Citrus Sinensis ID: 023659

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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-------28
Protein Sequence
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWRKR
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHccEEEEEcccccccccccHHHHHHHccccccHHHccccccccccHHHccccEEEcccccccccccEEEEccccccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHcccccccccHHHHHHHHHHcccHHcccccccccEEEEEEcccccccccccccEcccHHHHHHHccccccccccccHccccccccccccccEEEEEEcccccHHHHHHHHccccHHHHHHHHHcccEEEEEccccccccccHHHHHHHHccccHHHHHHHHccccccHHHHccccEEcccccccccccEEEEEccccccccEEEEccccEEEEEcccEEEEEcccccccccccccHHHHHHHHHHHHHcccccccccEEccccccccccc
Coil and Loop (DISEMBL)
MSSVSFSSIftnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFsssnrnfvceswkrhvfthtdTAAIaaattpssygypeyhrllpcpsqncpprvehlvvseggpVLEYICRelnlpplfvaDLIHFGAVYYAlvcpkppltatpeqmrvfkevtdpsvlskrssikgkTVREAQKTFRITHVDQIVEAGtylrvhvhpkrfprcydidwnsrIIAVTEshvvldkpagtsvggttdniEESCATFASRalglttplrtthqidnctegwrkr
Flexible Loop (DISEMBL)
MSSVSFSSIFtnngrslgaPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEqmrvfkevtdpsvlskrssikgktvreaqktfrithvdqiVEAGtylrvhvhpkrfPRCYDIDWNSRIIAVTeshvvldkpagtsvggttdNIEESCATFASRalglttplrtthqidnctegwrkr
Low Complexity Region (SEG)
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFthtdtaaiaaattPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWRKR
Disordered region (IsUnstruct)
***************SLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLT*******************************AQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNC*******
Disordered Region (DISOPRED)
******S*IFTNNGRSLGAPVSLLRTLASTHASCH**IY*****************ESWKRHVFTHTDT**********SYGYPEYHRLLPCPSQNC*PR***LVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKP***************************************RITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG****
Disordered Region (DISEMBL)
********IFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWRKR
Disordered Region (DISPRO)
*****FSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEG****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSVSFSSIFTNNGRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSSSNRNFVCESWKRHVFTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWRKR
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	279	2.2.26 [Sep-21-2011]
Q9SVS0	472	RNA pseudourine synthase	yes	no	0.939	0.555	0.642	1e-92
A3BN26	477	RNA pseudourine synthase	yes	no	0.709	0.415	0.712	4e-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 =  288 bits (736), Expect = 4e-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	279
224076324	470	predicted protein [Populus trichocarpa]	0.942	0.559	0.716	1e-106
255554955	476	ribosomal pseudouridine synthase, putati	0.956	0.560	0.707	1e-104
225444351	472	PREDICTED: RNA pseudourine synthase 6, c	0.899	0.531	0.716	1e-102
449467613	475	PREDICTED: RNA pseudourine synthase 6, c	0.878	0.515	0.705	2e-97
449488468	475	PREDICTED: LOW QUALITY PROTEIN: RNA pseu	0.878	0.515	0.705	3e-97
356546416	473	PREDICTED: RNA pseudourine synthase 6, c	0.910	0.536	0.639	2e-93
449471733	287	PREDICTED: RNA pseudourine synthase 6, c	0.903	0.878	0.653	3e-93
449454720	475	PREDICTED: RNA pseudourine synthase 6, c	0.903	0.530	0.653	3e-93
449488373	475	PREDICTED: RNA pseudourine synthase 6, c	0.903	0.530	0.653	3e-93
356557901	473	PREDICTED: RNA pseudourine synthase 6, c	0.939	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 (1003), 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   MASLNLASIFSYSYRSFSAPVTLLRTLAFTRA---YSLNKKALVWC-SLSKKKLSCESLK 56

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

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

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

Query: 241 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 =  384 bits (986), 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 (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 195/272 (71%), Positives = 219/272 (80%), Gaps = 21/272 (7%)

Query: 7   SSIFTNNGRSLGAPVSLLRTLASTHASCHRN---IYKSNVVLSFSSSNRNFVCESWKRHV 63
           SS++ +N RS G PV+L RTLAS++    R+   ++ SN          N  C       
Sbjct: 16  SSLWNSNCRSFGTPVALARTLASSNVFSRRHKRVVWCSN----------NPTC------- 58

Query: 64  FTHTDTAAIAAATTPSSYGYPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLP 123
            T   TA+  +A T S  GYPEYHRLLPCPSQN PPRVEHLVVSEGG VL+YI + L+LP
Sbjct: 59  -TRELTASSDSANTSSVNGYPEYHRLLPCPSQNGPPRVEHLVVSEGGCVLDYISKALDLP 117

Query: 124 PLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKT 183
           PLFVADLIHFGAVYYALVCP+PP +ATPEQ+R+FKEVT PSVL KR SIKGKT+REAQKT
Sbjct: 118 PLFVADLIHFGAVYYALVCPEPPPSATPEQVRLFKEVTAPSVLRKRPSIKGKTIREAQKT 177

Query: 184 FRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTD 243
           FRIT V++ VEAGTYLRVHVHPKRFPRCY+IDW SRIIAVTES+VVLDKPAGTSVGGTTD
Sbjct: 178 FRITDVNEFVEAGTYLRVHVHPKRFPRCYEIDWKSRIIAVTESYVVLDKPAGTSVGGTTD 237

Query: 244 NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
           NIEESCATFA+RALGLTTPLRTTHQIDNCTEG
Sbjct: 238 NIEESCATFATRALGLTTPLRTTHQIDNCTEG 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 =  361 bits (926), Expect = 2e-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 (925), Expect = 3e-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 (892), Expect = 2e-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 (891), Expect = 3e-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 =  347 bits (890), Expect = 3e-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 =  347 bits (890), Expect = 3e-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 =  344 bits (883), 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	279
TAIR|locus:2119073	472	AT4G21770 [Arabidopsis thalian	0.939	0.555	0.634	4.3e-86

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

 Score = 861 (308.1 bits), Expect = 4.3e-86, P = 4.3e-86
 Identities = 172/271 (63%), Positives = 206/271 (76%)

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 IEESCATFASRALGLTTPLRTTHQIDNCTEG 275
             IEESCATFASRAL L  PL+TTHQIDNCTEG
Sbjct:   236 IEESCATFASRALDLPEPLKTTHQIDNCTEG 266


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        0.320   0.134   0.416    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      279       266   0.00094  114 3  11 22  0.45    33
                                                     32  0.39    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:  218 KB (2120 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:  22.95u 0.24s 23.19t   Elapsed:  00:00:01
  Total cpu time:  22.95u 0.24s 23.19t   Elapsed:  00:00:01
  Start:  Fri May 10 13:34:11 2013   End:  Fri May 10 13:34:12 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	0.7096	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	279
pfam00849	149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	2e-04

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

 Score = 40.1 bits (94), 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	279
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	99.95
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	99.9
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	99.9
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	99.9
cd02558	246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	99.8
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	99.77
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	99.71
KOG1919	371	consensus RNA pseudouridylate synthases [RNA proce	99.68
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	99.65
cd02557	213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	99.57
TIGR01621	217	RluA-like pseudouridine synthase Rlu family protei	99.55
cd02563	223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	99.54
PRK10158	219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	99.54
PRK11112	257	tRNA pseudouridine synthase C; Provisional	99.53
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	99.06
cd02870	146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.05
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	98.98
PRK11394	217	23S rRNA pseudouridine synthase E; Provisional	98.6
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	98.32
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.03
smart00363	60	S4 S4 RNA-binding domain.	97.55
COG1188	100	Ribosome-associated heat shock protein implicated	97.29
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	97.26
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	97.01
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	96.64
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	96.35
COG2302	257	Uncharacterized conserved protein, contains S4-lik	96.35
PF00849	164	PseudoU_synth_2: RNA pseudouridylate synthase This	96.32
CHL00113	201	rps4 ribosomal protein S4; Reviewed	96.27
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	96.22
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	96.16
cd02550	154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	95.92
cd02555	177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	95.66
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	94.76
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	93.5
PF06353	142	DUF1062: Protein of unknown function (DUF1062); In	91.93
PRK04270	300	H/ACA RNA-protein complex component Cbf5p; Reviewe	91.65
PRK11507	70	ribosome-associated protein; Provisional	90.16
COG2501	73	S4-like RNA binding protein [Replication, recombin	90.08
PRK01851	303	truB tRNA pseudouridine synthase B; Provisional	89.45
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	85.57
PF13275	65	S4_2: S4 domain; PDB: 1P9K_A.	84.99
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	84.86
TIGR00425	322	CBF5 rRNA pseudouridine synthase, putative. This f	82.73
PRK01777	95	hypothetical protein; Validated	82.3

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

Probab=99.95  E-value=2.1e-27  Score=221.55  Aligned_cols=123  Identities=19%  Similarity=0.170  Sum_probs=102.3

Q ss_pred             CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      .|||.||++ +. +||++++++++.|+|.+||+                                  .+          .
T Consensus        13 ~rld~~L~~-l~~~sr~~~~~~i~~g~v~vNg~----------------------------------~v----------~   47 (289)
T COG0564          13 QRLDKFLAK-LLPISRSRIQKLIRKGRVRVNGK----------------------------------KV----------K   47 (289)
T ss_pred             CCHHHHHHH-ccCcCHHHHHHHHHCCCEEECCE----------------------------------Ec----------c
Confidence            389999999 65 99999999999999999986                                  22          3


Q ss_pred             CCceecCCCEEEEEcCCCCC-CCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC-CCCcccc
Q 023659          189 VDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTT  266 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~~~~~~~-~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~-~~~l~~V  266 (279)
                      .+++|+.||.|++..+.... ....+.+++++|||||||+||||||+||+|||+.++..+|+++++....+. ...+.+|
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            57899999999999865332 334456667999999999999999999999999999999999988765432 2235679


