.|.|||.                                  .         +..
T Consensus        90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk----------------------------------~---------v~~  126 (200)
T TIGR01017        90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK----------------------------------K---------VDI  126 (200)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCE----------------------------------E---------eCC
Confidence            57899996543 679999999999999999985                                  1         246


Q ss_pred             cCceecCCCEEEEEc
Q 023331          189 VDQIVEAGTYLRVHV  203 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~  203 (284)
                      +++.|++||.|+|.-
T Consensus       127 ps~~V~~GD~I~V~~  141 (200)
T TIGR01017       127 PSYQVRPGDIISIKE  141 (200)
T ss_pred             CCCCCCCCCEEEEee
Confidence            788999999999863

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=96.00  E-value=0.018  Score=49.30  Aligned_cols=32  Identities=13%  Similarity=0.129  Sum_probs=27.5

Q ss_pred             CcHHHHHH-HhcCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYIC-RELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~-~~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.||. ..|--+|+.++++|..|.|++||.
T Consensus         9 ~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~   41 (133)
T PRK10348          9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQ   41 (133)
T ss_pred             ccHHHHHHHcCccccHHHHHHHHHCCCEEECCE
Confidence            48999985 345579999999999999999985

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=95.89  E-value=0.016  Score=52.59  Aligned_cols=51  Identities=8%  Similarity=-0.057  Sum_probs=41.9

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.+|.+.. ..|+..++++|..|.|+|||..                                           +..
T Consensus        89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~-------------------------------------------v~~  125 (201)
T CHL00113         89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRI-------------------------------------------VDI  125 (201)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEE-------------------------------------------ecC
Confidence            47899997654 5799999999999999999851                                           246


Q ss_pred             cCceecCCCEEEEEc
Q 023331          189 VDQIVEAGTYLRVHV  203 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~  203 (284)
                      +++.|++||.|+|.-
T Consensus       126 ps~~Vk~GD~I~V~~  140 (201)
T CHL00113        126 PSYRCKPKDIITVKD  140 (201)
T ss_pred             ccccCCCCCEEEEcc
Confidence            788999999999863

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=95.89  E-value=0.015  Score=52.57  Aligned_cols=32  Identities=9%  Similarity=0.044  Sum_probs=27.1

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.+|.+. +..|+..++++|..|.|+|||.
T Consensus        93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk  125 (203)
T PRK05327         93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGK  125 (203)
T ss_pred             HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCE
Confidence            5788888643 4689999999999999999985

>TIGR00478 tly hemolysin TlyA family protein

Probab=95.75  E-value=0.017  Score=53.09  Aligned_cols=31  Identities=16%  Similarity=-0.130  Sum_probs=27.2

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~  141 (284)
                      +||.||.+.. ..||++++++|..|.|++||+
T Consensus         1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~   32 (228)
T TIGR00478         1 RLDILLVRRGLFESREKAKRLILKGFVLVNGK   32 (228)
T ss_pred             CHHHHHHHcCCccHHHHHHHHHHCCcEEECCE
Confidence            5889988765 578999999999999999985

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]

Probab=95.64  E-value=0.017  Score=54.10  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=44.4

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      -|||..+++.+++||++++++|+.|.|.||+.                                  .         +.++
T Consensus       181 lRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k----------------------------------~---------v~~~  217 (257)
T COG2302         181 LRLDVVISEGFGLSRAKAQQLIEKGKVKVNWK----------------------------------V---------VDKA  217 (257)
T ss_pred             hhHHHHHHHHHhhhHHHHHHHHHcCceEEeeE----------------------------------E---------eccc
Confidence            58999999999999999999999999999974                                  1         2467


Q ss_pred             CceecCCCEEEEE
Q 023331          190 DQIVEAGTYLRVH  202 (284)
Q Consensus       190 ~~~L~~GD~I~V~  202 (284)
                      ++.|+.||.|.+.
T Consensus       218 s~~v~~GDliSir  230 (257)
T COG2302         218 SYEVQEGDLISIR  230 (257)
T ss_pred             cceeccCCEEEEe
Confidence            8999999999886

>PRK00020 truB tRNA pseudouridine synthase B; Provisional

Probab=95.55  E-value=0.017  Score=53.86  Aligned_cols=49  Identities=22%  Similarity=0.304  Sum_probs=39.9

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+++||||.||.+|-        +++.+.+.++...- ....-||-..||||+++-.
T Consensus        10 ~Gil~vdKP~G~TS~d--------vv~~vkr~~~~kKv-GH~GTLDP~AtGvLiv~iG   58 (244)
T PRK00020         10 DGVLLLDKPVGLSSNH--------ALQRAKRTVDAAKA-GHTGTLDPFATGLLVCCMG   58 (244)
T ss_pred             CeEEEEecCCCCCHHH--------HHHHHHHHhCCCCC-CcCCcCCCcCeeEEEEEEC
Confidence            3699999999999874        56667777776654 4489999999999999864

>PRK05033 truB tRNA pseudouridine synthase B; Provisional

Probab=95.11  E-value=0.029  Score=54.07  Aligned_cols=49  Identities=20%  Similarity=0.233  Sum_probs=39.4

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+++||||.||.+|-        +++.+.+.++... +....-||-..||||+++-.
T Consensus        10 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kK-vGH~GTLDP~AtGvL~v~vG   58 (312)
T PRK05033         10 NGVLLLDKPQGMSSND--------ALQKVKRLFNANK-AGHTGALDPLATGMLPICLG   58 (312)
T ss_pred             CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCC-CCCCCcCCCcCeeEEEEEEC
Confidence            4799999999999884        5566777777654 34489999999999999854

>PRK05389 truB tRNA pseudouridine synthase B; Provisional

Probab=95.08  E-value=0.028  Score=53.98  Aligned_cols=49  Identities=16%  Similarity=0.182  Sum_probs=39.6

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+|+||||.||.+|-        +++.+.+.++... +....-||-..||||+++-.
T Consensus        13 ~Gil~i~KP~G~TS~d--------vv~~vrk~~~~kK-vGH~GTLDP~AtGvL~v~vG   61 (305)
T PRK05389         13 SGWLILDKPAGMTSTE--------AVSKVKWLFDAQK-AGHAGTLDPLASGVLPIALG   61 (305)
T ss_pred             CeEEEEeCCCCCCHHH--------HHHHHHHHhcccc-cCCcccCCCCCceEEEEEEC
Confidence            4799999999999874        5666777777654 34489999999999999854

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed

Probab=94.82  E-value=0.034  Score=53.01  Aligned_cols=50  Identities=22%  Similarity=0.216  Sum_probs=39.8

Q ss_pred             eCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       224 DedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      -+.+|+||||.||.+|-        +++.+.+.++... +....-||-..||+|+++-.
T Consensus        21 ~~g~l~i~Kp~g~tS~~--------~v~~~r~~~~~kk-vGH~GTLDp~A~GvL~v~~g   70 (300)
T PRK04270         21 KFGVVNLDKPPGPTSHE--------VAAWVRDILGVEK-AGHGGTLDPKVTGVLPVALG   70 (300)
T ss_pred             CCCEEEEECCCCCCHHH--------HHHHHHHHhcccc-ccCCCCCCCcCeEEEEEEEC
Confidence            35799999999999874        5566777776554 44599999999999999864

>PRK01851 truB tRNA pseudouridine synthase B; Provisional

Probab=94.33  E-value=0.058  Score=51.84  Aligned_cols=49  Identities=24%  Similarity=0.253  Sum_probs=39.2

