254780608

254780608

ribosomal large subunit pseudouridine synthase C

GeneID in NCBI database:8209607Locus tag:CLIBASIA_02475
Protein GI in NCBI database:254780608Protein Accession:YP_003065021.1
Gene range:+(667861, 668901)Protein Length:346aa
Gene description:ribosomal large subunit pseudouridine synthase C
COG prediction:[J] Pseudouridylate synthases, 23S RNA-specific
KEGG prediction:rluC; ribosomal large subunit pseudouridine synthase C; K06179 ribosomal large subunit pseudouridine synthase C [EC:5.4.99.12]
SEED prediction:Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70), LSU Psi955, Psi2504 and Psi2580
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Ribosome biogenesis bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340------
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
ccccccEEEEEEccccccccHHHHHHHHcccccHHHHHHHHHcccEEEccEEEccccccccccEEEEcccccccccccccccccccccccccccccccEEEEEccccEEEEEccccEEEcccccccccHHHHHHHHHHccccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHccccEEEEEEEEccccccccEEEccHHccccccccEEEEEEEccccccccccEEEEEEEccccEEEEEEEEcccccHHHHHHHHHHcccEEccccccccccccccccccccHHHHHHHcEEEcccccEEEEEccccHHHHHHHHHHcccccHHHHHHHHHcHHHHHHHcc
ccccccEEEEEEccHHcccHHHHHHHHHcccccHHHHHHHHHcccEEEcccEEccccEEccccEEEEccccccHHccccccccccccHHHcccHHHHcccEEEEcccEEEEEccccEEEEccccccHHHHHHHHHHcccccccccEEEEEccccccEEEEEccHHHHHHHHHHHHHccccEEEEEEEEcccccccccEcccccccccccccEEEEEEEEcccccccEEHEEHHHHccccEEEEEEEcccccccEEEEEHHHccccccccccccccccccccccccccHHHHHHHEccccccccEEEEEccccHHHHHHHHHHcccHHHHHHHHHHHcHHHHHHHcc
MSLMTYVQYVVVendeenmrldrwfknhyphinfVNLQKILRSgqvrvdkkrvkfnnriqsgqvvrippviNALNHIIKEQKIldssvnltkhsDFLKSILLYedskiyvfnkpagisvqggsgiaYHIDGFLKSwvdskgqkprlthrldqetsGILVVARTRAAAQHLTESFRMRRIQKIYWSLvwgipknkkECIANWLlkkshiggdYVHVVKQNEKGANYAISHFKVIDCFAQKFCwlemqphtgrthQLRVHALhmgcpivgdhkycanfkgnftspiqNKLYLHARymdlphpeggrlqitaplpahmVKTWdslgfkydrnLYIKRlysqdeckqnil
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKrvkfnnriqsgqvvrippvINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRlthrldqetsgilvVARTRAAAqhltesfrmrrIQKIYWSlvwgipknKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRlysqdeckqnil
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
****TYV*YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA*******************HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD**********GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR*****************L
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ********
****TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target346 ribosomal large subunit pseudouridine synthase C [Candi
254780610340 RNA-pseudouridylate synthase protein, ribosomal la 4e-27
>gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus str. psy62] Length = 340 Back     alignment
 Score =  113 bits (283), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 81/252 (32%), Positives = 121/252 (48%), Gaps = 30/252 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  I V NKPAG+ V    G         + YH    L S    K  +P + HRLD
Sbjct: 92  ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVK--RPGIVHRLD 149

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++T+G++VVA+   A Q L+E F    +  R+++ Y+++VWGIP      I N  L +  
Sbjct: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPL-PDSGIINAPLGRCK 208

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMG 263
                  V   ++K A+ AI+H++ I+ + +        L+    TGRTHQ+RVH  H G
Sbjct: 209 SNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKG 268

Query: 264 CPIVGDHKYCANFK-------GNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPA 313
            P++GD  Y   FK        N  S I +  +  LHA  +   HP   + +    P+P 
Sbjct: 269 NPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPE 328