Q ss_pred             ccCCcCccccc
Q 023659          267 HQIDNCTEGWR  277 (279)
Q Consensus       267 HRLDrdTSGLL  277 (279)
                      |||||||||||
T Consensus       128 HRLDkdTSGll  138 (289)
T COG0564         128 HRLDKDTSGLL  138 (289)
T ss_pred             ccCCCCCceEE
Confidence            99999999997

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=99.90  E-value=1.3e-23  Score=193.99  Aligned_cols=125  Identities=18%  Similarity=0.142  Sum_probs=99.3

Q ss_pred             CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      .+|++||++.+. +||+.++++|+.|.|+|||..                                           +..
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            389999999996 999999999999999999841                                           114


Q ss_pred             CCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC---CCCccc
Q 023659          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT  265 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~~l~~  265 (279)
                      .++.|+.||.|.+...+...+...+.+.+++|+|||++++|||||+||+|||+.++..+|+.+.+..+++.   ...+++
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            46789999999997643222222334456889999999999999999999999887778888887655431   133678


Q ss_pred             cccCCcCccccc
Q 023659          266 THQIDNCTEGWR  277 (279)
Q Consensus       266 VHRLDrdTSGLL  277 (279)
                      |||||++|||||
T Consensus       123 vhRLD~~TSGll  134 (299)
T TIGR00005       123 VHRLDRDTSGLM  134 (299)
T ss_pred             ECCCCCCCceEE
Confidence            999999999997

modifies uracil-65 in transfer RNAs to pseudouridine.

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=99.90  E-value=2.7e-23  Score=195.38  Aligned_cols=124  Identities=14%  Similarity=0.086  Sum_probs=98.0

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||+||++.+ .+||+.++++|+.|.|++||+.                                           +..+
T Consensus        19 RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~-------------------------------------------v~~~   55 (325)
T PRK11180         19 RLDQALAELFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------INKP   55 (325)
T ss_pred             cHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccCC
Confidence            8999999987 4899999999999999999861                                           1134


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC---CCCcccc
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTT  266 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~~l~~V  266 (279)
                      ++.|+.||.|.+...+.......+.+.+++|||||+++||||||+||+|||+.++..+|+.+.+..++..   ...+++|
T Consensus        56 ~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~v  135 (325)
T PRK11180         56 KEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIV  135 (325)
T ss_pred             CcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCccccee
Confidence            6788999999998643222222344567899999999999999999999999887778888877654321   1224579


Q ss_pred             ccCCcCccccc
Q 023659          267 HQIDNCTEGWR  277 (279)
Q Consensus       267 HRLDrdTSGLL  277 (279)
                      ||||++|||||
T Consensus       136 hRLD~~TSGll  146 (325)
T PRK11180        136 HRLDKDTTGLM  146 (325)
T ss_pred             ccCCCCCceeE
Confidence            99999999997

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=99.90  E-value=3.7e-23  Score=194.05  Aligned_cols=136  Identities=18%  Similarity=0.179  Sum_probs=96.6

Q ss_pred             CCCceEEEeeCC-CC-cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCccccccccccc
Q 023659           97 CPPRVEHLVVSE-GG-PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIK  173 (279)
Q Consensus        97 ~~~rv~~~v~~~-~g-rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~  173 (279)
                      .|++..+.+... +| ||++||++.+ .+||+.++++|+.|.|++||..                               
T Consensus         5 ~~~~~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~-------------------------------   53 (317)
T PRK11025          5 TPSVKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKR-------------------------------   53 (317)
T ss_pred             CCccEEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEE-------------------------------
Confidence            344434444333 34 9999999888 5899999999999999999851                               


Q ss_pred             CcceeeccccccccCCCceecCCCEEEEEcCCCCC---CCCC-----CCCCccceEEecCcEEEEeCCCCCcccCCCCCC
Q 023659          174 GKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRF---PRCY-----DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNI  245 (279)
Q Consensus       174 GK~v~~~q~~~rv~~~~~~Lk~GD~I~V~~~~~~~---~~~~-----~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~  245 (279)
                         +          ..+++|+.||.|++.......   .+..     ...++++|||||+++||||||+||+|||+.+..
T Consensus        54 ---v----------~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~  120 (317)
T PRK11025         54 ---I----------KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS  120 (317)
T ss_pred             ---c----------CcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC
Confidence               1          346789999999986422111   1010     123567999999999999999999999987653


Q ss_pred             cCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          246 EESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       246 ~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      . ++.+.+.........+++||||||+|||||
T Consensus       121 ~-~~~~~~~~~~~~~~~~~~vhRLD~~TSGll  151 (317)
T PRK11025        121 F-GVIEGLRALRPEARFLELVHRLDRDTSGVL  151 (317)
T ss_pred             c-cHHHHHHHhccCCCcCceeCCCCCCCceEE
Confidence            3 455555433222223467999999999997

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

Probab=99.80  E-value=1e-19  Score=165.54  Aligned_cols=86  Identities=22%  Similarity=0.215  Sum_probs=68.9

Q ss_pred             CCCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccc
Q 023659          188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH  267 (279)
Q Consensus       188 ~~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VH  267 (279)
                      ..+++|+.||.|.++....+.   .+.+.+++|||||++++|||||+||+|||+.++..+|+.+.+....+.. .+.+||
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            568899999999998532211   1334568999999999999999999999998888888888776555543 356799


Q ss_pred             cCCcCccccc
Q 023659          268 QIDNCTEGWR  277 (279)
Q Consensus       268 RLDrdTSGLL  277 (279)
                      |||++|||||
T Consensus        88 RLD~~TSGll   97 (246)
T cd02558          88 RLDRLTAGLV   97 (246)
T ss_pred             cCCCCceeEE
Confidence            9999999997

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=99.77  E-value=4.9e-19  Score=158.78  Aligned_cols=108  Identities=13%  Similarity=0.089  Sum_probs=80.2

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCCC
Q 023659          111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD  190 (279)
Q Consensus       111 rLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~~  190 (279)
                      +|++||++.+.+||+.++++|+.|.|++||+.                                  +         ...+
T Consensus         2 rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~----------------------------------~---------~~~~   38 (232)
T PRK10839          2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEI----------------------------------V---------KNGA   38 (232)
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE----------------------------------e---------ccCC
Confidence            68999998888999999999999999999851                                  1         1356


Q ss_pred             ceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCC
Q 023659          191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID  270 (279)
Q Consensus       191 ~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLD  270 (279)
                      ++|+.||.|.+...+..             ..+|+++||||||+||+|||+.. ...|+..++..  +....+++|||||
T Consensus        39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~-~~~tl~~~l~~--~~~~~~~~v~RLD  102 (232)
T PRK10839         39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDP-DHPTVLYFLDE--PVAYKLHAAGRLD  102 (232)
T ss_pred             cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCC-CCCeEEEeccc--ccccCceecCCCC
Confidence            78999999988632100             11467999999999999999844 23555443321  1112356899999


Q ss_pred             cCccccc
Q 023659          271 NCTEGWR  277 (279)
Q Consensus       271 rdTSGLL  277 (279)
                      +||||||
T Consensus       103 ~~TSGll  109 (232)
T PRK10839        103 IDTTGLV  109 (232)
T ss_pred             CCceeEE
Confidence            9999997

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=99.71  E-value=3.5e-17  Score=153.26  Aligned_cols=108  Identities=16%  Similarity=0.149  Sum_probs=83.0

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      .+|++||++....||..+.+||+.|.|+|||+.                                  +          ..
T Consensus         7 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~----------------------------------v----------~~   42 (290)
T PRK10475          7 TRLNKYISESGICSRREADRYIEQGNVFINGKR----------------------------------A----------TI   42 (290)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEE----------------------------------c----------cC
Confidence            389999997655799999999999999999861                                  1          34


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL  269 (279)
                      +++|.+||.|.|....     ..+.      .+||+++||+|||+|+++|+... ...|+.+++...    ..+++||||
T Consensus        43 ~~~V~~gD~V~v~g~~-----i~~~------~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~VgRL  106 (290)
T PRK10475         43 GDQVKAGDVVKVNGQL-----IEPR------EAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIGRL  106 (290)
T ss_pred             CCCcCCCCEEEECCEE-----cccc------ccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccccC
Confidence            5678999999886311     1010      14899999999999999998764 457777766431    235689999


Q ss_pred             CcCccccc
Q 023659          270 DNCTEGWR  277 (279)
Q Consensus       270 DrdTSGLL  277 (279)
                      |+||||||
T Consensus       107 DrdTsGLL  114 (290)
T PRK10475        107 DKDSQGLI  114 (290)
T ss_pred             CCCCcceE
Confidence            99999997

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

Probab=99.68  E-value=1.9e-16  Score=152.99  Aligned_cols=119  Identities=24%  Similarity=0.277  Sum_probs=91.1

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      .+.+++..+| ..++.+.+..|+.|.|++||+                                  .+          ..
T Consensus        45 ~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~----------------------------------~~----------~v   80 (371)
T KOG1919|consen   45 KLVDVFVSEFRLRERAYYESAIKLGRVTVNGE----------------------------------QV----------RV   80 (371)
T ss_pred             chHHHHHHHHhcCchHhhhhhhhcCceEECcE----------------------------------ee----------ee
Confidence            4667776666 689999999999999999986                                  11          24


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL  269 (279)
                      +..++.||.|...++..+.+   ...+++.|+|||+++||||||+|++|||++....+++...+....... .+++||||
T Consensus        81 ~~i~k~~d~l~~~vhrh~p~---~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~-~~~~~hRL  156 (371)
T KOG1919|consen   81 SLIVKNGDVLCHTVHRHEPP---VAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVE-GLRPCHRL  156 (371)
T ss_pred             EEEeccCCEEEEeeccCCCC---ccccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhcccc-cccccccc
Confidence            67899999998877643222   123578999999999999999999999988766666655554432222 36789999