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+++||||.||.+|-        +++.+.+.++... +...--||-..||||+++-.
T Consensus        16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kK-vGH~GTLDP~AtGvL~v~vG   64 (303)
T PRK01851         16 DGVLLLDKPLGLSSND--------ALQRAKRLLRAKK-AGHTGTLDPLATGLLPLCFG   64 (303)
T ss_pred             CeEEEEeCCCCCCHHH--------HHHHHHHHhCccc-CCCCCCCCCCCceEEEEEEC
Confidence            4799999999999874        5666777777654 33478999999999999854

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE

Probab=94.07  E-value=0.036  Score=47.99  Aligned_cols=27  Identities=15%  Similarity=0.281  Sum_probs=20.8

Q ss_pred             EEEEECCCCCccCCCCC-CccchHHHHH
Q 023331          227 HVVLDKPAGTSVGGTTD-NIEESCATFA  253 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~-~~~~TL~~~l  253 (284)
                      ++|+|||+|++||++.. ....++.+.+
T Consensus         1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l   28 (168)
T cd02566           1 LILFNKPYGVLSQFTDESEKHKTLKDYI   28 (168)
T ss_pred             CEEEECCCCCEEecCCCcCCCccHHHHc
Confidence            58999999999998764 4456776655

This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=94.00  E-value=0.096  Score=47.73  Aligned_cols=51  Identities=14%  Similarity=0.151  Sum_probs=39.8

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      +|+..+.+. |.-|+.++.+||..|.|.|||+                                           +|..+
T Consensus        95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk-------------------------------------------~V~iP  131 (205)
T COG0522          95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGK-------------------------------------------RVNIP  131 (205)
T ss_pred             HHHHHHHHhcccccHHHHHHHhhcceEEECCE-------------------------------------------EeccC
Confidence            455555432 3468889999999999999985                                           24688


Q ss_pred             CceecCCCEEEEEcC
Q 023331          190 DQIVEAGTYLRVHVH  204 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~  204 (284)
                      ++.|++||++.|..-
T Consensus       132 Sy~V~~gdei~V~~k  146 (205)
T COG0522         132 SYLVSPGDEISVREK  146 (205)
T ss_pred             cEEecCCCEEEeeec
Confidence            999999999999854

>PRK04642 truB tRNA pseudouridine synthase B; Provisional

Probab=92.30  E-value=0.19  Score=48.38  Aligned_cols=49  Identities=27%  Similarity=0.280  Sum_probs=39.1

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+++||||.||.+|-        +++.+.+.++...- ...-=||-..||+|+++-.
T Consensus        10 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKv-GH~GTLDP~AtGvL~v~~G   58 (300)
T PRK04642         10 DGILLLDKPAGLSSNN--------ALQAARRLLRAEKG-GHTGSLDPLATGLLPLCFG   58 (300)
T ss_pred             CeEEEEecCCCCCHHH--------HHHHHHHHhCCCcc-cCCCccCCcCeeeEEEEEC
Confidence            4799999999999874        56777777776543 3377899999999999854

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative

Probab=92.28  E-value=0.19  Score=48.53  Aligned_cols=49  Identities=22%  Similarity=0.236  Sum_probs=38.4

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+|+||||.||.+|-        +++.+.+.++... +...-=||-..+|||+++-.
T Consensus        34 ~G~l~i~KP~g~tS~~--------~v~~vr~~~~~kk-vGH~GTLDP~A~GvL~v~~G   82 (322)
T TIGR00425        34 YGVVNLDKPSGPSSHE--------VVAWVRRILNVEK-TGHGGTLDPKVTGVLPVCIE   82 (322)
T ss_pred             CCEEEEeCCCCCCHHH--------HHHHHHHHhcccc-cCCCCCCCCCCceEEEEEEC
Confidence            4799999999999874        5566777776554 33477899999999999854

This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=92.26  E-value=0.24  Score=46.39  Aligned_cols=32  Identities=16%  Similarity=-0.032  Sum_probs=28.1

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .|||.+|.++ +--||++++++|..|.|++||.
T Consensus         3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~   35 (245)
T COG1189           3 MRLDALLVERGLFESREKAKELILAGNVLVNGE   35 (245)
T ss_pred             chHHHHHHHccchhhHHHHHHHHHcCeEEECCE
Confidence            4789999876 4579999999999999999985

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=90.18  E-value=0.34  Score=45.93  Aligned_cols=48  Identities=21%  Similarity=0.290  Sum_probs=39.1

Q ss_pred             cEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      .++++|||.|+.+|-        ++..+.+.++...-.+ .--||-..||+|++|-.
T Consensus        16 Gil~ldKP~G~tS~~--------~v~~vkkil~~~K~GH-~GTLDP~atGvLpi~ig   63 (271)
T COG0130          16 GVINLDKPPGPTSHE--------VVAWVKRILGVEKAGH-GGTLDPLATGVLPICLG   63 (271)
T ss_pred             ceEEeeCCCCCCHHH--------HHHHHHHHhCcccccc-ccccCCcccceEEEEec
Confidence            899999999999874        5667778887665444 77899999999999853

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=88.96  E-value=1.2  Score=34.87  Aligned_cols=68  Identities=21%  Similarity=0.254  Sum_probs=43.8

Q ss_pred             CCCccccccCCCCCCCCceEEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCC
Q 023331           83 YPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTD  162 (284)
Q Consensus        83 ~~~~~~~~~~~~~~~~~rv~~~vv~~~g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~  162 (284)
                      |++.+..+|-....  ..+. ....+..++.+.+ +.+|+|...+      |.|.+||+                     
T Consensus         9 ~~~L~~flp~~~r~--~~~~-~~~~~~~tvkd~I-EsLGVP~tEV------~~i~vNG~---------------------   57 (81)
T PF14451_consen    9 YAELNDFLPPERRG--GPFT-HPFDGGATVKDVI-ESLGVPHTEV------GLILVNGR---------------------   57 (81)
T ss_pred             chHHhhhcChhhcC--CceE-EecCCCCcHHHHH-HHcCCChHHe------EEEEECCE---------------------
Confidence            45555566643322  1122 2233345777755 6799998654      78999985                     


Q ss_pred             cccccccccccCcchhhccccccccCcCceecCCCEEEEEcC
Q 023331          163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVH  204 (284)
Q Consensus       163 ~~~~~kr~~~~Gk~vr~~~~~~r~~~~~~~L~~GD~I~V~~~  204 (284)
                                   .          ...++.++.||.|.|+..
T Consensus        58 -------------~----------v~~~~~~~~Gd~v~V~P~   76 (81)
T PF14451_consen   58 -------------P----------VDFDYRLKDGDRVAVYPV   76 (81)
T ss_pred             -------------E----------CCCcccCCCCCEEEEEec
Confidence                         1          366889999999999853

>PRK11507 ribosome-associated protein; Provisional

Probab=88.43  E-value=1.2  Score=34.21  Aligned_cols=31  Identities=10%  Similarity=-0.182  Sum_probs=24.9

Q ss_pred             CcHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~  141 (284)
                      -.|+.||+- .+  -|=..++.+|..|.|.+||+
T Consensus        12 I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGe   44 (70)
T PRK11507         12 VELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGA   44 (70)
T ss_pred             EEHHHHHhh-hCcccChHHHHHHHHcCceEECCE
Confidence            478888863 34  36669999999999999996

>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]

Probab=87.35  E-value=1.7  Score=33.75  Aligned_cols=35  Identities=14%  Similarity=-0.130  Sum_probs=26.4