Query: 314 HMVKTWDSLGFK 325
            M+     L  K
Sbjct: 329 DMLTVIRKLNEK 340

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target346 ribosomal large subunit pseudouridine synthase C [Candi
315121808336 ribosomal large subunit pseudouridine synthase C [Candi 1 1e-148
325292801329 ribosomal large subunit pseudouridine synthase C [Agrob 1 1e-103
159184771329 ribosomal large subunit pseudouridine synthase C [Agrob 1 1e-102
222086089332 pseudouridylate synthase [Agrobacterium radiobacter K84 1 1e-101
190891935330 RNA-pseudouridine synthase, ribosomal large subunit C [ 1 4e-99
241204807330 pseudouridine synthase, RluA family [Rhizobium legumino 1 3e-98
327191042330 RNA-pseudouridine synthase protein, ribosomal large sub 1 4e-98
116252313330 ribosomal large subunit pseudouridine synthase C [Rhizo 1 4e-98
227821788330 ribosomal large subunit pseudouridine synthase C [Sinor 1 5e-98
15965142330 ribosomal large subunit pseudouridine synthase C protei 1 9e-98
>gi|315121808|ref|YP_004062297.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 336 Back     alignment and organism information
 Score =  530 bits (1366), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 252/336 (75%), Positives = 292/336 (86%), Gaps = 1/336 (0%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  MT V+++++END ENMR DRWFK HYPHINF NLQK+LRSGQ+R+DK+RVK N+R+Q
Sbjct: 1   MLFMTCVKHIIIENDVENMRFDRWFKLHYPHINFGNLQKLLRSGQIRLDKRRVKSNDRVQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQVVRIPP+I+ L+H  +++  LDSSV+  K+S FLK+ILLYED+K+Y+FNKP GISVQ
Sbjct: 61  SGQVVRIPPIIDVLDHATEKRYSLDSSVDFLKNSAFLKNILLYEDNKLYIFNKPPGISVQ 120

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+ YHIDGFLKSW DSKGQKPRL HRLD+ETSGILVVARTRAAAQ LTESFRMRRI+
Sbjct: 121 GGSGVTYHIDGFLKSWSDSKGQKPRLIHRLDRETSGILVVARTRAAAQSLTESFRMRRIR 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYWSLV G+P+NKKECI+ WL KK+ IGGDYV VV QNEKGA+YAISHFKVID F  KF
Sbjct: 181 KIYWSLVRGVPQNKKECISGWLFKKAKIGGDYVQVVDQNEKGAHYAISHFKVIDRFEYKF 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
           CWLEMQP+TGRTHQLRVHALH+G PIVGD KY  N  K  F++ IQNKLYLHARY+D PH
Sbjct: 241 CWLEMQPYTGRTHQLRVHALHVGHPIVGDKKYRINDSKEIFSNHIQNKLYLHARYIDFPH 300

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           PEGGRLQITAPLP HM KTWDS GFKY++++ IKRL
Sbjct: 301 PEGGRLQITAPLPVHMAKTWDSFGFKYNQDIDIKRL 336