Q ss_pred             CcCccccc
Q 023659          270 DNCTEGWR  277 (279)
Q Consensus       270 DrdTSGLL  277 (279)
                      |+.|||||
T Consensus       157 Dr~tSGll  164 (371)
T KOG1919|consen  157 DRLTSGLL  164 (371)
T ss_pred             CccccceE
Confidence            99999998

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=99.65  E-value=7e-16  Score=144.14  Aligned_cols=114  Identities=11%  Similarity=0.027  Sum_probs=79.6

Q ss_pred             CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      .||++||++ ++ .||+.+.+||+.|.|+|||+.                                  +          .
T Consensus         3 ~RL~k~La~-~g~~SRr~a~~lI~~G~V~VNG~~----------------------------------~----------~   37 (289)
T PRK10700          3 EKLQKVLAR-AGHGSRREIESIIEAGRVSVDGKI----------------------------------A----------T   37 (289)
T ss_pred             hhHHHHHHH-CCCCCHHHHHHHHHcCCEEECCEe----------------------------------c----------c
Confidence            479999997 45 899999999999999999862                                  1          2


Q ss_pred             CCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCcccccc
Q 023659          189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ  268 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHR  268 (279)
                      ..+.|..+|...|.+..+....  ..     ..-||++++++|||+|+++|++......|+.+++....  ...+.+|||
T Consensus        38 ~g~~V~~~~~d~I~v~g~~~~~--~~-----~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--~~~~~~VgR  108 (289)
T PRK10700         38 LGDRVEVTPGLKIRIDGHLISV--KE-----SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR--GARWIAVGR  108 (289)
T ss_pred             CCCEeCCCCCeEEEECCEEeec--cc-----ccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc--CCceeEccC
Confidence            3456766643333332211000  00     00167789999999999999987666678888775321  123568999


Q ss_pred             CCcCccccc
Q 023659          269 IDNCTEGWR  277 (279)
Q Consensus       269 LDrdTSGLL  277 (279)
                      ||+||||||
T Consensus       109 LD~dTsGLL  117 (289)
T PRK10700        109 LDVNTCGLL  117 (289)
T ss_pred             CCCCCceEE
Confidence            999999997

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like

Probab=99.57  E-value=4.3e-15  Score=132.38  Aligned_cols=60  Identities=28%  Similarity=0.415  Sum_probs=50.4

Q ss_pred             ccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       217 ~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      .++|||||++++|||||+||+|||+......++...+....+.. .+.+|||||++|||||
T Consensus        15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~-~~~~vhRLD~~TSGll   74 (213)
T cd02557          15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLT-ELRPCHRLDRLTSGLL   74 (213)
T ss_pred             CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCC-CccCccCCCCCCceEE
Confidence            57899999999999999999999987666778888776655432 3567999999999997

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.

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

Probab=99.55  E-value=4.9e-15  Score=132.64  Aligned_cols=57  Identities=21%  Similarity=0.295  Sum_probs=45.2

Q ss_pred             cceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|||||++++|||||+||+|||+.+  ..++...+....+.. .+++|||||++|||||
T Consensus         2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~~~-~~~~VhRLDr~TSGll   58 (217)
T TIGR01621         2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLGVG-QVWLVHRLDKMTSGIL   58 (217)
T ss_pred             ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcCCC-CccEecCCCCCCceEE
Confidence            57999999999999999999999764  345665554443322 3678999999999997

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=99.54  E-value=6.7e-15  Score=131.69  Aligned_cols=58  Identities=24%  Similarity=0.283  Sum_probs=43.1

Q ss_pred             cceEEecCcEEEEeCCCCCcccCCCCCCcCcH--HHHHHHHhCCCCCccccccCCcCccccc
Q 023659          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|||||++|||||||+||+|||+..+...+.  ...+....+  ..+++|||||++|||||
T Consensus         1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGll   60 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVL   60 (223)
T ss_pred             CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEE
Confidence            36999999999999999999999865433332  222322223  23568999999999997

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

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

Probab=99.54  E-value=6.8e-15  Score=131.78  Aligned_cols=57  Identities=23%  Similarity=0.227  Sum_probs=45.2

Q ss_pred             cceEEecCcEEEEeCCCCCcccCCCC-CCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       218 l~ILYEDedlLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|||||++++|||||+|++|||+.. ....++.+.+...+  . .+.+|||||++|||||
T Consensus        14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~-~~~~vhRLDr~TSGll   71 (219)
T PRK10158         14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--P-QAESVHRLDMATSGVI   71 (219)
T ss_pred             CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--C-CCCEECCCCCCCceEE
Confidence            68999999999999999999999764 33456666554332  2 2567999999999997

>PRK11112 tRNA pseudouridine synthase C; Provisional

Probab=99.53  E-value=9.4e-15  Score=133.86  Aligned_cols=58  Identities=26%  Similarity=0.260  Sum_probs=43.3

Q ss_pred             cceEEecCcEEEEeCCCCCcccCCCCCCcCcH--HHHHHHHhCCCCCccccccCCcCccccc
Q 023659          218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|||||+++||||||+||+|||+..+..++.  ...+....+  ..+++|||||++|||||
T Consensus         2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGll   61 (257)
T PRK11112          2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVL   61 (257)
T ss_pred             CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEE
Confidence            57999999999999999999999864444432  222322222  23568999999999997

>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=99.06  E-value=7.5e-10  Score=78.16  Aligned_cols=68  Identities=16%  Similarity=0.128  Sum_probs=54.4

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      +|+.||.+.+ ..|++.++++|+.|.|++||+.                                           ++.+
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            6899999874 6899999999999999999861                                           1244


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEe
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD  231 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVN  231 (279)
                      ++.+..||.|.+...+   .       +.+|+|||+++||||
T Consensus        39 ~~~v~~~d~i~i~~~~---~-------~~~i~~ed~~~lvv~   70 (70)
T cd00165          39 SYKVKPGDVIEVDGKS---I-------EEDIVYEDKKLLVVN   70 (70)
T ss_pred             ccCcCCCCEEEEcCCC---c-------ccceeeccCCEEEeC
Confidence            6788999998886421   1       128999999999997

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

Probab=99.05  E-value=4.3e-11  Score=100.43  Aligned_cols=48  Identities=19%  Similarity=0.194  Sum_probs=36.4

Q ss_pred             EEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       227 lLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|+|||+||++||+......++.+.+..   ....+.+|||||++|||||
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---~~~~~~~vhRLD~~TsGll   48 (146)
T cd02870           1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---VGERLFPVGRLDYDTEGLL   48 (146)
T ss_pred             CEEEECCCCcEecccCCCCCCEEeeeccc---cCCCEEECCCCCCCCeeEE
Confidence            58999999999999876656666554432   1223678999999999997

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=98.98  E-value=1.1e-09  Score=101.24  Aligned_cols=111  Identities=19%  Similarity=0.125  Sum_probs=74.1

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      .||++||++.--.||..+.+||..|.|.|||++                                  +         +..
T Consensus         3 ~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v----------------------------------~---------~~~   39 (248)
T COG1187           3 MRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKV----------------------------------A---------TLG   39 (248)
T ss_pred             cchHHHHHHcCCCCHHHHHHHHHcCCEEECCEE----------------------------------e---------ccC
Confidence            379999998555899999999999999999862                                  0         012


Q ss_pred             CceecCCC-EEEEEcCCCCCCCCCCCCCccceEE-ecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccc
Q 023659          190 DQIVEAGT-YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH  267 (279)
Q Consensus       190 ~~~Lk~GD-~I~V~~~~~~~~~~~~~~~~l~ILY-EDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VH  267 (279)
                      ...+.+++ .|.+.-  .            .+.+ +..-+++.|||.|+++.-..+....|+..++.........+++|-
T Consensus        40 ~~~v~~~~~~i~v~g--~------------~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvG  105 (248)
T COG1187          40 GVVVDPDDDVVEVDG--K------------RIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG  105 (248)
T ss_pred             CeEeCCCCcEEEECC--E------------EeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeecc
Confidence            23445553 444431  0            1233 223399999999999986644455666555432111122367899


Q ss_pred             cCCcCccccc
Q 023659          268 QIDNCTEGWR  277 (279)
Q Consensus       268 RLDrdTSGLL  277 (279)
                      |||+||+|||
T Consensus       106 RLD~dTeGLL  115 (248)
T COG1187         106 RLDKDTEGLL  115 (248)
T ss_pred             ccCCCCeeEE
Confidence            9999999997

>PRK11394 23S rRNA pseudouridine synthase E; Provisional

Probab=98.60  E-value=2.9e-08  Score=90.12  Aligned_cols=48  Identities=15%  Similarity=0.199  Sum_probs=36.2

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      -.++++|||+|+++|+.......++...+.    .. .+++|||||+||||||
T Consensus        39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~----~~-~~~~vgRLD~~TsGll   86 (217)
T PRK11394         39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP----VQ-GVYAAGRLDRDSEGLL   86 (217)
T ss_pred             CEEEEEECCCCCEEeeCCccCCcchHHhcc----cC-CeEEecCCCCCCeeEE
Confidence            358999999999999654444566666542    12 3568999999999997

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=98.32  E-value=1.6e-06  Score=62.94  Aligned_cols=31  Identities=3%  Similarity=-0.212  Sum_probs=28.7

Q ss_pred             CcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.||++. ++  ||+.+++||+.|.|+|||.
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            4899999987 77  9999999999999999986

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=98.03  E-value=1.1e-05  Score=55.71  Aligned_cols=31  Identities=16%  Similarity=-0.001  Sum_probs=27.4

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      |||.||.+.. ..||+++++||+.|.|+|||+
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            7999998544 578999999999999999986

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 ....