Q ss_pred             eCCCCcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023331          106 VSEGGPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       106 v~~~g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~  141 (284)
                      ..+.-.|.+||+ ..++  |=.+++..|..|.|++||+
T Consensus         8 ~~e~I~L~qlLK-~~g~i~sGG~AK~~i~eg~V~vNGe   44 (73)
T COG2501           8 KTEFITLGQLLK-LAGLIESGGQAKAFIAEGEVKVNGE   44 (73)
T ss_pred             ccceEEHHHHHH-HhCcccCcHHHHHHHHCCeEEECCe
Confidence            333357888886 3553  5559999999999999996

>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=86.91  E-value=1.9  Score=37.32  Aligned_cols=62  Identities=16%  Similarity=0.151  Sum_probs=44.4

Q ss_pred             CCCCCCCccccccCCCCCCC-CceE-EEeeCCC--CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcC
Q 023331           79 SSYGYPEYHRLLPCPSQNCP-PRVE-HLVVSEG--GPVLEYICRELNLPPLFVADLIHFGAVYYAL  140 (284)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~-~rv~-~~vv~~~--g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng  140 (284)
                      ...++|+|.=....+..... ..++ ++..+..  -+++..|++.|++|++.+++|+..|.|..+.
T Consensus        68 ~~~~~~~~~v~~~~~~~~~~~~~~~v~i~~~~~~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~  133 (142)
T PF06353_consen   68 ELDEFPEYDVEKRLDTEDDDWADIEVEIRFPFPFPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP  133 (142)
T ss_pred             eeCCCCceEEEEEeccCCccccceEEEEEeCCCCCccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence            34478888766554443322 2244 3333333  4899999999999999999999999999884

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=83.00  E-value=2.6  Score=37.74  Aligned_cols=31  Identities=16%  Similarity=0.139  Sum_probs=24.1

Q ss_pred             cHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      +|+.+|.+ .|--|+.++++||..|.|.|||.
T Consensus       104 RLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~  135 (177)
T PRK04051        104 RLQTIVYRKGLARTPKQARQFIVHGHIAVNGR  135 (177)
T ss_pred             HHHHHHHHccCcCCHHHHHHHHHcCCEEECCE
Confidence            56665543 23478999999999999999985

>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like

Probab=81.93  E-value=1.4  Score=38.59  Aligned_cols=27  Identities=19%  Similarity=0.298  Sum_probs=20.6

Q ss_pred             EEEEECCCCCccCCCCCCccchHHHHHH
Q 023331          227 HVVLDKPAGTSVGGTTDNIEESCATFAS  254 (284)
Q Consensus       227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~  254 (284)
                      ++++|||+|++++++.. ...++.+++.
T Consensus         2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~   28 (164)
T cd02554           2 YIAYNKPVGIDCTLERA-DEDNIIDFVN   28 (164)
T ss_pred             EEEEECCCCcEeecCCC-CCCcHHHHhc
Confidence            68999999999998754 3467766553

This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	284
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.6 bits (107), Expect = 1e-05
 Identities = 43/263 (16%), Positives = 70/263 (26%), Gaps = 71/263 (26%)

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--WNSRII-----------------------AVTESHVVLD 231
            LR  +  K +  C  +     N++                         A T +H+ LD
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 232 KPAGTSVGGTTDNIEESCATFAS 254
                S+  T D ++     +  
Sbjct: 293 HH---SMTLTPDEVKSLLLKYLD 312

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	284
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	99.92
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	99.9
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	99.89
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	99.84
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	99.7
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	99.69
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	99.68
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	99.67
2gml_A	237	Ribosomal large subunit pseudouridine synthase F;	99.22
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	98.28
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	97.9
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.3
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	96.98
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	96.77
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	96.19
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	96.18
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	95.59
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	95.53
2aus_C	334	Pseudouridine synthase; isomerase, structural prot	94.44
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	94.42
1k8w_A	327	TRNA pseudouridine synthase B; protein-RNA complex	94.23
2apo_A	357	Probable tRNA pseudouridine synthase B; protein-pr	93.51
3u28_A	400	H/ACA ribonucleoprotein complex subunit 4; pseudou	93.07
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	92.55
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	89.21
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	86.61
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	81.57

>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

Probab=99.92  E-value=2.2e-26  Score=215.20  Aligned_cols=131  Identities=13%  Similarity=0.075  Sum_probs=59.3

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+|++||++.+ .+||+.++++|+.|.|++||+.                                           +++
T Consensus        17 ~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~-------------------------------------------v~~   53 (325)
T 1v9f_A           17 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------CDK   53 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccC
Confidence            48999999887 7999999999999999999851                                           135


Q ss_pred             cCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhC---CCCCCcc
Q 023331          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALG---LTTPLRT  265 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg---~~~pl~~  265 (284)
                      +++.|++||.|+|..++.......+.+++++|||||++++|||||+||+|||+.++..+|+.+.+..++.   ....+++
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            6778999999999765432212223455689999999999999999999999988777888887765442   1224678


Q ss_pred             ccCCCcccceeeeeeeeC
Q 023331          266 THQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       266 VHRLDRdTSGLLlfAKT~  283 (284)
                      |||||++||||||||||.
T Consensus       134 vhRLD~~TSGlll~ak~~  151 (325)
T 1v9f_A          134 VHRLDKDTTGLMVVAKTV  151 (325)
T ss_dssp             CCCCCTTCEEEEEEESSH
T ss_pred             ecCCCCCCeeEEEEEcCH
Confidence            999999999999999984

>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*

Probab=99.90  E-value=1.9e-24  Score=193.01  Aligned_cols=114  Identities=11%  Similarity=0.070  Sum_probs=92.9

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|++||++...+||+.++++|+.|.|++||+.                                           +.++
T Consensus         4 ~RLd~~L~~~~~~SR~~~~~li~~G~V~VNG~~-------------------------------------------v~~~   40 (234)
T 1ksk_A            4 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEI-------------------------------------------VRNA   40 (234)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEE-------------------------------------------CCCT
T ss_pred             ccHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE-------------------------------------------eCCC
Confidence            479999998777999999999999999999851                                           1246


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEe-eCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccC
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAV-TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ  268 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYE-DedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHR  268 (284)
                      ++.|++||.|++..              ..|+|| |++++|||||+||+|||+.++ ..|+.+++....+  ..+++|||
T Consensus        41 ~~~v~~gD~I~v~~--------------~~i~~e~d~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~~--~~~~~vhR  103 (234)
T 1ksk_A           41 AFKLLPEHDVAYDG--------------NPLAQQHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEPVA--WKLHAAGR  103 (234)
T ss_dssp             TCEECTTCCEEETT--------------EEECCCCCCCEEEEEECTTCBSSSSCSS-SCBGGGGCCCTTG--GGCEESSC
T ss_pred             CCCCCCCCEEEEeC--------------eEeecCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHhhhhhc--CCeeEcCC
Confidence            78999999988741              148999 999999999999999998764 6777665432211  24678999


Q ss_pred             CCcccceeeeeeeeC
Q 023331          269 IDNCTEGWYCYFTTL  283 (284)
Q Consensus       269 LDRdTSGLLlfAKT~  283 (284)
                      ||+|||||||||||.
T Consensus       104 LD~~TsGlll~ak~~  118 (234)
T 1ksk_A          104 LDIDTTGLVLMTDDG  118 (234)
T ss_dssp             CCTTCEEEEEEESCH
T ss_pred             CCCCCeeEEEEEcCH
Confidence            999999999999984