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325292801|ref|YP_004278665.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium sp. H13-3] Length = 329 Back     alignment and organism information
>gi|159184771|ref|NP_354476.2| ribosomal large subunit pseudouridine synthase C [Agrobacterium tumefaciens str. C58] Length = 329 Back     alignment and organism information
>gi|222086089|ref|YP_002544621.1| pseudouridylate synthase [Agrobacterium radiobacter K84] Length = 332 Back     alignment and organism information
>gi|190891935|ref|YP_001978477.1| RNA-pseudouridine synthase, ribosomal large subunit C [Rhizobium etli CIAT 652] Length = 330 Back     alignment and organism information
>gi|241204807|ref|YP_002975903.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 330 Back     alignment and organism information
>gi|327191042|gb|EGE58095.1| RNA-pseudouridine synthase protein, ribosomal large subunit C [Rhizobium etli CNPAF512] Length = 330 Back     alignment and organism information
>gi|116252313|ref|YP_768151.1| ribosomal large subunit pseudouridine synthase C [Rhizobium leguminosarum bv. viciae 3841] Length = 330 Back     alignment and organism information
>gi|227821788|ref|YP_002825758.1| ribosomal large subunit pseudouridine synthase C [Sinorhizobium fredii NGR234] Length = 330 Back     alignment and organism information
>gi|15965142|ref|NP_385495.1| ribosomal large subunit pseudouridine synthase C protein [Sinorhizobium meliloti 1021] Length = 330 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target346 ribosomal large subunit pseudouridine synthase C [Candi
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C 1e-44
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, RluA fa 2e-43
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA-speci 1e-59
cd02869185 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/R 9e-42
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomera 5e-24
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthas 7e-22
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; Prov 1e-21
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Prov 9e-20
cd02557213 cd02557, PseudoU_synth_ScRIB2, PseudoU_synth_ScRIB2_lik 1e-18
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu family 2e-18
cd02558246 cd02558, PSRA_1, PSRA_1: Pseudouridine synthase, a subg 3e-14
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_ 2e-13
cd02870146 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthas 0.004
pfam00849151 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthas 1e-26
KOG1919371 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthase 1e-26
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|30910 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|30029 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>gnl|CDD|30016 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>gnl|CDD|73313 cd02557, PseudoU_synth_ScRIB2, PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|30015 cd02558, PSRA_1, PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|30008 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>gnl|CDD|30030 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>gnl|CDD|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase Back     alignment and domain information
>gnl|CDD|37130 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 346 ribosomal large subunit pseudouridine synthase C [Candi
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisional 100.0
TIGR00005337 rluA_subfam pseudouridine synthase, RluA family; InterP 100.0
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [Trans 100.0
KOG1919371 consensus 100.0
PRK11112257 tRNA pseudouridine synthase C; Provisional 100.0
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisional 100.0
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseu 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudou 100.0
TIGR01621222 RluA-like pseudouridine synthase Rlu family protein, TI 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of th 100.0
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseud 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseud 100.0
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine sy 99.79
TIGR00093185 TIGR00093 conserved hypothetical protein; InterPro: IPR 99.6
pfam00849151 PseudoU_synth_2 RNA pseudouridylate synthase. Members o 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases are res 99.97
PRK11394207 23S rRNA pseudouridine synthase E; Provisional 99.62
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine sy 99.61
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine sy 99.59
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of th 99.53
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridi 99.47
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthases ca 96.41
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase and 99.93
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 99.93
PRK10700291 23S rRNA pseudouridylate synthase B; Provisional 99.91
PRK10839231 16S rRNA pseudouridylate synthase A; Provisional 99.91
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The doma 98.99
smart0036360 S4 S4 RNA-binding domain. 98.5
pfam0147948 S4 S4 domain. The S4 domain is a small domain consistin 98.41
COG1188100 Ribosome-associated heat shock protein implicated in th 98.28
PRK10348133 ribosome-associated heat shock protein Hsp15; Provision 98.27
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members of t 98.14
COG2302257 Uncharacterized conserved protein, contains S4-like dom 97.94
TIGR01017217 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Rib 97.81
PRK12565197 30S ribosomal protein S4; Provisional 97.64
CHL00113201 rps4 ribosomal protein S4; Reviewed 97.56
COG1189245 Predicted rRNA methylase [Translation, ribosomal struct 97.46
COG0522205 RpsD Ribosomal protein S4 and related proteins [Transla 97.43
PRK05327201 rpsD 30S ribosomal protein S4; Validated 97.28
TIGR00478240 tly hemolysin A; InterPro: IPR004538 Hemolysins are exo 97.15
TIGR0298860 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014 95.33
COG250173 S4-like RNA binding protein [Replication, recombination 94.53
PRK04313237 30S ribosomal protein S4e; Validated 93.32
PRK1150770 hypothetical protein; Provisional 93.16
TIGR0168793 moaD_arch MoaD family protein; InterPro: IPR010038 Memb 93.08
PTZ00223273 40S ribosomal protein S4; Provisional 92.5
PTZ00118262 40S ribosomal protein S4; Provisional 92.29
pfam06353142 DUF1062 Protein of unknown function (DUF1062). This fam 91.94
PRK04051177 rps4p 30S ribosomal protein S4; Validated 91.26
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: P 96.8
PRK00989235 truB tRNA pseudouridine synthase B; Provisional 96.43
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridi 96.42
PRK01851310 truB tRNA pseudouridine synthase B; Provisional 96.2
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 96.13
PRK02484293 truB tRNA pseudouridine synthase B; Provisional 96.05
PRK00130289 truB tRNA pseudouridine synthase B; Provisional 95.99
PRK04099272 truB tRNA pseudouridine synthase B; Provisional 95.99
PRK02755291 truB tRNA pseudouridine synthase B; Provisional 95.89
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 95.77
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 95.72
PRK01550307 truB tRNA pseudouridine synthase B; Provisional 95.64
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: P 95.53
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 95.52
PRK01528293 truB tRNA pseudouridine synthase B; Provisional 95.45
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 95.41
COG0130271 TruB Pseudouridine synthase [Translation, ribosomal str 95.34
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridin 95.31
PRK05033314 truB tRNA pseudouridine synthase B; Provisional 95.3
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewed 95.26
TIGR00431236 TruB tRNA pseudouridine synthase B; InterPro: IPR014780 93.75
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridin 94.3
KOG2559318 consensus 92.65
COG4332203 Uncharacterized protein conserved in bacteria [Function 93.53
PRK13354 405 tyrosyl-tRNA synthetase; Provisional 92.36
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1919 consensus Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621; InterPro: IPR006508 These sequences represent a clade within the pseudouridine synthase superfamily Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>TIGR00093 TIGR00093 conserved hypothetical protein; InterPro: IPR000748 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase Back     alignment and domain information
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>pfam01479 S4 S4 domain Back     alignment and domain information
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK12565 30S ribosomal protein S4; Provisional Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PRK11507 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038 Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>pfam06353 DUF1062 Protein of unknown function (DUF1062) Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4; Validated Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine synthase B; InterPro: IPR014780 TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs of all three domains of life Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>KOG2559 consensus Back     alignment and domain information
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target346 ribosomal large subunit pseudouridine synthase C [Candi
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 5e-44
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 2e-41
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 2e-18
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 3e-18
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 4e-15
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 7e-13
1i94_D208 Crystal Structures Of The Small Ribosomal Subunit W 1e-06
1fjg_D209 Structure Of The Thermus Thermophilus 30s Ribosomal 2e-06
1fka_D209 Structure Of Functionally Activated Small Ribosomal 2e-06
3dh3_A290 Crystal Structure Of Rluf In Complex With A 22 Nucl 9e-05
1vio_A243 Crystal Structure Of Pseudouridylate Synthase Lengt 1e-04
1ksk_A234 Structure Of Rsua Length = 234 8e-04
>gi|49259508|pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325 Back     alignment and structure
 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 130/331 (39%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I  
Sbjct: 9   TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                         +   ++YED  I + NKP  + V  G+G     
Sbjct: 69  EIEEEARF---------------EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGT 113