>smart00363 S4 S4 RNA-binding domain

Probab=97.55  E-value=0.00026  Score=48.22  Aligned_cols=31  Identities=19%  Similarity=0.112  Sum_probs=27.7

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      +|+.||.+. +..|+..+++++..|.|++||+
T Consensus         2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~   33 (60)
T smart00363        2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGK   33 (60)
T ss_pred             cHHHHHHHcCcccCHHHHHHHHHcCCEEECCE
Confidence            689999876 3689999999999999999986

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

Probab=97.29  E-value=0.00066  Score=55.41  Aligned_cols=52  Identities=13%  Similarity=0.124  Sum_probs=43.0

Q ss_pred             cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||.||.- +|==+|+.++++++.|.|.|||..                                            .++
T Consensus        10 RLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~--------------------------------------------aKp   45 (100)
T COG1188          10 RLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQR--------------------------------------------AKP   45 (100)
T ss_pred             ehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEE--------------------------------------------ccc
Confidence            89999954 455689999999999999999862                                            156


Q ss_pred             CceecCCCEEEEEcCCC
Q 023659          190 DQIVEAGTYLRVHVHPK  206 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~  206 (279)
                      ++.|+.||+|+|++...
T Consensus        46 S~~VK~GD~l~i~~~~~   62 (100)
T COG1188          46 SKEVKVGDILTIRFGNK   62 (100)
T ss_pred             ccccCCCCEEEEEeCCc
Confidence            78899999999997643

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

Probab=97.26  E-value=0.00055  Score=64.22  Aligned_cols=32  Identities=16%  Similarity=0.054  Sum_probs=30.6

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+++..+++||+.+++||+.|.|.+|+.
T Consensus       192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~  223 (267)
T PLN00051        192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWR  223 (267)
T ss_pred             ccHHHHHHHHhccCHHHHHHHHHcCcEEECCE
Confidence            49999999999999999999999999999986

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=97.01  E-value=0.0013  Score=61.31  Aligned_cols=32  Identities=13%  Similarity=0.038  Sum_probs=30.2

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+++..+++||+.+++||+.|.|.|||.
T Consensus       184 ~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~  215 (257)
T TIGR03069       184 LRIDAIASAGFGLSRSKIVDQIKAGRLRLNWK  215 (257)
T ss_pred             ccHHHHHHhhhhhhHHHHHHHHHCCeEEECCE
Confidence            49999999999999999999999999999986

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=96.64  E-value=0.0037  Score=56.20  Aligned_cols=32  Identities=9%  Similarity=0.091  Sum_probs=27.9

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|... +..||..++.||..|.|.|||+
T Consensus        90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk  122 (200)
T TIGR01017        90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK  122 (200)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCE
Confidence            4899999654 3689999999999999999986

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

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=96.35  E-value=0.0064  Score=54.77  Aligned_cols=32  Identities=9%  Similarity=0.065  Sum_probs=27.7

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+ .+..||..+++||..|.|+|||+
T Consensus        93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk  125 (203)
T PRK05327         93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGK  125 (203)
T ss_pred             HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCE
Confidence            489999964 34689999999999999999985

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

Probab=96.35  E-value=0.0055  Score=57.35  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=44.4

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      =|||..+++.+++||+..++||+.|.|.||++.                                           +.++
T Consensus       181 lRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~-------------------------------------------v~~~  217 (257)
T COG2302         181 LRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKV-------------------------------------------VDKA  217 (257)
T ss_pred             hhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEE-------------------------------------------eccc
Confidence            489999999999999999999999999999751                                           2356


Q ss_pred             CceecCCCEEEEE
Q 023659          190 DQIVEAGTYLRVH  202 (279)
Q Consensus       190 ~~~Lk~GD~I~V~  202 (279)
                      ++.|+.||.|.+.
T Consensus       218 s~~v~~GDliSir  230 (257)
T COG2302         218 SYEVQEGDLISIR  230 (257)
T ss_pred             cceeccCCEEEEe
Confidence            8999999999986

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

Probab=96.32  E-value=0.0018  Score=54.07  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=11.8

Q ss_pred             CCCCccccccCCcCccccc
Q 023659          259 LTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       259 ~~~~l~~VHRLDrdTSGLL  277 (279)
                      ....+++|||||++|||||
T Consensus        37 ~~~~~~~v~RLD~~TsGll   55 (164)
T PF00849_consen   37 DPPELYPVHRLDRDTSGLL   55 (164)
T ss_dssp             TSGGGEESS---TT-EEEE
T ss_pred             CCCceEECCCCCccccCCe
Confidence            3345778999999999997

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 ....

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=96.27  E-value=0.0082  Score=54.28  Aligned_cols=32  Identities=9%  Similarity=-0.069  Sum_probs=28.0

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+.. ..||..+++||..|.|.|||.
T Consensus        89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk  121 (201)
T CHL00113         89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGR  121 (201)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCE
Confidence            37999997654 579999999999999999986

>TIGR00478 tly hemolysin TlyA family protein

Probab=96.22  E-value=0.0074  Score=55.27  Aligned_cols=31  Identities=16%  Similarity=-0.130  Sum_probs=27.8

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      |||.||.+.. ..||+.+++||+.|.|++||+
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            6899998765 578999999999999999986

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).

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=96.16  E-value=0.013  Score=50.15  Aligned_cols=32  Identities=13%  Similarity=0.129  Sum_probs=27.8

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.||.. .|--+|+.+++||..|.|.+||.
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            389999964 44579999999999999999986

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

Probab=95.92  E-value=0.0057  Score=51.64  Aligned_cols=28  Identities=21%  Similarity=0.291  Sum_probs=22.8

Q ss_pred             EEEEeCCCCCcccCCCCCCcCcHHHHHH
Q 023659          227 HVVLDKPAGTSVGGTTDNIEESCATFAS  254 (279)
Q Consensus       227 lLVVNKPaGl~VHPt~~~~~~TL~~~l~  254 (279)
                      ++|+|||+|+++|++.....+++...+.
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~   28 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLD   28 (154)
T ss_pred             CEEEECCCCCEEecCCCCCCCcHHHhhh
Confidence            5899999999999988766677766553

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.

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

Probab=95.66  E-value=0.0038  Score=54.84  Aligned_cols=15  Identities=20%  Similarity=0.244  Sum_probs=13.7

Q ss_pred             ccccccCCcCccccc
Q 023659          263 LRTTHQIDNCTEGWR  277 (279)
Q Consensus       263 l~~VHRLDrdTSGLL  277 (279)
                      +.+|||||+||||||
T Consensus        47 l~~VgRLD~dTsGLL   61 (177)
T cd02555          47 LAPIGPLDKDASGLL   61 (177)
T ss_pred             eeEecCCCCCCeeEE
Confidence            568999999999997

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.

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

Probab=94.76  E-value=0.051  Score=49.41  Aligned_cols=51  Identities=12%  Similarity=0.132  Sum_probs=40.4

Q ss_pred             cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||..+.. .|.-|+.++++||..|+|.|||+                                  .         ++.+
T Consensus        95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk----------------------------------~---------V~iP  131 (205)
T COG0522          95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGK----------------------------------R---------VNIP  131 (205)
T ss_pred             HHHHHHHHhcccccHHHHHHHhhcceEEECCE----------------------------------E---------eccC
Confidence            66666643 23468999999999999999986                                  2         4577


Q ss_pred             CceecCCCEEEEEcC
Q 023659          190 DQIVEAGTYLRVHVH  204 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~  204 (279)
                      ++.|++||++.|..-
T Consensus       132 Sy~V~~gdei~V~~k  146 (205)
T COG0522         132 SYLVSPGDEISVREK  146 (205)
T ss_pred             cEEecCCCEEEeeec
Confidence            999999999999753

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

Probab=93.50  E-value=0.12  Score=48.22  Aligned_cols=32  Identities=16%  Similarity=-0.032  Sum_probs=28.5

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.++ +--||+.++++|..|.|++||.
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            3799999886 4579999999999999999986

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

Probab=91.93  E-value=0.48  Score=40.90  Aligned_cols=62  Identities=16%  Similarity=0.138  Sum_probs=43.1

Q ss_pred             CCCCCccccccccCCCCCCC-CceEE-EeeCC--CCcHHHHHHHhcCCCHHHHHHHHHcCcEEEcc
Q 023659           79 SSYGYPEYHRLLPCPSQNCP-PRVEH-LVVSE--GGPVLEYICRELNLPPLFVADLIHFGAVYYAL  140 (279)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~-~rv~~-~v~~~--~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~  140 (279)
                      ...++|+|.=....+..... +.++. +..+.  .-+|+.+|++.|++||+.+++|+..|.|....
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            34478888766544333322 22442 22222  24899999999999999999999999999873

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

Probab=91.65  E-value=0.2  Score=47.69  Aligned_cols=44  Identities=25%  Similarity=0.288  Sum_probs=35.4

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      +.||+||||.|+.+|.        +++.+.+.++.....| ..-||-..||+|
T Consensus        22 ~g~l~i~Kp~g~tS~~--------~v~~~r~~~~~kkvGH-~GTLDp~A~GvL   65 (300)
T PRK04270         22 FGVVNLDKPPGPTSHE--------VAAWVRDILGVEKAGH-GGTLDPKVTGVL   65 (300)
T ss_pred             CCEEEEECCCCCCHHH--------HHHHHHHHhccccccC-CCCCCCcCeEEE
Confidence            5799999999998873        4566777777665454 999999999997

>PRK11507 ribosome-associated protein; Provisional

Probab=90.16  E-value=0.66  Score=35.72  Aligned_cols=31  Identities=10%  Similarity=-0.182  Sum_probs=25.7

Q ss_pred             CcHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~  141 (279)
                      -+|+.||+- .+  -|=..++.+|..|.|.|||+
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            379999974 45  35569999999999999997

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

Probab=90.08  E-value=0.91  Score=35.29  Aligned_cols=38  Identities=16%  Similarity=-0.070  Sum_probs=28.9