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

Probab=99.89  E-value=4.2e-24  Score=192.22  Aligned_cols=114  Identities=14%  Similarity=0.113  Sum_probs=90.9

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|++||++...+||+.++++|+.|.|++||+.                                           +.++
T Consensus         3 ~RLd~~L~~~~~~SR~~~~~lI~~G~V~VNG~~-------------------------------------------v~~~   39 (243)
T 1vio_A            3 LRLDKFIAENVGLTRSQATKAIRQSAVKINGEI-------------------------------------------VKSG   39 (243)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEE-------------------------------------------CCCT
T ss_pred             ccHHHHHHHcCCCCHHHHHHHHHcCcEEECCEE-------------------------------------------eCCC
Confidence            379999998777999999999999999999851                                           1246


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCc-EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccC
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTES-HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ  268 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDed-LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHR  268 (284)
                      ++.|++||.|.+.  +            ..|+|||++ ++|||||+||+|||+.+. ..|+.+++.....  ..+++|||
T Consensus        40 ~~~v~~gD~I~v~--~------------~~i~~ed~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~~--~~~~~vhR  102 (243)
T 1vio_A           40 SVQISQEDEIYFE--D------------ELLTWIEEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYPLA--GKLHSAGR  102 (243)
T ss_dssp             TCEECTTSCEEET--T------------EECCSSCCCCEEEEEECTTCBSSCCC---CCBGGGGSCTTGG--GGCEESSC
T ss_pred             CCCcCCCCEEEEe--c------------cccccCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHHhHHhc--CCEeEccC
Confidence            7799999987763  1            248999999 999999999999998764 6677665432221  23678999


Q ss_pred             CCcccceeeeeeeeC
Q 023331          269 IDNCTEGWYCYFTTL  283 (284)
Q Consensus       269 LDRdTSGLLlfAKT~  283 (284)
                      ||+|||||||||||.
T Consensus       103 LD~~TsGlll~ak~~  117 (243)
T 1vio_A          103 LDVDTTGLVLLTDDG  117 (243)
T ss_dssp             CCTTCEEEEEEESCH
T ss_pred             CCCCCeEEEEEEECH
Confidence            999999999999984

>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}

Probab=99.84  E-value=1.9e-21  Score=180.81  Aligned_cols=114  Identities=14%  Similarity=0.134  Sum_probs=91.6

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      .+|+.||++....||..++++|..|.|+|||+.                                            ...
T Consensus         7 ~RLdk~La~~g~~SR~~a~~lI~~G~V~VNG~~--------------------------------------------v~~   42 (290)
T 3dh3_A            7 VRLNKYISESGICSRREADRYIEQGNVFLNGKR--------------------------------------------ATI   42 (290)
T ss_dssp             EEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEE--------------------------------------------CCT
T ss_pred             hHHHHHHHhCCCCCHHHHHHHHHCCCEEECCEE--------------------------------------------ccC
Confidence            489999998755899999999999999999851                                            255


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCC
Q 023331          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRL  269 (284)
                      ++.|.+||.|+|...+..     +      ..|||++++|||||+||+||++..+ ..|+.+++..    ...+++||||
T Consensus        43 ~~~V~~gD~I~v~~~~i~-----~------~~~ed~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~----~~~~~~VhRL  106 (290)
T 3dh3_A           43 GDQVKPGDVVKVNGQLIE-----P------REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH----SKRVFPIGRL  106 (290)
T ss_dssp             TCEECTTCCEEETTEEEC-----C------CCGGGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTC----SSCCEESSCC
T ss_pred             CcCcCCCCEEEecccccc-----c------cccccceEEEEECCCccccCCCCCC-CCcHHHHhhc----cCceeeeccC
Confidence            678999999988642110     0      1389999999999999999998754 5677775532    3457889999


Q ss_pred             CcccceeeeeeeeC
Q 023331          270 DNCTEGWYCYFTTL  283 (284)
Q Consensus       270 DRdTSGLLlfAKT~  283 (284)
                      |+|||||||||++.
T Consensus       107 D~dTSGLllla~d~  120 (290)
T 3dh3_A          107 DKDSQGLIFLTNHG  120 (290)
T ss_dssp             CTTCEEEEEEESCT
T ss_pred             CCCCcceEEEcCCH
Confidence            99999999999985

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

Probab=99.70  E-value=1.2e-17  Score=147.96  Aligned_cols=63  Identities=21%  Similarity=0.178  Sum_probs=53.6

Q ss_pred             cceEEeeCcEEEEECCCCCccCCCCC-CccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       218 l~ILYEDedLLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++|||||++++|||||+||+|||+.+ ...+++.+.+...+.   .+++|||||++||||||||||.
T Consensus        12 ~~ilyed~~~lvvnKP~G~~~~~~~~~~~~~tl~~~l~~~~~---~~~~vhRLD~~TSGlll~ak~~   75 (217)
T 2i82_A           12 LVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYP---QAESVHRLDMATSGVIVVALTK   75 (217)
T ss_dssp             CCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCT---TCEESSCCCTTCEEEEEEESSH
T ss_pred             ceEEEECCCEEEEECCCCCeEeCCCCCCchhHHHHHHHHHCC---CCceeecCCCCCeEEEEEEeCH
Confidence            68999999999999999999999765 456788887765542   3578999999999999999984

>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

Probab=99.69  E-value=1.8e-17  Score=147.80  Aligned_cols=64  Identities=22%  Similarity=0.202  Sum_probs=52.9

Q ss_pred             ceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       219 ~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      +|+|||++++|||||+||+|||+.+ ...++...+....+....+++|||||+|||||||||||.
T Consensus         3 ~Ilyed~~~lvvnKP~G~~~~~~~~-~~~~l~~~l~~~~~~~~~~~~VhRLD~~TSGlll~ak~~   66 (228)
T 1v9k_A            3 VIMYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKR   66 (228)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSS-SBCCHHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSH
T ss_pred             CEEEECCCEEEEECCCCCeEecCCC-hHHHHHHHHHHHcCCCCccceEecCCCCCeEEEEEEeCH
Confidence            6999999999999999999999776 456677766555443334678999999999999999984

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

Probab=99.68  E-value=6.2e-18  Score=146.72  Aligned_cols=60  Identities=12%  Similarity=0.117  Sum_probs=48.5

Q ss_pred             ceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       219 ~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      .|||||++++|||||+||+|||+.+....|+.+++.    . ..+++|||||+|||||||||||.
T Consensus         5 ~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~----~-~~~~~vhRLD~~TSGlll~ak~~   64 (189)
T 2oml_A            5 KPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP----V-QGVYAAGRLDRDSEGLLVLTNNG   64 (189)
T ss_dssp             ---CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC----C-SSCEESSCCCTTCEEEEEEESCH
T ss_pred             ccccCCCeEEEEECCCCCEecCCCCCCCCCHHHHcC----C-CCceECCCCCCCCeeEEEEEcCH
Confidence            699999999999999999999988766777765432    1 24678999999999999999984

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

Probab=99.67  E-value=9e-18  Score=149.41  Aligned_cols=62  Identities=11%  Similarity=0.114  Sum_probs=47.2

Q ss_pred             CcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       217 ~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      .++|||||++++|||||+||+|||+.+....|+.+++.    . ..+++|||||+|||||||||||.
T Consensus        31 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~tl~~~l~----~-~~~~~VhRLDr~TSGllllAk~~   92 (217)
T 2olw_A           31 RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP----V-QGVYAAGRLDRDSEGLLVLTNNG   92 (217)
T ss_dssp             ------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCC----C-CSCEESSCCCTTCEEEEEEESCH
T ss_pred             cCceEeeCCcEEEEECCCCCEeccCCCCCCccHHHHhC----c-CCceECCCCCCCCeeEEEEEcCH
Confidence            46899999999999999999999988766677665432    1 24678999999999999999984