Query: 130 DGF---LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                       +   +  + HRLD++T+G++VVA+T  A   L ES + R I + Y ++
Sbjct: 114 VLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G                                    A++H+++++ F      L ++
Sbjct: 174 AIGHMTAGGTVDE------PISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 227 LETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLY 286

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 287 HPISGIEMEWHAPIPQDMVELIEVMRADFEE 317


>gi|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349 Back     alignment and structure
>gi|38492837|pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 Back     alignment and structure
>gi|78100963|pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 Back     alignment and structure
>gi|49259509|pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of Pseudouridine Synthase Rluc From Escherichia Coli Length = 228 Back     alignment and structure
>gi|119390059|pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-Induced Rna Structure Length = 217 Back     alignment and structure
>gi|14278533|pdb|1I94|D Chain D, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 208 Back     alignment and structure
>gi|10835588|pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 209 Back     alignment and structure
gi|10120567|pdb|1FKA|D Chain D, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 209 Back     alignment and structure
gi|228312012|pdb|3DH3|A Chain A, Crystal Structure Of Rluf In Complex With A 22 Nucleotide Rna Substrate Length = 290 Back     alignment and structure
>gi|40890007|pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase Length = 243 Back     alignment and structure
>gi|20664188|pdb|1KSK|A Chain A, Structure Of Rsua Length = 234 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target346 ribosomal large subunit pseudouridine synthase C [Candi
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; RNA b 4e-32
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; pseud 7e-29
2i82_A217 Ribosomal large subunit pseudouridine synthase A; lyase 6e-20
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 2e-09
2oml_A189 Ribosomal large subunit pseudouridine synthase E; bifur 2e-09
2olw_A217 Ribosomal large subunit pseudouridine synthase E; bifur 2e-09
2gml_A237 Ribosomal large subunit pseudouridine synthase F; RLUF, 2e-04
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; RSUA, 4e-09
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325 Back     alignment and structure
 Score =  133 bits (336), Expect = 4e-32
 Identities = 76/333 (22%), Positives = 135/333 (40%), Gaps = 35/333 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I 
Sbjct: 8   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAIN 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        +   LD                +YED  I + NKP  + V  G+G    
Sbjct: 68  AEIEEEARFEPQDIPLDI---------------VYEDEDIIIINKPRDLVVHPGAGNPDG 112

Query: 129 IDGFLKSWVDS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                            +  + HRLD++T+G++VVA+T  A   L ES + R I + Y +
Sbjct: 113 TVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G                +      VH           A++H+++++ F +    L +
Sbjct: 173 VAIGHMTAGGTVDEPISRHPTKRTHMAVH------PMGKPAVTHYRIMEHF-RVHTRLRL 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L
Sbjct: 226 RLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRL 285

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
            HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 286 YHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 318