Q ss_pred             EEeeCCCCcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659          103 HLVVSEGGPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       103 ~~v~~~~grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~  141 (279)
                      +.+..+.-.|.+||+. .|+  |=.+++..|..|.|+|||+
T Consensus         5 ~~i~~e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe   44 (73)
T COG2501           5 VLIKTEFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGE   44 (73)
T ss_pred             EEeccceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCe
Confidence            3344444589999975 564  4559999999999999997

>PRK01851 truB tRNA pseudouridine synthase B; Provisional

Probab=89.45  E-value=0.44  Score=45.82  Aligned_cols=44  Identities=27%  Similarity=0.312  Sum_probs=35.2

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      +-||+||||.||.+|.        +++.+.+.++....+| .--||-..||+|
T Consensus        16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH-~GTLDP~AtGvL   59 (303)
T PRK01851         16 DGVLLLDKPLGLSSND--------ALQRAKRLLRAKKAGH-TGTLDPLATGLL   59 (303)
T ss_pred             CeEEEEeCCCCCCHHH--------HHHHHHHHhCcccCCC-CCCCCCCCceEE
Confidence            4799999999998873        4566777777665444 889999999997

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=85.57  E-value=1.7  Score=38.88  Aligned_cols=32  Identities=16%  Similarity=0.124  Sum_probs=25.6

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+ .|--|+.+++.||..|.|.|||.
T Consensus       103 rRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~  135 (177)
T PRK04051        103 RRLQTIVYRKGLARTPKQARQFIVHGHIAVNGR  135 (177)
T ss_pred             hHHHHHHHHccCcCCHHHHHHHHHcCCEEECCE
Confidence            367777754 23469999999999999999976

>PF13275 S4_2: S4 domain; PDB: 1P9K_A

Probab=84.99  E-value=0.28  Score=37.11  Aligned_cols=31  Identities=16%  Similarity=-0.093  Sum_probs=23.7

Q ss_pred             CcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~  141 (279)
                      -+|+.||+. .++  |=..++.+|..|.|++||+
T Consensus         8 I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe   40 (65)
T PF13275_consen    8 ITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGE   40 (65)
T ss_dssp             --HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB
T ss_pred             EEHHHHHhH-cCCcccHHHHHHHHHcCceEECCE
Confidence            479999975 453  4448999999999999997

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=84.86  E-value=2.8  Score=32.81  Aligned_cols=67  Identities=22%  Similarity=0.307  Sum_probs=43.8

Q ss_pred             CccccccccCCCCCCCCceEEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCC
Q 023659           83 YPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTD  162 (279)
Q Consensus        83 ~~~~~~~~~~~~~~~~~rv~~~v~~~~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~  162 (279)
                      |++++..+|-.....+  + ..-..+..++.+.+ +.||+|...      -|.|.+||+                     
T Consensus         9 ~~~L~~flp~~~r~~~--~-~~~~~~~~tvkd~I-EsLGVP~tE------V~~i~vNG~---------------------   57 (81)
T PF14451_consen    9 YAELNDFLPPERRGGP--F-THPFDGGATVKDVI-ESLGVPHTE------VGLILVNGR---------------------   57 (81)
T ss_pred             chHHhhhcChhhcCCc--e-EEecCCCCcHHHHH-HHcCCChHH------eEEEEECCE---------------------
Confidence            6667777774222111  1 11223334788877 569999854      578999986                     


Q ss_pred             cccccccccccCcceeeccccccccCCCceecCCCEEEEEc
Q 023659          163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHV  203 (279)
Q Consensus       163 ~~~~~~r~~~~GK~v~~~q~~~rv~~~~~~Lk~GD~I~V~~  203 (279)
                                   .+          ..++.++.||.|.|+.
T Consensus        58 -------------~v----------~~~~~~~~Gd~v~V~P   75 (81)
T PF14451_consen   58 -------------PV----------DFDYRLKDGDRVAVYP   75 (81)
T ss_pred             -------------EC----------CCcccCCCCCEEEEEe
Confidence                         22          5578999999999984

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative

Probab=82.73  E-value=1.6  Score=42.17  Aligned_cols=44  Identities=25%  Similarity=0.280  Sum_probs=34.1

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      +.+|+||||.||.+|.        +++.+.+.++....+| .-=||-.-+|+|
T Consensus        34 ~G~l~i~KP~g~tS~~--------~v~~vr~~~~~kkvGH-~GTLDP~A~GvL   77 (322)
T TIGR00425        34 YGVVNLDKPSGPSSHE--------VVAWVRRILNVEKTGH-GGTLDPKVTGVL   77 (322)
T ss_pred             CCEEEEeCCCCCCHHH--------HHHHHHHHhcccccCC-CCCCCCCCceEE
Confidence            4799999999998873        4566777777655444 788999999987

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.

>PRK01777 hypothetical protein; Validated

Probab=82.30  E-value=2.3  Score=34.20  Aligned_cols=58  Identities=17%  Similarity=0.111  Sum_probs=39.7

Q ss_pred             EEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeecc
Q 023659          102 EHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ  181 (279)
Q Consensus       102 ~~~v~~~~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q  181 (279)
                      ..+-++++.++.+.|.. +|+...+-.--+..+.|-|||+                                  .+    
T Consensus        19 ~~l~vp~GtTv~dal~~-sgi~~~~pei~~~~~~vgI~Gk----------------------------------~v----   59 (95)
T PRK01777         19 QRLTLQEGATVEEAIRA-SGLLELRTDIDLAKNKVGIYSR----------------------------------PA----   59 (95)
T ss_pred             EEEEcCCCCcHHHHHHH-cCCCccCcccccccceEEEeCe----------------------------------EC----
Confidence            34445556689998864 7877763222235678888875                                  22    


Q ss_pred             ccccccCCCceecCCCEEEEEcC
Q 023659          182 KTFRITHVDQIVEAGTYLRVHVH  204 (279)
Q Consensus       182 ~~~rv~~~~~~Lk~GD~I~V~~~  204 (279)
                            ..++.|+.||.|+|+.+
T Consensus        60 ------~~d~~L~dGDRVeIyrP   76 (95)
T PRK01777         60 ------KLTDVLRDGDRVEIYRP   76 (95)
T ss_pred             ------CCCCcCCCCCEEEEecC
Confidence                  45789999999999854

---

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	279
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 = 46.0 bits (108), 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	279
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	99.9
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	99.86
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	99.85
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	99.79
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	99.58
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	99.56
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	99.53
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	99.53
2gml_A	237	Ribosomal large subunit pseudouridine synthase F;	98.93
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	98.38
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	98.0
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.58
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	97.2
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	97.03
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	96.71
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	96.57
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	96.17
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	96.0
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	95.29
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	94.2
2aus_C	334	Pseudouridine synthase; isomerase, structural prot	90.86
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	90.78
1k8w_A	327	TRNA pseudouridine synthase B; protein-RNA complex	90.32
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	89.44
2apo_A	357	Probable tRNA pseudouridine synthase B; protein-pr	88.37
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	86.69
3u28_A	400	H/ACA ribonucleoprotein complex subunit 4; pseudou	86.65

>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=99.90  E-value=7.6e-25  Score=203.88  Aligned_cols=124  Identities=13%  Similarity=0.075  Sum_probs=54.2

Q ss_pred             cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||+||++.+ .+||+.+++||+.|.|+|||+.                                           +.++
T Consensus        18 RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~-------------------------------------------v~~~   54 (325)
T 1v9f_A           18 RLDQALAEMFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------CDKP   54 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccCC
Confidence            8999999987 7999999999999999999861                                           1245


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhC---CCCCcccc
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALG---LTTPLRTT  266 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg---~~~~l~~V  266 (279)
                      +++|++||.|.|..++.+.....+.+++++|||||+++||||||+||+|||+.++..+|+.+.+..++.   ....+++|
T Consensus        55 ~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~v  134 (325)
T 1v9f_A           55 KEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIV  134 (325)
T ss_dssp             ---------------------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBC
T ss_pred             CCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceeee
Confidence            678999999999865432222334556789999999999999999999999988778899888754432   11236789


Q ss_pred             ccCCcCccccc
Q 023659          267 HQIDNCTEGWR  277 (279)
Q Consensus       267 HRLDrdTSGLL  277 (279)
                      ||||++|||||
T Consensus       135 hRLD~~TSGll  145 (325)
T 1v9f_A          135 HRLDKDTTGLM  145 (325)
T ss_dssp             CCCCTTCEEEE
T ss_pred             cCCCCCCeeEE
Confidence            99999999997

>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=99.86  E-value=1.4e-22  Score=180.11  Aligned_cols=108  Identities=13%  Similarity=0.098  Sum_probs=87.4

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      .|||+||++...+||+.++++|+.|.|++||+.                                  +         .++
T Consensus         4 ~RLd~~L~~~~~~SR~~~~~li~~G~V~VNG~~----------------------------------v---------~~~   40 (234)
T 1ksk_A            4 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEI----------------------------------V---------RNA   40 (234)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEE----------------------------------C---------CCT
T ss_pred             ccHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE----------------------------------e---------CCC
Confidence            389999998878999999999999999999861                                  1         135


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEe-cCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCcccccc
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAV-TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ  268 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYE-DedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHR  268 (279)
                      +++|++||.|.+..              ..|+|| |++++|||||+||+|||+.++ .+|+.+.+....+  ..+++|||
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            78899999988741              148999 999999999999999998764 7777765532211  13568999


Q ss_pred             CCcCccccc
Q 023659          269 IDNCTEGWR  277 (279)
Q Consensus       269 LDrdTSGLL  277 (279)
                      ||++|||||
T Consensus       104 LD~~TsGll  112 (234)
T 1ksk_A          104 LDIDTTGLV  112 (234)
T ss_dssp             CCTTCEEEE
T ss_pred             CCCCCeeEE
Confidence            999999997