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

Probab=99.22  E-value=3.6e-12  Score=115.69  Aligned_cols=55  Identities=13%  Similarity=0.172  Sum_probs=44.1

Q ss_pred             eCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       224 DedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      ++++||+|||+|++||+... ...|+.+++.    ....+++|||||+|||||||||++-
T Consensus        13 ~~~~lvlnKPaG~vs~~~~~-~~~tv~dll~----~~~rl~~VgRLD~dTSGLLLlT~dg   67 (237)
T 2gml_A           13 DLVLIALNKPVGIVSTTEDG-ERDNIVDFVN----HSKRVFPIGRLDKDSQGLIFLTNHG   67 (237)
T ss_dssp             CCCEEEEEECTTCBCCSSSS-CSSBHHHHSC----CSSCCEEESCCCTTCEEEEEEESCH
T ss_pred             CCEEEEEECCCCCEeCCCCC-CCCCHHHHhh----ccCCeeEecCCCCCCeeEEEEEcCH
Confidence            46799999999999999765 4567766442    2234789999999999999999973

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

Probab=98.28  E-value=9e-08  Score=73.71  Aligned_cols=73  Identities=12%  Similarity=0.147  Sum_probs=52.5

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       111 ~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      +|+.||++.. ..|++++++||..|.|++||..                                            .++
T Consensus         2 RLD~~L~~~~~~~sR~~~~~li~~G~V~VNg~~--------------------------------------------~~~   37 (92)
T 2k6p_A            2 RIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSC--------------------------------------------AKA   37 (92)
T ss_dssp             BHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEE--------------------------------------------CCT
T ss_pred             hHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEE--------------------------------------------cCC
Confidence            6899998653 3599999999999999999851                                            255


Q ss_pred             CceecCCCEEEEEcCCCCCCC--------CCCCCCCcceEEeeCcE
Q 023331          190 DQIVEAGTYLRVHVHPKRFPR--------CYDIDWNSRIIAVTESH  227 (284)
Q Consensus       190 ~~~L~~GD~I~V~~~~~~~~~--------~~~~~~~l~ILYEDedL  227 (284)
                      ++.|++||.|.|..+++....        .......++|+|||+++
T Consensus        38 ~~~v~~gd~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~lyed~~~   83 (92)
T 2k6p_A           38 SKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYIAPKTK   83 (92)
T ss_dssp             TCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSEEECCC
T ss_pred             CCCcCCCCEEEEEeCCceEEEEEeccccccCCCHHHHHHHHHhcCC
Confidence            678999999999865432110        01112347899999975

>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

Probab=97.90  E-value=7e-06  Score=68.04  Aligned_cols=73  Identities=11%  Similarity=0.068  Sum_probs=52.3

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+|+.||... +..|++.++++|..|.|.|||..                                            .+
T Consensus         9 ~RLDk~L~~~~~~~SRs~a~~li~~G~V~VNG~~--------------------------------------------vk   44 (133)
T 1dm9_A            9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR--------------------------------------------SK   44 (133)
T ss_dssp             CBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEE--------------------------------------------CC
T ss_pred             hhHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEE--------------------------------------------cC
Confidence            5899999876 45799999999999999999851                                            25


Q ss_pred             cCceecCCCEEEEEcCCCCCCC-CCC-----C-CCCcceEEeeCc
Q 023331          189 VDQIVEAGTYLRVHVHPKRFPR-CYD-----I-DWNSRIIAVTES  226 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~~~~~~-~~~-----~-~~~l~ILYEDed  226 (284)
                      +++.|+.||.|.|...+..... ...     . .-..+++|||..
T Consensus        45 ~s~~V~~GD~I~I~~~~~~~~~~v~~~~~~r~~a~~a~~lYed~~   89 (133)
T 1dm9_A           45 PSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYEETA   89 (133)
T ss_dssp             TTCBCCTTCEEEEEETTEEEEEEECEEESCCCCHHHHGGGEEECH
T ss_pred             CCCEeCCCCEEEEEeCCceeeEEEccccccCCCcHHhhhheEECC
Confidence            6778999999999875432110 000     0 012578999874

>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

Probab=97.30  E-value=8.3e-05  Score=55.75  Aligned_cols=31  Identities=13%  Similarity=-0.091  Sum_probs=27.7

Q ss_pred             CcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~  141 (284)
                      .+|+.||++. ++  ||+.+++||..|.|++||+
T Consensus        21 ~RLdk~L~~~-g~~~SR~~a~~lI~~G~V~VNG~   53 (79)
T 1p9k_A           21 VELCDLLKLE-GWSESGAQAKIAIAEGQVKVDGA   53 (79)
T ss_dssp             CCHHHHHHHH-TSCSSSSTTSHHHHHHHHEETTB
T ss_pred             chHHHHHHHC-CCCCCHHHHHHHHHCCEEEECCE
Confidence            5899999875 53  9999999999999999985

>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

Probab=96.98  E-value=0.0013  Score=55.89  Aligned_cols=52  Identities=13%  Similarity=0.105  Sum_probs=42.8

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.+|.+. ++.||..+++||..|.|.|||+.                                           +.+
T Consensus        51 ~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VNG~~-------------------------------------------v~~   87 (159)
T 1c05_A           51 SRLDNLVYRLGLARTRRQARQLVTHGHILVDGSR-------------------------------------------VNI   87 (159)
T ss_dssp             HBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTEE-------------------------------------------CCC
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHHCCCEEECCEE-------------------------------------------eCc
Confidence            4799999865 36899999999999999999851                                           236


Q ss_pred             cCceecCCCEEEEEcC
Q 023331          189 VDQIVEAGTYLRVHVH  204 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~  204 (284)
                      +++.|++||.|+|...
T Consensus        88 ps~~V~~gD~I~V~~~  103 (159)
T 1c05_A           88 PSYRVKPGQTIAVREK  103 (159)
T ss_dssp             SSCBCCTTCEEEECGG
T ss_pred             CCcEeCCCCEEEEeCc
Confidence            7789999999998653

>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* ...

Probab=96.77  E-value=0.0021  Score=57.01  Aligned_cols=52  Identities=12%  Similarity=0.080  Sum_probs=43.1

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.+|.+. ++.|+..+++||..|.|.|||..                                           +..
T Consensus        99 ~RLD~~L~~~g~~~SR~~arqLI~~G~V~VNG~~-------------------------------------------v~~  135 (209)
T 2vqe_D           99 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRR-------------------------------------------VDL  135 (209)
T ss_dssp             TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEE-------------------------------------------CCC
T ss_pred             HHHHHHHHHhcCcCCHHHHHHHHHCCCEEECCEE-------------------------------------------eCc
Confidence            5899999865 46899999999999999999851                                           235


Q ss_pred             cCceecCCCEEEEEcC
Q 023331          189 VDQIVEAGTYLRVHVH  204 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~  204 (284)
                      +++.|++||.|+|...
T Consensus       136 ps~~V~~gD~I~V~~~  151 (209)
T 2vqe_D          136 PSYRVRPGDEIAVAEK  151 (209)
T ss_dssp             TTCBCCTTCEEEECGG
T ss_pred             CCcCcCCCCEEEEcCc
Confidence            7789999999998743

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

Probab=96.19  E-value=0.0059  Score=56.46  Aligned_cols=31  Identities=13%  Similarity=-0.056  Sum_probs=27.8