>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Length = 228 Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217 Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Length = 92 Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189 Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Length = 217 Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Length = 237 Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Length = 234 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 ribosomal large subunit pseudouridine synthase C [Candi
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; RNA b 100.0
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; pseud 100.0
2i82_A217 Ribosomal large subunit pseudouridine synthase A; lyase 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; struc 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; RSUA, 100.0
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; prote 99.98
2oml_A189 Ribosomal large subunit pseudouridine synthase E; bifur 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; bifur 100.0
2gml_A237 Ribosomal large subunit pseudouridine synthase F; RLUF, 99.83
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 99.54
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 98.61
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 98.04
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-binding, m 97.75
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, unique t 97.73
3ofo_D205 30S ribosomal protein S4; protein biosynthesis, ribosom 97.58
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spinach 97.5
3hp7_A291 Hemolysin, putative; structural genomics, APC64019, PSI 97.13
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protein IMP 96.6
3jyv_D158 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 96.11
1s1h_D179 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal 95.64
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, pseudo 96.84
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA modi 96.69
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex, T s 96.67
2aus_C334 Pseudouridine synthase; isomerase, structural protein, 95.79
2apo_A357 Probable tRNA pseudouridine synthase B; protein-protein 95.67
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
Probab=100.00  E-value=0  Score=540.00  Aligned_cols=299  Identities=25%  Similarity=0.384  Sum_probs=239.9

Q ss_pred             EEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             999841136866899999876788989999999849903887884-5112117998899935655422233222234554
Q gi|254780608|r    9 YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS   87 (346)
Q Consensus         9 ~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~   87 (346)
                      .++|+++++|+|||+||++.||++||++++++|++|.|+|||+++ +++++|..||.|.+........            
T Consensus         7 t~tV~~~~~G~RLD~~L~~~~~~~sr~~i~k~i~~g~V~vNg~~~~k~~~~l~~gD~I~i~~~~~~~~------------   74 (325)
T 1v9f_A            7 TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEA------------   74 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCC------------
T ss_conf             99989775886799999986687799999999986998999999378541656999999826766654------------


Q ss_pred             CCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCCCC--CCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             33432223454307861785688417653112235785332-33201101111--1001333544534222404621231
Q gi|254780608|r   88 VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTR  164 (346)
Q Consensus        88 ~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~--~~~~~~lVHRLDr~TSGlll~AK~~  164 (346)
                         .......++.|||||++++|||||+|++|||+++.... +.+.+..+...  ....+++|||||++||||||||||.
T Consensus        75 ---~~~~~~~~~~ilyed~~~ivvnKP~Gl~~~p~~~~~~~tl~~~~~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~  151 (325)
T 1v9f_A           75 ---RFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTV  151 (325)
T ss_dssp             ----CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSH
T ss_pred             ---CCCCCCCCCCEEEEECCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCCEEEEEECC
T ss_conf             ---46755688607996088999989998725899998887499999986343137765216657898874269974000


Q ss_pred             CHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEE
Q ss_conf             01222102333322111200013456541000000012234655432111335555555303430101343202442045
Q gi|254780608|r  165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE  244 (346)
Q Consensus       165 ~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~  244 (346)
                      .+++.|+++|+++.|.|+|+|+|.|.++. .+.+..++........ .    ....++|+.|+|+|++++..+ .+|||+
T Consensus       152 ~~~~~l~~~f~~~~v~K~Y~A~v~G~~~~-~~~~~~~~~~~~~~~~-~----~~v~~~gk~a~T~~~~~~~~~-~~slv~  224 (325)
T 1v9f_A          152 PAQTRLVESLQRREITREYEAVAIGHMTA-GGTVDEPISRHPTKRT-H----MAVHPMGKPAVTHYRIMEHFR-VHTRLR  224 (325)
T ss_dssp             HHHHHHHHHHHTTCSEEEEEEEEESCCCC-CEEEECCEEECSSCTT-C----EEECTTSBCCEEEEEEEEECS-SEEEEE
T ss_pred             HHHHHHHHHHHHCEEEEEEEEEEECCCCC-CCCEECCCCCCCCCCC-E----EEECCCCEEEEEEEEEEEECC-CCEEEE
T ss_conf             57899988764070205899999764276-6505044323777762-7----997889803589999744238-844689