>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=99.85  E-value=2.4e-22  Score=179.93  Aligned_cols=107  Identities=15%  Similarity=0.156  Sum_probs=85.3

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCCC
Q 023659          111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD  190 (279)
Q Consensus       111 rLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~~  190 (279)
                      |||+||++...+||+.+++||+.|.|+|||+.                                           +.+++
T Consensus         4 RLd~~L~~~~~~SR~~~~~lI~~G~V~VNG~~-------------------------------------------v~~~~   40 (243)
T 1vio_A            4 RLDKFIAENVGLTRSQATKAIRQSAVKINGEI-------------------------------------------VKSGS   40 (243)
T ss_dssp             EHHHHHHHHHTCCHHHHHHHHHTTCEEETTEE-------------------------------------------CCCTT
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHcCcEEECCEE-------------------------------------------eCCCC
Confidence            79999998878999999999999999999861                                           11356


Q ss_pred             ceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCc-EEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659          191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTES-HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (279)
Q Consensus       191 ~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDed-lLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL  269 (279)
                      ++|++||.|.+.  +            ..|+|||++ ++|||||+||+|||+.++ ..|+.+.+.....  ..+++||||
T Consensus        41 ~~v~~gD~I~v~--~------------~~i~~ed~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~~--~~~~~vhRL  103 (243)
T 1vio_A           41 VQISQEDEIYFE--D------------ELLTWIEEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYPLA--GKLHSAGRL  103 (243)
T ss_dssp             CEECTTSCEEET--T------------EECCSSCCCCEEEEEECTTCBSSCCC---CCBGGGGSCTTGG--GGCEESSCC
T ss_pred             CCcCCCCEEEEe--c------------cccccCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHHhHHhc--CCEeEccCC
Confidence            789999987763  1            248999999 999999999999998764 6677665532221  135689999


Q ss_pred             CcCccccc
Q 023659          270 DNCTEGWR  277 (279)
Q Consensus       270 DrdTSGLL  277 (279)
                      |+||||||
T Consensus       104 D~~TsGll  111 (243)
T 1vio_A          104 DVDTTGLV  111 (243)
T ss_dssp             CTTCEEEE
T ss_pred             CCCCeEEE
Confidence            99999997

>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=99.79  E-value=7.4e-20  Score=169.53  Aligned_cols=108  Identities=15%  Similarity=0.147  Sum_probs=85.9

Q ss_pred             CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      .|||.||++...+||+.+++||+.|.|+|||+.                                  +          ..
T Consensus         7 ~RLdk~La~~g~~SR~~a~~lI~~G~V~VNG~~----------------------------------v----------~~   42 (290)
T 3dh3_A            7 VRLNKYISESGICSRREADRYIEQGNVFLNGKR----------------------------------A----------TI   42 (290)
T ss_dssp             EEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEE----------------------------------C----------CT
T ss_pred             hHHHHHHHhCCCCCHHHHHHHHHCCCEEECCEE----------------------------------c----------cC
Confidence            389999998756899999999999999999861                                  1          44


Q ss_pred             CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659          190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI  269 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL  269 (279)
                      ++.|.+||.|.|...+.     .+      ..|||+++||||||+||++||+.++ ..|+.+.+..    ...+++||||
T Consensus        43 ~~~V~~gD~I~v~~~~i-----~~------~~~ed~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~----~~~~~~VhRL  106 (290)
T 3dh3_A           43 GDQVKPGDVVKVNGQLI-----EP------REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH----SKRVFPIGRL  106 (290)
T ss_dssp             TCEECTTCCEEETTEEE-----CC------CCGGGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTC----SSCCEESSCC
T ss_pred             CcCcCCCCEEEeccccc-----cc------cccccceEEEEECCCccccCCCCCC-CCcHHHHhhc----cCceeeeccC
Confidence            67899999999864211     01      1389999999999999999998754 6677776532    2346789999


Q ss_pred             CcCccccc
Q 023659          270 DNCTEGWR  277 (279)
Q Consensus       270 DrdTSGLL  277 (279)
                      |+||||||
T Consensus       107 D~dTSGLl  114 (290)
T 3dh3_A          107 DKDSQGLI  114 (290)
T ss_dssp             CTTCEEEE
T ss_pred             CCCCcceE
Confidence            99999997

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

Probab=99.58  E-value=1.6e-15  Score=133.75  Aligned_cols=57  Identities=21%  Similarity=0.212  Sum_probs=48.0

Q ss_pred             cceEEecCcEEEEeCCCCCcccCCCC-CCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       218 l~ILYEDedlLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++|||||+++||||||+||+|||+.+ ...+++.+.+.....   .+.+|||||++|||||
T Consensus        12 ~~ilyed~~~lvvnKP~G~~~~~~~~~~~~~tl~~~l~~~~~---~~~~vhRLD~~TSGll   69 (217)
T 2i82_A           12 LVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYP---QAESVHRLDMATSGVI   69 (217)
T ss_dssp             CCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCT---TCEESSCCCTTCEEEE
T ss_pred             ceEEEECCCEEEEECCCCCeEeCCCCCCchhHHHHHHHHHCC---CCceeecCCCCCeEEE
Confidence            68999999999999999999999765 456788887765432   2568999999999997

>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=99.56  E-value=2.5e-15  Score=133.36  Aligned_cols=58  Identities=24%  Similarity=0.250  Sum_probs=46.9

Q ss_pred             ceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       219 ~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      +|+|||+++||||||+||+|||+.+ ...++...+....+....+++|||||++|||||
T Consensus         3 ~Ilyed~~~lvvnKP~G~~~~~~~~-~~~~l~~~l~~~~~~~~~~~~VhRLD~~TSGll   60 (228)
T 1v9k_A            3 VIMYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPEARFLELVHRLDRDTSGVL   60 (228)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSS-SBCCHHHHHHHHSTTCSCCEESSCCCTTCEEEE
T ss_pred             CEEEECCCEEEEECCCCCeEecCCC-hHHHHHHHHHHHcCCCCccceEecCCCCCeEEE
Confidence            6999999999999999999999776 456677766554442234668999999999997

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

Probab=99.53  E-value=1.1e-15  Score=132.08  Aligned_cols=54  Identities=13%  Similarity=0.151  Sum_probs=42.9

Q ss_pred             ceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       219 ~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      .|||||+++||||||+||+|||+.++...|+.+.+.    .. .+++|||||++|||||
T Consensus         5 ~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~----~~-~~~~vhRLD~~TSGll   58 (189)
T 2oml_A            5 KPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP----VQ-GVYAAGRLDRDSEGLL   58 (189)
T ss_dssp             ---CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC----CS-SCEESSCCCTTCEEEE
T ss_pred             ccccCCCeEEEEECCCCCEecCCCCCCCCCHHHHcC----CC-CceECCCCCCCCeeEE
Confidence            699999999999999999999998776777765442    22 3578999999999997

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

Probab=99.53  E-value=1.4e-15  Score=134.85  Aligned_cols=56  Identities=13%  Similarity=0.146  Sum_probs=41.6

Q ss_pred             ccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       217 ~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      .++|||||+++||||||+||+|||+.+....|+.+.+.    .. .+++|||||++|||||
T Consensus        31 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~tl~~~l~----~~-~~~~VhRLDr~TSGll   86 (217)
T 2olw_A           31 RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP----VQ-GVYAAGRLDRDSEGLL   86 (217)
T ss_dssp             ------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCC----CC-SCEESSCCCTTCEEEE
T ss_pred             cCceEeeCCcEEEEECCCCCEeccCCCCCCccHHHHhC----cC-CceECCCCCCCCeeEE
Confidence            46899999999999999999999988766777665442    22 3578999999999997

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

Probab=98.93  E-value=3e-10  Score=102.82  Aligned_cols=49  Identities=14%  Similarity=0.230  Sum_probs=38.7

Q ss_pred             cCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       224 DedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ++++||+|||+|++||+... ...|+.+++.    ....+++|||||+||||||
T Consensus        13 ~~~~lvlnKPaG~vs~~~~~-~~~tv~dll~----~~~rl~~VgRLD~dTSGLL   61 (237)
T 2gml_A           13 DLVLIALNKPVGIVSTTEDG-ERDNIVDFVN----HSKRVFPIGRLDKDSQGLI   61 (237)
T ss_dssp             CCCEEEEEECTTCBCCSSSS-CSSBHHHHSC----CSSCCEEESCCCTTCEEEE
T ss_pred             CCEEEEEECCCCCEeCCCCC-CCCCHHHHhh----ccCCeeEecCCCCCCeeEE
Confidence            56899999999999999765 4667766542    1224678999999999997

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

Probab=98.38  E-value=3e-08  Score=76.21  Aligned_cols=73  Identities=12%  Similarity=0.156  Sum_probs=52.9

Q ss_pred             cHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||.||++... .||+.+++||..|.|+|||+.                                  +          ++
T Consensus         2 RLD~~L~~~~~~~sR~~~~~li~~G~V~VNg~~----------------------------------~----------~~   37 (92)
T 2k6p_A            2 RIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSC----------------------------------A----------KA   37 (92)
T ss_dssp             BHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEE----------------------------------C----------CT
T ss_pred             hHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEE----------------------------------c----------CC
Confidence            79999987533 599999999999999999861                                  1          44


Q ss_pred             CceecCCCEEEEEcCCCCCC----C----CCCCCCccceEEecCcE
Q 023659          190 DQIVEAGTYLRVHVHPKRFP----R----CYDIDWNSRIIAVTESH  227 (279)
Q Consensus       190 ~~~Lk~GD~I~V~~~~~~~~----~----~~~~~~~l~ILYEDedl  227 (279)
                      ++.|++||.|.|.++++...    .    ..+..-.++|+|||+++
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            67899999999987543211    0    01122347899999875