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYAL  140 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng  140 (284)
                      .|||.||.+. +..||+++++||..|.|++||
T Consensus         7 ~RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng   38 (291)
T 3hp7_A            7 ERVDVLAYKQGLFETREQAKRGVMAGLVVNVI   38 (291)
T ss_dssp             EEHHHHHHHTTSSSSHHHHHHHHHTTCEEETT
T ss_pred             hhHHHHHHHcCCcccHHHHHHHHHCCeEEECC
Confidence            4899999875 468999999999999999998

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.59  E-value=0.011  Score=43.70  Aligned_cols=32  Identities=6%  Similarity=-0.043  Sum_probs=27.1

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.+|.+. +.-|+.++++||..|.|.+||+
T Consensus         8 ~RLD~~l~~~gla~SR~~A~~lI~~G~V~Vng~   40 (71)
T 2cqj_A            8 RRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPD   40 (71)
T ss_dssp             EEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTB
T ss_pred             HHHHHHHHHhCCcCCHHHHHHHHHCCcEEECCE
Confidence            4799998754 3459999999999999999985

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

Probab=95.53  E-value=0.0049  Score=54.53  Aligned_cols=51  Identities=4%  Similarity=-0.117  Sum_probs=40.5

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.+|.+. +..|+..+++||..|.|.|||..                                           +..
T Consensus        89 ~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VNG~~-------------------------------------------V~~  125 (201)
T 3bbn_D           89 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRI-------------------------------------------VDI  125 (201)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEE-------------------------------------------CCC
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHhCCcEEeCCEE-------------------------------------------Eee
Confidence            3677777653 24799999999999999999851                                           246


Q ss_pred             cCceecCCCEEEEEc
Q 023331          189 VDQIVEAGTYLRVHV  203 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~  203 (284)
                      +++.|++||.|+|.-
T Consensus       126 pS~~V~~gD~I~V~~  140 (201)
T 3bbn_D          126 PSYRCKPQDTIMARD  140 (201)
T ss_dssp             TTCBCCTTEEEEECS
T ss_pred             cceecCCCCEEEEcc
Confidence            778999999999864

>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

Probab=94.44  E-value=0.022  Score=53.79  Aligned_cols=52  Identities=19%  Similarity=0.224  Sum_probs=41.6

Q ss_pred             EeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       222 YEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      |-.+.+|+||||.||.+|-        +++.+.+.++... +....-||-..||+|+++-.
T Consensus        43 ~~~~Gil~vdKP~g~tS~~--------vv~~vr~~~~~~K-vGH~GTLDP~atGvL~v~~g   94 (334)
T 2aus_C           43 HIQYGVINLDKPPGPTSHE--------VVAWIKRILNLEK-AGHGGTLDPKVSGVLPVALE   94 (334)
T ss_dssp             HHHTEEEEEEECSSSCHHH--------HHHHHHHHTTCSC-EEESSCCCTTCEEEEEEEEG
T ss_pred             hccCcEEEEECCCCCCHHH--------HHHHHHHHhCcce-eccccccCCccceeEEEEeC
Confidence            4457899999999998874        5666777777543 44589999999999999854

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

Probab=94.42  E-value=0.033  Score=48.51  Aligned_cols=32  Identities=13%  Similarity=0.019  Sum_probs=26.6

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+|+.+|.+ .+.-|+..+++||..|.|.|||.
T Consensus       103 ~RLD~~L~~~G~a~SR~~Ar~LI~~G~V~VNg~  135 (180)
T 3j20_D          103 RRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQ  135 (180)
T ss_dssp             TSHHHHHHHHTSSSSHHHHHHHHHHTCCEESSS
T ss_pred             hhhhheeecCcccCcHHHHHHHHHcCCeEECCE
Confidence            478888864 34569999999999999999985

>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

Probab=94.23  E-value=0.026  Score=53.34  Aligned_cols=49  Identities=20%  Similarity=0.220  Sum_probs=39.6

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      +.+++||||+||.+|-        +++.+.+.++... +.....||-..||+|+++-.
T Consensus        25 ~Gil~vdKP~G~TS~d--------vv~~vr~~l~~kK-vGH~GTLDP~AtGvL~i~~G   73 (327)
T 1k8w_A           25 NGVLLLDKPQGMSSND--------ALQKVKRIYNANR-AGHTGALDPLATGMLPICLG   73 (327)
T ss_dssp             CEEEEEEECTTCCHHH--------HHHHHHHHTTCSC-EEESSCCCTTCEEEEEEEEG
T ss_pred             CeEEEEECCCCCCHHH--------HHHHHHHhhccce-eccCCCCCCCCeeEEEEEEC
Confidence            4699999999999874        5666777776554 44599999999999999854

>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

Probab=93.51  E-value=0.041  Score=52.50  Aligned_cols=52  Identities=21%  Similarity=0.250  Sum_probs=41.8

Q ss_pred             EeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       222 YEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      |-.+.+|+||||+||.+|-        +++.+.+.++... +....-||-..||+|+++-.
T Consensus        63 ~~~~Gil~vdKP~G~TS~~--------vv~~vr~~l~~~K-vGH~GTLDP~AtGvL~v~~G  114 (357)
T 2apo_A           63 LIKYGVVVVDKPRGPTSHE--------VSTWVKKILNLDK-AGHGGTLDPKVTGVLPVALE  114 (357)
T ss_dssp             HHHTEEEEEEECSSSCHHH--------HHHHHHHHTTCSC-EEESSCCCTTCEEEEEEEEG
T ss_pred             hccCcEEEEECCCCCCHHH--------HHHHHHHHhCccc-cccccccCCCceeEEEEEeC
Confidence            4567899999999999874        5667777777553 44589999999999999854

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

Probab=93.07  E-value=0.052  Score=52.62  Aligned_cols=52  Identities=17%  Similarity=0.221  Sum_probs=42.2

Q ss_pred             EeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       222 YEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      |-.+.+|+||||.||.+|-        +++.+.+.++... +....-||-..||||+++-.
T Consensus        56 ~~~~Gil~ldKP~G~TS~d--------vv~~vrr~l~~kK-vGH~GTLDP~AtGvL~v~iG  107 (400)
T 3u28_A           56 YISSGVINLDKPSNPSSHE--------VVAWIKRILRCEK-TGHSGTLDPKVTGCLIVCID  107 (400)
T ss_dssp             HHHTEEEEEEECSSSCHHH--------HHHHHHHHHTCSC-EEESSCCCTTCEEEEEEEEG
T ss_pred             hccCcEEEEECCCCCCHHH--------HHHHHHHHhCcCc-ccccCCCCCCCeEEEEEEEC
Confidence            5568999999999999874        5667777777654 44589999999999999864

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

Probab=92.55  E-value=0.042  Score=47.78  Aligned_cols=32  Identities=9%  Similarity=-0.092  Sum_probs=27.3

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.+|.+. +..|+..+++||..|.|.|||.
T Consensus       107 ~RLD~vL~~~G~a~SR~~Ar~LI~~G~V~VNg~  139 (181)
T 2xzm_D          107 RRLQTRVFKLNLANSIHHSRVLIRQRHIKVGKN  139 (181)
T ss_dssp             TBHHHHHHHTTCSSSTTHHHHHTTTTCCEETTE
T ss_pred             cchhHHHHhccccCCHHHHHHHHHCCEEEECCE
Confidence            5899998643 4569999999999999999985

>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*

Probab=89.21  E-value=0.15  Score=44.94  Aligned_cols=32  Identities=9%  Similarity=-0.062  Sum_probs=26.1