Q ss_pred             EEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHH--------CCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHH
Q ss_conf             786123789999999963980004644466522100--------013446241311000437588964-99983997899
Q gi|254780608|r  245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM  315 (346)
Q Consensus       245 ~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~--------~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f  315 (346)
                      |+|+||||||||+||+++||||+||.+||+......        .....+||+|||++|+|+||.+++ ++|+||||+||
T Consensus       225 ~~~~TGRtHQIRvHla~lG~PIlGD~~YG~~~~~~~~~~~~~~~~~~~~~r~~LHA~~L~f~hP~t~~~~~~~aplP~df  304 (325)
T 1v9f_A          225 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDM  304 (325)
T ss_dssp             EEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCCHHH
T ss_pred             EEECCCCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCHHHH
T ss_conf             99788886799999998599375861348765565432056676650586412534806966699998899991797999


Q ss_pred             HHHHHHHCCCCCCC
Q ss_conf             99999808987520
Q gi|254780608|r  316 VKTWDSLGFKYDRN  329 (346)
Q Consensus       316 ~~~l~~l~~~~d~~  329 (346)
                      +++|+.|.+.++++
T Consensus       305 ~~~l~~L~~~~~~~  318 (325)
T 1v9f_A          305 VELIEVMRADFEEH  318 (325)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             99999974156554



>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} SCOP: d.66.1.6 Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>3ofo_D 30S ribosomal protein S4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ... Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3jyv_D 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1 Back     alignment and structure
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Back     alignment and structure
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 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 3hjw_A* 3hjy_A Back     alignment and structure
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 346 ribosomal large subunit pseudouridine synthase C [Candi
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridine sy 2e-29
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridine sy 8e-24
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]
 Score =  123 bits (309), Expect = 2e-29
 Identities = 74/225 (32%), Positives = 119/225 (52%), Gaps = 9/225 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  I V NKP+G +V GGSG+++ +   L++    + +   L HRLD++TSG+L+VA
Sbjct: 4   MYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRP-EARFLELVHRLDRDTSGVLLVA 62

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + R+A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V Q  K
Sbjct: 63  KKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGK 122

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y         
Sbjct: 123 ---PSETRFKVEERYAF-ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQL 178

Query: 282 SPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +      N+L+LHA  +   HP  G  ++I AP+   + +    +
Sbjct: 179 TEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKM 223


>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 ribosomal large subunit pseudouridine synthase C [Candi
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, RluD 100.0
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, RluC 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase RsuA 99.94
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase RsuA 99.87
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 562] 98.63
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Escheric 98.55
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Haemophi 98.52
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId: 562 98.14
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562]} 97.85
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus [TaxI 97.8
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 274] 97.72
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {The 95.25
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bac 92.41
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [TaxId 96.85
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritima [Ta 96.73
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tuberculo 96.6
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanococcus 96.26
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcus fur 96.23
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=433.87  Aligned_cols=228  Identities=27%  Similarity=0.433  Sum_probs=181.7

Q ss_pred             CCCCCEEEEECCCEEEECCCCCCEEECCCCCCC-CCCCCHHHCCCC--CCCCCCCCCCCCCCCCCEEEEECCCCHHHHHC
Q ss_conf             345430786178568841765311223578533-233201101111--10013335445342224046212310122210
Q gi|254780608|r   95 DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLT  171 (346)
Q Consensus        95 ~~~~~~IiyED~~livinKPaGl~vhp~~g~~~-~~~~~l~~~~~~--~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~  171 (346)
                      +.++++|||||++|||||||+||+|||+++... ++.+.+......  ....+++|||||++||||||||||+.+++.|+
T Consensus         4 ~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~~a~~~l~   83 (250)
T d1v9fa_           4 QDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLV   83 (250)
T ss_dssp             CCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHH
T ss_pred             CCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCEEEEECCCHHHHHHH
T ss_conf             88997789978999999999998780799999845999999973650488742577514888765178851527888632


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHH
Q ss_conf             23333221112000134565410000000122346554321113355555553034301013432024420457861237
Q gi|254780608|r  172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR  251 (346)
Q Consensus       172 ~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR  251 (346)
                      ++|+++.|.|+|+|+|.|.+.. .+.++.++....... ..    ....++||.|+|+|++++..+ .+||++|+|.|||
T Consensus        84 ~~f~~~~v~K~Y~a~~~g~~~~-~~~~~~~~~~~~~~~-~~----~~~~~~gk~a~T~~~~l~~~~-~~slv~~~~~TGR  156 (250)
T d1v9fa_          84 ESLQRREITREYEAVAIGHMTA-GGTVDEPISRHPTKR-TH----MAVHPMGKPAVTHYRIMEHFR-VHTRLRLRLETGR  156 (250)
T ss_dssp             HHHHTTCSEEEEEEEEESCCCC-CEEEECCEEECSSCT-TC----EEECTTSBCCEEEEEEEEECS-SEEEEEEEESCCC
T ss_pred             HHHCCCEEEEEEEEEECCCCCC-CCCCCCCCCCCCCCC-CE----EEECCCCEECCCCCHHHHCCC-CCEEEEEEECCCC
T ss_conf             3304545767744321135464-566235533577666-30----687789834441011344056-7426887863663