>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=98.00  E-value=3.5e-06  Score=69.69  Aligned_cols=52  Identities=15%  Similarity=0.135  Sum_probs=43.5

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      .+||.||... +..||+.+++||..|.|.|||..                                  +          +
T Consensus         9 ~RLDk~L~~~~~~~SRs~a~~li~~G~V~VNG~~----------------------------------v----------k   44 (133)
T 1dm9_A            9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR----------------------------------S----------K   44 (133)
T ss_dssp             CBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEE----------------------------------C----------C
T ss_pred             hhHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEE----------------------------------c----------C
Confidence            4899999986 45799999999999999999861                                  1          4


Q ss_pred             CCceecCCCEEEEEcCC
Q 023659          189 VDQIVEAGTYLRVHVHP  205 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~~~~  205 (279)
                      +++.|++||.|.|.+++
T Consensus        45 ~s~~V~~GD~I~I~~~~   61 (133)
T 1dm9_A           45 PSKIVELNATLTLRQGN   61 (133)
T ss_dssp             TTCBCCTTCEEEEEETT
T ss_pred             CCCEeCCCCEEEEEeCC
Confidence            56789999999998754

>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=97.58  E-value=1.9e-05  Score=59.12  Aligned_cols=31  Identities=13%  Similarity=-0.091  Sum_probs=27.9

Q ss_pred             CcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||+||++. ++  ||+.+++||+.|.|+|||+
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            4899999975 64  9999999999999999986

>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=97.20  E-value=0.00058  Score=57.88  Aligned_cols=32  Identities=9%  Similarity=-0.004  Sum_probs=28.4

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+.. +.||..+++||..|.|.|||+
T Consensus        51 ~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VNG~   83 (159)
T 1c05_A           51 SRLDNLVYRLGLARTRRQARQLVTHGHILVDGS   83 (159)
T ss_dssp             HBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTE
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHHCCCEEECCE
Confidence            37999998753 689999999999999999986

>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=97.03  E-value=0.00094  Score=59.10  Aligned_cols=32  Identities=9%  Similarity=0.075  Sum_probs=28.5

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+. ++.||..+++||..|.|.|||+
T Consensus        99 ~RLD~~L~~~g~~~SR~~arqLI~~G~V~VNG~  131 (209)
T 2vqe_D           99 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGR  131 (209)
T ss_dssp             TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTE
T ss_pred             HHHHHHHHHhcCcCCHHHHHHHHHCCCEEECCE
Confidence            4899999865 4689999999999999999986

>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=96.71  E-value=0.0019  Score=59.62  Aligned_cols=30  Identities=13%  Similarity=-0.050  Sum_probs=27.6

Q ss_pred             cHHHHHHHh-cCCCHHHHHHHHHcCcEEEcc
Q 023659          111 PVLEYICRE-LNLPPLFVADLIHFGAVYYAL  140 (279)
Q Consensus       111 rLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~  140 (279)
                      |||.||.+. +..||+++++||..|.|+|||
T Consensus         8 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng   38 (291)
T 3hp7_A            8 RVDVLAYKQGLFETREQAKRGVMAGLVVNVI   38 (291)
T ss_dssp             EHHHHHHHTTSSSSHHHHHHHHHTTCEEETT
T ss_pred             hHHHHHHHcCCcccHHHHHHHHHCCeEEECC
Confidence            899999875 467999999999999999998

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

Probab=96.17  E-value=0.0048  Score=45.73  Aligned_cols=32  Identities=6%  Similarity=-0.095  Sum_probs=27.4

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+.- .-||..+++||..|.|.|||+
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            38999998633 359999999999999999986

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

Probab=96.00  E-value=0.0022  Score=56.71  Aligned_cols=32  Identities=6%  Similarity=-0.178  Sum_probs=26.9

Q ss_pred             CcHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.+.. ..||..+++||..|.|.|||.
T Consensus        89 ~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VNG~  121 (201)
T 3bbn_D           89 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGR  121 (201)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTE
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHhCCcEEeCCE
Confidence            37888886532 479999999999999999986

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

Probab=95.29  E-value=0.014  Score=50.90  Aligned_cols=32  Identities=13%  Similarity=0.019  Sum_probs=27.1

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      -|||.+|.+ .|.-||..+++||..|.|.|||.
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            479999854 44569999999999999999986

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

Probab=94.20  E-value=0.015  Score=50.53  Aligned_cols=32  Identities=9%  Similarity=-0.054  Sum_probs=27.6

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      -|||.+|.. .+..||..++.||..|.|.|||.
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            489999965 34569999999999999999986

>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=90.86  E-value=0.13  Score=48.42  Aligned_cols=47  Identities=21%  Similarity=0.295  Sum_probs=37.2

Q ss_pred             EecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       222 YEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      |-.+.+|+||||.||.+|        .+++.+.+.++... +....-||-..||+|
T Consensus        43 ~~~~Gil~vdKP~g~tS~--------~vv~~vr~~~~~~K-vGH~GTLDP~atGvL   89 (334)
T 2aus_C           43 HIQYGVINLDKPPGPTSH--------EVVAWIKRILNLEK-AGHGGTLDPKVSGVL   89 (334)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHTTCSC-EEESSCCCTTCEEEE
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhCcce-eccccccCCccceeE
Confidence            446789999999999887        35566777777654 344999999999997

>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=90.78  E-value=0.085  Score=46.54  Aligned_cols=31  Identities=10%  Similarity=-0.026  Sum_probs=26.6

Q ss_pred             CcHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|||.+|.. ++  -|+..+++||..|.|.|||+
T Consensus       107 ~RLD~~L~r-~G~a~Sr~~ArqLI~~GhV~VNG~  139 (197)
T 3u5c_J          107 RRLQTQVYK-LGLAKSVHHARVLITQRHIAVGKQ  139 (197)
T ss_dssp             TSHHHHHHH-SSTTSSHHHHHHHHHTSCCBSSSC
T ss_pred             HHHHHHHHH-ccccCCHHHHHHHHHcCCEEECCE
Confidence            479988875 44  49999999999999999986

>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=90.32  E-value=0.15  Score=48.00  Aligned_cols=44  Identities=23%  Similarity=0.284  Sum_probs=35.0

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      +-||+||||+||.+|        .+++.+.+.++... +.....||-..||+|
T Consensus        25 ~Gil~vdKP~G~TS~--------dvv~~vr~~l~~kK-vGH~GTLDP~AtGvL   68 (327)
T 1k8w_A           25 NGVLLLDKPQGMSSN--------DALQKVKRIYNANR-AGHTGALDPLATGML   68 (327)
T ss_dssp             CEEEEEEECTTCCHH--------HHHHHHHHHTTCSC-EEESSCCCTTCEEEE
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHhhccce-eccCCCCCCCCeeEE
Confidence            469999999999887        35567777777654 444999999999997

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

Probab=89.44  E-value=0.64  Score=42.20  Aligned_cols=31  Identities=13%  Similarity=0.066  Sum_probs=28.7

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~  141 (279)
                      +|.-||.++|+  .++..+++++..|.|.|||+
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            79999999997  68899999999999999986

>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=88.37  E-value=0.25  Score=46.95  Aligned_cols=47  Identities=23%  Similarity=0.324  Sum_probs=37.2

Q ss_pred             EecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       222 YEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      |-.+.+|+||||+||.+|        .+++.+.+.++... +....-||-..||+|
T Consensus        63 ~~~~Gil~vdKP~G~TS~--------~vv~~vr~~l~~~K-vGH~GTLDP~AtGvL  109 (357)
T 2apo_A           63 LIKYGVVVVDKPRGPTSH--------EVSTWVKKILNLDK-AGHGGTLDPKVTGVL  109 (357)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHTTCSC-EEESSCCCTTCEEEE
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhCccc-cccccccCCCceeEE
Confidence            456789999999999887        35567777777654 344999999999997

>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=86.69  E-value=0.99  Score=40.23  Aligned_cols=31  Identities=19%  Similarity=0.012  Sum_probs=28.1

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~  141 (279)
                      +|.-||.++|+  .++..+++++..|.|.|||+
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            68999999886  67889999999999999986

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

Probab=86.65  E-value=0.25  Score=47.73  Aligned_cols=47  Identities=19%  Similarity=0.247  Sum_probs=37.7

Q ss_pred             EecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          222 AVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       222 YEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      |-.+.+|+||||.||.+|        .+++.+.+.++....+ ...-||-..||||
T Consensus        56 ~~~~Gil~ldKP~G~TS~--------dvv~~vrr~l~~kKvG-H~GTLDP~AtGvL  102 (400)
T 3u28_A           56 YISSGVINLDKPSNPSSH--------EVVAWIKRILRCEKTG-HSGTLDPKVTGCL  102 (400)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHHTCSCEE-ESSCCCTTCEEEE
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhCcCccc-ccCCCCCCCeEEE
Confidence            556889999999999888        3556777777766544 4999999999997

---

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	279
d1v9fa_	250	Ribosomal large subunit pseudouridine synthase D,	99.72
d1v9ka_	227	Ribosomal large subunit pseudouridine synthase C,	99.65
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.25
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.24
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	97.47
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	96.94
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	96.21
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	96.2
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	95.54
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	93.84
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	89.56
d2ey4a2	245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	87.67
d2apoa2	230	Pseudouridine synthase II TruB {Archaeon Methanoco	86.75

>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=99.72  E-value=1.3e-18  Score=154.86  Aligned_cols=65  Identities=17%  Similarity=0.153  Sum_probs=54.3

Q ss_pred             CCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC---CCCccccccCCcCccccc
Q 023659          213 DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       213 ~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~~l~~VHRLDrdTSGLL  277 (279)
                      |.+++++|||||++|||||||+||+|||+.++..+|+.+.+..++..   ...+++||||||+|||||
T Consensus         3 P~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~~~~~~~vHRLDr~TSGll   70 (250)
T d1v9fa_           3 PQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLM   70 (250)
T ss_dssp             CCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEE
T ss_pred             CCCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhccCCCceeEEeecCCCCcceE
Confidence            45667899999999999999999999999988888998877655421   123567999999999997