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+|+.+|.+. +.-|+..+++||..|.|.|||.
T Consensus       107 ~RLD~~L~r~G~a~Sr~~ArqLI~~GhV~VNG~  139 (197)
T 3u5c_J          107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQ  139 (197)
T ss_dssp             TSHHHHHHHSSTTSSHHHHHHHHHTSCCBSSSC
T ss_pred             HHHHHHHHHccccCCHHHHHHHHHcCCEEECCE
Confidence            4788888652 3359999999999999999985

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

Probab=86.61  E-value=0.9  Score=41.26  Aligned_cols=31  Identities=13%  Similarity=0.066  Sum_probs=28.0

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~  141 (284)
                      +|.-||.+.|+  .+...+++++.+|.|.|||+
T Consensus        44 PL~i~LRdrLgyA~t~rEar~Iv~~~~I~VdGK   76 (243)
T 3j20_E           44 PLLYIVRDYLGYAKTAREARKILNEGKFLVDGR   76 (243)
T ss_dssp             EHHHHHHTTSCCCSSHHHHHHHHHHCSCEETTE
T ss_pred             eehhhhhhhhccccCHHHHHHHHHCCcEEECCE
Confidence            68889999887  78889999999999999985

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=81.57  E-value=1.4  Score=39.28  Aligned_cols=31  Identities=19%  Similarity=0.012  Sum_probs=27.2

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~  141 (284)
                      +|.-||.+.|+  .+...+++++..|.|.|||+
T Consensus         9 PL~i~LRdrLgyA~t~rEarkIv~~~~I~VDGK   41 (213)
T 3kbg_A            9 TLLSIIRDYLKLSDKEREAARILANGLVKVDGK   41 (213)
T ss_dssp             EHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTE
T ss_pred             eeHHHHhhhhcccccHHHHHHHHHCCCEEECCE
Confidence            67888888876  67889999999999999986

---

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	Length	Definition	Probability
Query	284
d1v9fa_	250	Ribosomal large subunit pseudouridine synthase D,	99.81
d1v9ka_	227	Ribosomal large subunit pseudouridine synthase C,	99.78
d1vioa1	174	Ribosomal small subunit pseudouridine 516 synthase	99.25
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.09
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.08
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	97.3
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	96.75
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	95.85
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	95.8
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	95.12
d2apoa2	230	Pseudouridine synthase II TruB {Archaeon Methanoco	93.68
d2ey4a2	245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	93.41
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	92.24
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	90.69

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]}

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=99.81  E-value=8.8e-21  Score=169.76  Aligned_cols=70  Identities=17%  Similarity=0.158  Sum_probs=59.4

Q ss_pred             CCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC---CCCCccccCCCcccceeeeeeeeC
Q 023331          214 IDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       214 ~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      .+++++|||||++|||||||+||+|||+.++..+|+.+.+...+..   ...+++||||||+||||||||||.
T Consensus         4 ~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~   76 (250)
T d1v9fa_           4 QDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTV   76 (250)
T ss_dssp             CCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSH
T ss_pred             CCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhccCCCceeEEeecCCCCcceEEEeccc
Confidence            4567899999999999999999999999988888988877655422   223568999999999999999985

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]}

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=99.78  E-value=6.6e-20  Score=160.97  Aligned_cols=64  Identities=22%  Similarity=0.156  Sum_probs=52.4

Q ss_pred             ceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023331          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL  283 (284)
Q Consensus       219 ~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~  283 (284)
                      .||||||+|||||||+||+|||+.++..+ +.+.+....+....+++||||||+||||||||||.
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~~-~~~~l~~~~~~~~~~~~vHRLD~~TSGlll~Ak~~   65 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKR   65 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBCC-HHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSH
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcch-HHHHHHHhCCCCcccceeeeccceeeeeeeeecch
Confidence            49999999999999999999998766555 44545554444455678999999999999999985

>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal small subunit pseudouridine 516 synthase RsuA
species: Haemophilus influenzae [TaxId: 727]

Probab=99.25  E-value=4.6e-13  Score=112.39  Aligned_cols=57  Identities=18%  Similarity=0.212  Sum_probs=41.3

Q ss_pred             eeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          223 VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       223 EDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      ||..++|+|||+|++|+...++ ..++.+++...  ....+++|||||+|||||||||++
T Consensus         1 e~~~Yi~lNKP~G~~~~~~~~~-~~~v~~~l~~~--~~~~l~~V~RLD~~TsGLll~t~d   57 (174)
T d1vioa1           1 EEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYP--LAGKLHSAGRLDVDTTGLVLLTDD   57 (174)
T ss_dssp             CCCCEEEEEECTTCBSSCCC---CCBGGGGSCTT--GGGGCEESSCCCTTCEEEEEEESC
T ss_pred             CCCEEEEEECCCCEEeCCCCCC-CCcHHHhCccc--ccCceEEEecCChhHhceEEEeec
Confidence            7889999999999999875543 34444432111  123467899999999999999976

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.09  E-value=2.5e-06  Score=59.46  Aligned_cols=32  Identities=16%  Similarity=0.045  Sum_probs=29.7

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      .+||.||++....||+++++||+.|.|.+||.
T Consensus         2 mRLD~~Ls~~~~~SR~~a~~lI~~g~V~Vng~   33 (58)
T d1vioa2           2 LRLDKFIAENVGLTRSQATKAIRQSAVKINGE   33 (58)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTE
T ss_pred             cHHHHHHHHcCCCCHHHHHHHHHcCeEEECCE
Confidence            37999999988899999999999999999985

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.08  E-value=2.6e-06  Score=59.49  Aligned_cols=31  Identities=13%  Similarity=0.076  Sum_probs=29.3

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      +|+.||++...+||+.+++||..|.|.|||.
T Consensus         2 RLdk~l~~~~~~SR~~a~~lI~~g~V~Vng~   32 (59)
T d1kska3           2 RLDKFIAQQLGVSRAIAGREIRGNRVTVDGE   32 (59)
T ss_dssp             EHHHHHHHHHTCCHHHHHHHHHTTCEEETTE
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHcCcEEECCE
Confidence            6899999988899999999999999999985

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=97.30  E-value=0.00022  Score=55.12  Aligned_cols=52  Identities=15%  Similarity=0.166  Sum_probs=42.6

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||.||.. .+--||+.++++|..|.|.|||.                                  .          ++
T Consensus         5 mRlD~~L~~~r~~ktR~~A~~~i~~G~V~vNg~----------------------------------~----------vK   40 (104)
T d1dm9a_           5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQ----------------------------------R----------SK   40 (104)
T ss_dssp             CBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTE----------------------------------E----------CC
T ss_pred             EeHHHHHHHhhhHhhHHHHHHHHHcCCeeeCCe----------------------------------e----------cc
Confidence            589999954 34469999999999999999985                                  1          36


Q ss_pred             cCceecCCCEEEEEcCC
Q 023331          189 VDQIVEAGTYLRVHVHP  205 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~~~  205 (284)
                      +++.|++||+|.|....
T Consensus        41 ps~~vk~GDvI~i~~~~   57 (104)
T d1dm9a_          41 PSKIVELNATLTLRQGN   57 (104)
T ss_dssp             TTCBCCTTCEEEEEETT
T ss_pred             ccccCCCCCEEEEEeCC
Confidence            67899999999997643

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.00016  Score=53.28  Aligned_cols=32  Identities=13%  Similarity=-0.112  Sum_probs=27.9