Q ss_pred             HHHHHHHHHHCCCCEECCCCCCCCCCCHH--------CCCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHHHHHHHHH
Q ss_conf             89999999963980004644466522100--------01344624131100043758896-4999839978999999980
Q gi|254780608|r  252 THQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL  322 (346)
Q Consensus       252 ~HQIRvhl~~~g~PivGD~~Yg~~~~~~~--------~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f~~~l~~l  322 (346)
                      |||||+||+++||||+||.+||+......        ......||+|||++|+|.||.++ +++|+||+|+||.++|+.|
T Consensus       157 ~HQIRvHla~lG~PIlGD~~YG~~~~~~~~~~~~~~~~~~~~~r~~LHA~~L~f~hP~t~~~~~~~aplP~df~~~l~~L  236 (250)
T d1v9fa_         157 THQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM  236 (250)
T ss_dssp             TTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCHHHHHHHHCCCHHHHHCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHH
T ss_conf             27999999985983001115762113544455878887742526456407115326899986999807909999999997


Q ss_pred             CCCCCCC
Q ss_conf             8987520
Q gi|254780608|r  323 GFKYDRN  329 (346)
Q Consensus       323 ~~~~d~~  329 (346)
                      ++.+++.
T Consensus       237 ~~~~~~~  243 (250)
T d1v9fa_         237 RADFEEH  243 (250)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHC
T ss_conf             5177756



>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 346 ribosomal large subunit pseudouridine synthase C [
1v9k_A_228 (A:) Ribosomal large subunit pseudouridine synthas 4e-31
2i82_A_217 (A:) Ribosomal large subunit pseudouridine synthas 4e-29
2gml_A_237 (A:) Ribosomal large subunit pseudouridine synthas 6e-24
3dh3_A_64-290227 (A:64-290) Ribosomal large subunit pseudouridine s 9e-23
2oml_A_189 (A:) Ribosomal large subunit pseudouridine synthas 5e-18
1vio_A_58-243186 (A:58-243) Ribosomal small subunit pseudouridine s 3e-17
1ksk_A_59-234176 (A:59-234) Ribosomal small subunit pseudouridine s 3e-17
1v9f_A_325 (A:) Ribosomal large subunit pseudouridine synthas 2e-27
2olw_A_103-20098 (A:103-200) Ribosomal large subunit pseudouridine 4e-15
2olw_A_1-102_201-217119 (A:1-102,A:201-217) Ribosomal large subunit pseudo 3e-10
1dm9_A_133 (A:) Hypothetical 15.5 KD protein in MRCA-PCKA int 2e-08
2k6p_A_92 (A:) Uncharacterized protein HP_1423; alpha-L moti 6e-09
3dh3_A_1-6363 (A:1-63) Ribosomal large subunit pseudouridine syn 2e-05
>1v9k_A (A:) Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli}Length = 228 Back     alignment and structure
 Score =  129 bits (325), Expect = 4e-31
 Identities = 70/222 (31%), Positives = 108/222 (48%), Gaps = 9/222 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I V NKP+G +V GGSG+++ +   L++    + +   L HRLD++TSG+L+VA+
Sbjct: 6   YEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRP-EARFLELVHRLDRDTSGVLLVAK 64

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            R+A + L E  R +  QK Y +LV G  ++  + +   LLK     G+ +  V Q  K 
Sbjct: 65  KRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKP 124

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGN 279
           +                   +   P TGRTHQ+RVH  + G PI  D +Y     + +  
Sbjct: 125 SETRFKVE----ERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLT 180

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
                 N+L+LHA  +   HP  G   +I AP    + +   
Sbjct: 181 EAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEGLKRCLQ 222