>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=99.65  E-value=4.4e-17  Score=142.13  Aligned_cols=58  Identities=24%  Similarity=0.198  Sum_probs=46.0

Q ss_pred             ceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          219 RIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       219 ~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      .||||||+|||||||+||+|||+.++..+ +.+.+....+....+++||||||+|||||
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~~-~~~~l~~~~~~~~~~~~vHRLD~~TSGll   59 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRPEARFLELVHRLDRDTSGVL   59 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBCC-HHHHHHHHSTTCSCCEESSCCCTTCEEEE
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcch-HHHHHHHhCCCCcccceeeeccceeeeee
Confidence            49999999999999999999998766554 44545444443344678999999999997

>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=98.25  E-value=8.2e-07  Score=61.94  Aligned_cols=31  Identities=16%  Similarity=0.094  Sum_probs=29.6

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      |||.||++...+||+.+++||+.|.|+|||+
T Consensus         3 RLD~~Ls~~~~~SR~~a~~lI~~g~V~Vng~   33 (58)
T d1vioa2           3 RLDKFIAENVGLTRSQATKAIRQSAVKINGE   33 (58)
T ss_dssp             EHHHHHHHHHTCCHHHHHHHHHTTCEEETTE
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHcCeEEECCE
Confidence            7999999988999999999999999999986

>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=98.24  E-value=8.6e-07  Score=61.95  Aligned_cols=31  Identities=13%  Similarity=0.076  Sum_probs=29.7

Q ss_pred             cHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRELNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      |||.||++...+||+.+++||..|.|.|||+
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            6999999999999999999999999999986

>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=97.47  E-value=9.8e-05  Score=57.11  Aligned_cols=52  Identities=15%  Similarity=0.137  Sum_probs=42.4

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      -|||.||.. .+--||+.++++|..|.|.|||+.                                  +          +
T Consensus         5 mRlD~~L~~~r~~ktR~~A~~~i~~G~V~vNg~~----------------------------------v----------K   40 (104)
T d1dm9a_           5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR----------------------------------S----------K   40 (104)
T ss_dssp             CBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEE----------------------------------C----------C
T ss_pred             EeHHHHHHHhhhHhhHHHHHHHHHcCCeeeCCee----------------------------------c----------c
Confidence            489999964 344599999999999999999861                                  1          5


Q ss_pred             CCceecCCCEEEEEcCC
Q 023659          189 VDQIVEAGTYLRVHVHP  205 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~~~~  205 (279)
                      +++.|++||.|.|....
T Consensus        41 ps~~vk~GDvI~i~~~~   57 (104)
T d1dm9a_          41 PSKIVELNATLTLRQGN   57 (104)
T ss_dssp             TTCBCCTTCEEEEEETT
T ss_pred             ccccCCCCCEEEEEeCC
Confidence            57889999999997643

>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=96.94  E-value=8.9e-05  Score=54.55  Aligned_cols=32  Identities=13%  Similarity=-0.112  Sum_probs=27.9

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      -||++||+.. +--||..+++||..|.|.|||+
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            3899999875 2349999999999999999987

>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=96.21  E-value=0.0036  Score=51.48  Aligned_cols=49  Identities=14%  Similarity=0.145  Sum_probs=40.7

Q ss_pred             cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659          111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV  189 (279)
Q Consensus       111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~  189 (279)
                      |||..+.+ .|..|+..+++||..|.|.|||+                                  .         +..+
T Consensus        52 RlD~vv~r~gfa~t~~~arQ~v~Hghi~vNgk----------------------------------~---------v~iP   88 (159)
T d1c06a_          52 RLDNLVYRLGLARTRRQARQLVTHGHILVDGS----------------------------------R---------VNIP   88 (159)
T ss_dssp             CHHHHHHHHTSSSSHHHHHHHHHTSCEEETTE----------------------------------E---------CCCS
T ss_pred             HhhhhhccCcccCCHHHHHHHHHhcceEccce----------------------------------E---------EEec
Confidence            78887764 33479999999999999999986                                  1         3467


Q ss_pred             CceecCCCEEEEE
Q 023659          190 DQIVEAGTYLRVH  202 (279)
Q Consensus       190 ~~~Lk~GD~I~V~  202 (279)
                      ++.|++||.|.+.
T Consensus        89 Sy~vk~GDvIsvk  101 (159)
T d1c06a_          89 SYRVKPGQTIAVR  101 (159)
T ss_dssp             SCCCCSSCEEEEC
T ss_pred             ceeecCCcEEeec
Confidence            9999999999996

>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=96.20  E-value=0.0035  Score=53.49  Aligned_cols=50  Identities=10%  Similarity=0.106  Sum_probs=41.7

Q ss_pred             CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659          110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH  188 (279)
Q Consensus       110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~  188 (279)
                      .|||..|.. .|.-|+.++++||..|.|.|||+                                  .         +..
T Consensus        94 ~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk----------------------------------~---------VnI  130 (204)
T d2gy9d1          94 GRLDNVVYRMGFGATRAEARQLVSHKAIMVNGR----------------------------------V---------VNI  130 (204)
T ss_dssp             TBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSS----------------------------------B---------CCC
T ss_pred             HHHHHHHhhccccccHHHHHHHHHhcceecCCE----------------------------------E---------EEe
Confidence            489998865 23479999999999999999986                                  1         346


Q ss_pred             CCceecCCCEEEEE
Q 023659          189 VDQIVEAGTYLRVH  202 (279)
Q Consensus       189 ~~~~Lk~GD~I~V~  202 (279)
                      +++.|++||+|.|.
T Consensus       131 PSy~vk~GDvIsvk  144 (204)
T d2gy9d1         131 ASYQVSPNDVVSIR  144 (204)
T ss_dssp             TTCBCCTTCBEEEC
T ss_pred             ccEeecCCCEEEec
Confidence            78999999999997

>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=95.54  E-value=0.0086  Score=51.17  Aligned_cols=50  Identities=14%  Similarity=0.129  Sum_probs=41.4

Q ss_pred             CcHHHHHHHhcC--CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeecccccccc
Q 023659          110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT  187 (279)
Q Consensus       110 grLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~  187 (279)
                      .|||..|.. +|  -|+..+++||..|.|.|||+                                  .         +.
T Consensus        98 ~Rld~vv~r-~g~a~t~~~ARQ~v~Hg~i~vNg~----------------------------------~---------v~  133 (208)
T d2uubd1          98 SRLDNVVYR-LGFAVSRRQARQLVRHGHITVNGR----------------------------------R---------VD  133 (208)
T ss_dssp             TBHHHHHHH-TTSSSSHHHHHHHHHTTCEEETTE----------------------------------E---------CC
T ss_pred             HHHHHHHHh-ccccccHHHHHHHHHhcCeecCCe----------------------------------E---------EE
Confidence            378888864 44  69999999999999999986                                  1         34


Q ss_pred             CCCceecCCCEEEEEc
Q 023659          188 HVDQIVEAGTYLRVHV  203 (279)
Q Consensus       188 ~~~~~Lk~GD~I~V~~  203 (279)
                      .+++.|++||+|.|.-
T Consensus       134 ips~~~~~gd~I~vre  149 (208)
T d2uubd1         134 LPSYRVRPGDEIAVAE  149 (208)
T ss_dssp             CTTCBCCTTCEEEECG
T ss_pred             eccEEecCCceeehhh
Confidence            6789999999999974

>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=93.84  E-value=0.06  Score=38.73  Aligned_cols=30  Identities=10%  Similarity=-0.159  Sum_probs=26.2

Q ss_pred             cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659          111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~  141 (279)
                      .|.++|.+ .+  -|++.+++||..|+|+||++
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            68888875 55  49999999999999999986

>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=89.56  E-value=0.47  Score=34.87  Aligned_cols=32  Identities=19%  Similarity=0.241  Sum_probs=26.3

Q ss_pred             CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659          110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV  141 (279)
Q Consensus       110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~  141 (279)
                      -.|.++|.+. +--|++.+++||+.|+|+||++
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            3688888653 3359999999999999999986

>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=87.67  E-value=0.15  Score=44.19  Aligned_cols=44  Identities=20%  Similarity=0.266  Sum_probs=36.0

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ..||+||||.|+.+|        .+++.+.+.++....+| ..-||=.-||+|
T Consensus        42 ~G~l~idKP~G~TS~--------~vv~~vkk~l~~kKvGH-~GTLDP~AtGvL   85 (245)
T d2ey4a2          42 FGVINLDKPPGPTSH--------EVVAWIKKILNLEKAGH-GGTLDPKVSGVL   85 (245)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTTCSCEEE-SSCCCTTCEEEE
T ss_pred             CcEEEEeCCCCCCHH--------HHHHHHHHHhCcCCCCc-CccCCCcceeeE
Confidence            479999999999877        45677777788766444 999999999987

>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=86.75  E-value=0.18  Score=43.15  Aligned_cols=44  Identities=25%  Similarity=0.323  Sum_probs=35.7

Q ss_pred             CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659          225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR  277 (279)
Q Consensus       225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL  277 (279)
                      ..||+||||.|+.+|        .+++.+.+.++....+| ..-||-.-||||
T Consensus        29 ~G~l~idKP~G~TS~--------~vv~~ikk~l~~kKvGH-~GTLDP~AtGvL   72 (230)
T d2apoa2          29 YGVVVVDKPRGPTSH--------EVSTWVKKILNLDKAGH-GGTLDPKVTGVL   72 (230)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTTCSCEEE-SSCCCTTCEEEE
T ss_pred             CcEEEEECCCCCCHH--------HHHHHHHHHcCCCCCCc-ccccCccceeee
Confidence            479999999999877        35667777888765444 999999999987