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      -+|++||... +--||.++++||..|.|.|||+
T Consensus        21 irL~k~L~~~gl~~Sr~eAk~lI~~G~V~VNG~   53 (79)
T d1p9ka_          21 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGA   53 (79)
T ss_dssp             CCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTB
T ss_pred             EEHHHHHHHCCCccCHHHHHHHHHhCCcccCCE
Confidence            4899999875 3359999999999999999985

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

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.85  E-value=0.007  Score=49.74  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=40.7

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023331          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (284)
Q Consensus       111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~  189 (284)
                      +||..+.+. +..|+..+++++..|.|.|||.                                           ++..+
T Consensus        52 RlD~vv~r~gfa~t~~~arQ~v~Hghi~vNgk-------------------------------------------~v~iP   88 (159)
T d1c06a_          52 RLDNLVYRLGLARTRRQARQLVTHGHILVDGS-------------------------------------------RVNIP   88 (159)
T ss_dssp             CHHHHHHHHTSSSSHHHHHHHHHTSCEEETTE-------------------------------------------ECCCS
T ss_pred             HhhhhhccCcccCCHHHHHHHHHhcceEccce-------------------------------------------EEEec
Confidence            677776542 3479999999999999999985                                           23678


Q ss_pred             CceecCCCEEEEEc
Q 023331          190 DQIVEAGTYLRVHV  203 (284)
Q Consensus       190 ~~~L~~GD~I~V~~  203 (284)
                      ++.|++||.|++.-
T Consensus        89 Sy~vk~GDvIsvke  102 (159)
T d1c06a_          89 SYRVKPGQTIAVRE  102 (159)
T ss_dssp             SCCCCSSCEEEECG
T ss_pred             ceeecCCcEEeecc
Confidence            99999999999963

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=95.80  E-value=0.0071  Score=51.60  Aligned_cols=50  Identities=10%  Similarity=0.085  Sum_probs=41.4

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||..+.+. |.-|+..+++||..|.|.|||+                                           ++..
T Consensus        94 ~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk-------------------------------------------~VnI  130 (204)
T d2gy9d1          94 GRLDNVVYRMGFGATRAEARQLVSHKAIMVNGR-------------------------------------------VVNI  130 (204)
T ss_dssp             TBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSS-------------------------------------------BCCC
T ss_pred             HHHHHHHhhccccccHHHHHHHHHhcceecCCE-------------------------------------------EEEe
Confidence            5788887652 3478889999999999999985                                           1357


Q ss_pred             cCceecCCCEEEEE
Q 023331          189 VDQIVEAGTYLRVH  202 (284)
Q Consensus       189 ~~~~L~~GD~I~V~  202 (284)
                      +++.|++||+|+|.
T Consensus       131 PSy~vk~GDvIsvk  144 (204)
T d2gy9d1         131 ASYQVSPNDVVSIR  144 (204)
T ss_dssp             TTCBCCTTCBEEEC
T ss_pred             ccEeecCCCEEEec
Confidence            88999999999997

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=95.12  E-value=0.014  Score=49.81  Aligned_cols=51  Identities=14%  Similarity=0.122  Sum_probs=40.9

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~  188 (284)
                      .+||..+.+. |.-|+..+++|+..|.|.|||+                                           ++..
T Consensus        98 ~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i~vNg~-------------------------------------------~v~i  134 (208)
T d2uubd1          98 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGR-------------------------------------------RVDL  134 (208)
T ss_dssp             TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTE-------------------------------------------ECCC
T ss_pred             HHHHHHHHhccccccHHHHHHHHHhcCeecCCe-------------------------------------------EEEe
Confidence            3677776642 2368999999999999999985                                           1367


Q ss_pred             cCceecCCCEEEEEc
Q 023331          189 VDQIVEAGTYLRVHV  203 (284)
Q Consensus       189 ~~~~L~~GD~I~V~~  203 (284)
                      +++.|++||.|.|..
T Consensus       135 ps~~~~~gd~I~vre  149 (208)
T d2uubd1         135 PSYRVRPGDEIAVAE  149 (208)
T ss_dssp             TTCBCCTTCEEEECG
T ss_pred             ccEEecCCceeehhh
Confidence            889999999999974

>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.68  E-value=0.018  Score=49.68  Aligned_cols=49  Identities=22%  Similarity=0.252  Sum_probs=40.4

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      ..+++||||.|+.+|-        +++.+.+.++... +....-||=-.||||+++-.
T Consensus        29 ~G~l~idKP~G~TS~~--------vv~~ikk~l~~kK-vGH~GTLDP~AtGvL~v~iG   77 (230)
T d2apoa2          29 YGVVVVDKPRGPTSHE--------VSTWVKKILNLDK-AGHGGTLDPKVTGVLPVALE   77 (230)
T ss_dssp             TEEEEEEECSSSCHHH--------HHHHHHHHTTCSC-EEESSCCCTTCEEEEEEEEG
T ss_pred             CcEEEEECCCCCCHHH--------HHHHHHHHcCCCC-CCcccccCccceeeeeeeec
Confidence            4799999999998874        6677788887765 44589999999999999854

>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.41  E-value=0.021  Score=49.77  Aligned_cols=49  Identities=18%  Similarity=0.211  Sum_probs=40.3

Q ss_pred             CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023331          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT  282 (284)
Q Consensus       225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT  282 (284)
                      ..+++||||.|+.+|-        +++.+.+.++...- ...--||=..||+|+++-.
T Consensus        42 ~G~l~idKP~G~TS~~--------vv~~vkk~l~~kKv-GH~GTLDP~AtGvL~i~iG   90 (245)
T d2ey4a2          42 FGVINLDKPPGPTSHE--------VVAWIKKILNLEKA-GHGGTLDPKVSGVLPVALE   90 (245)
T ss_dssp             TEEEEEEECSSSCHHH--------HHHHHHHHTTCSCE-EESSCCCTTCEEEEEEEEG
T ss_pred             CcEEEEeCCCCCCHHH--------HHHHHHHHhCcCCC-CcCccCCCcceeeEEEEec
Confidence            4799999999998873        66778888877653 4489999999999999864

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.24  E-value=0.14  Score=36.77  Aligned_cols=30  Identities=10%  Similarity=-0.159  Sum_probs=25.7

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023331          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~  141 (284)
                      .|.++|.+ .+  -|++.++++|+.|+|++||+
T Consensus        19 ~l~~ll~~-~gl~~S~searRlI~~g~V~iN~~   50 (81)
T d1h3fa2          19 WVARLFTL-AGLTPSNAEARRLIQNRGLRLDGE   50 (81)
T ss_dssp             EHHHHHHH-TTSSSSHHHHHHHHHTTCEEETTE
T ss_pred             cHHHHHHH-cCCCcCHHHHHHHHHcCCEEECCE
Confidence            58888865 44  59999999999999999985

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.69  E-value=0.36  Score=35.65  Aligned_cols=32  Identities=19%  Similarity=0.241  Sum_probs=26.5

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023331          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (284)
Q Consensus       110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~  141 (284)
                      -.+.++|.+. +--|++.+++||+.|+|+||++
T Consensus        32 ~~l~~ll~~~~l~~S~seaRrlI~~ggv~iN~~   64 (99)
T d1jh3a_          32 VPLVELLVSAGISPSKRQAREDIQNGAIYVNGE   64 (99)
T ss_dssp             CCHHHHHHHHTSCCSHHHHHHHHHSTTEEETTE
T ss_pred             CCHHHHHHHcCCCcCHHHHHHHHHcCCEEECCE
Confidence            4688888643 3469999999999999999986