>2i82_A (A:) Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}Length = 217 Back     alignment and structure
>2gml_A (A:) Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}Length = 237 Back     alignment and structure
>3dh3_A (A:64-290) 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}Length = 227 Back     alignment and structure
>2oml_A (A:) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}Length = 189 Back     alignment and structure
>1vio_A (A:58-243) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae}Length = 186 Back     alignment and structure
>1ksk_A (A:59-234) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli}Length = 176 Back     alignment and structure
>1v9f_A (A:) Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli}Length = 325 Back     alignment and structure
>2olw_A (A:103-200) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}Length = 98 Back     alignment and structure
>2olw_A (A:1-102,A:201-217) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}Length = 119 Back     alignment and structure
>1dm9_A (A:) Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli}Length = 133 Back     alignment and structure
>2k6p_A (A:) Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}Length = 92 Back     alignment and structure
>3dh3_A (A:1-63) 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}Length = 63 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 ribosomal large subunit pseudouridine synthase C [Candi
1v9f_A_325 Ribosomal large subunit pseudouridine synthase D; 100.0
1v9k_A_228 Ribosomal large subunit pseudouridine synthase C; 100.0
2i82_A_217 Ribosomal large subunit pseudouridine synthase A; 100.0
2gml_A_237 Ribosomal large subunit pseudouridine synthase F; 100.0
3dh3_A_64-290227 Ribosomal large subunit pseudouridine synthase F; 100.0
1ksk_A_59-234176 Ribosomal small subunit pseudouridine synthase A; 100.0
1vio_A_58-243186 Ribosomal small subunit pseudouridine synthase A; 100.0
2oml_A_189 Ribosomal large subunit pseudouridine synthase E; 100.0
1dm9_A_133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 99.86
2olw_A_1-102_201-217119 Ribosomal large subunit pseudouridine synthase E; 99.86
2olw_A_103-20098 Ribosomal large subunit pseudouridine synthase E; 99.8
2k6p_A_92 Uncharacterized protein HP_1423; alpha-L motif, RN 99.77
3dh3_A_1-6363 Ribosomal large subunit pseudouridine synthase F; 99.03
1p9k_A_79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.9
1ksk_A_1-5858 Ribosomal small subunit pseudouridine synthase A; 98.58
1vio_A_1-5757 Ribosomal small subunit pseudouridine synthase A; 98.53
2vqe_D_100-19394 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.09
3hp7_A_1-6565 Hemolysin, putative; structural genomics, APC64019 98.08
3bbn_D_82-201120 Ribosomal protein S4; small ribosomal subunit, spi 97.9
3i1m_D_97-19094 30S ribosomal protein S4; ribosome structure, prot 97.9
1h3f_A_350-43283 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 97.57
1s1h_D_81-17999 40S ribosomal protein S9-A; 80S ribosome, 40S ribo 97.53
2cqj_A_71 BRMS2, U3 small nucleolar ribonucleoprotein protei 97.29
2jan_A_345-43288 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 95.82
1jil_A_247-420174 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; 91.13
3kbg_A_1-8181 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 90.41
2apo_A_51-266216 Probable tRNA pseudouridine synthase B; protein-pr 96.45
2aus_C_31-245215 Pseudouridine synthase; isomerase, structural prot 96.38
1sgv_A_1-60_206-23287 TRNA pseudouridine synthase B; hinged motion, tRNA 92.49
1k8w_A_1-79_225-253108 TRNA pseudouridine synthase B; protein-RNA complex 92.08
1r3e_A_1-57_190-22492 TRNA pseudouridine synthase B; RNA modification, p 92.05
1c05_A_77-15983 Ribosomal protein S4 delta 41; two subdomains, uni 91.4
>1v9f_A (A:) Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=0  Score=453.24  Aligned_cols=300  Identities=25%  Similarity=0.368  Sum_probs=235.6

Q ss_pred             EEE-EEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCC-CCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             049-9984113686689999987678898999999984990388788451121179-98899935655422233222234
Q gi|254780608|r    7 VQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKIL   84 (346)
Q Consensus         7 ~~~-~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~-GD~I~i~~~~~~~~~~~~~~~~~   84 (346)
                      |++ ++|+++++|+|||+||++.++++||+.++++|++|+|+|||+++...+.+.. ++.+........           
T Consensus         4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~-----------   72 (325)
T 1v9f_A            4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEE-----------   72 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCC-----------
T ss_conf             899999897648866999999866867999999999869989999991783206258989973254332-----------


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCC--CCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             55433432223454307861785688417653112235785332-332011011--111001333544534222404621
Q gi|254780608|r   85 DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVA  161 (346)
Q Consensus        85 ~~~~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~--~~~~~~~~lVHRLDr~TSGlll~A  161 (346)
                          .........+..|||||++++|+|||+|++|||+.+.... +...+....  ......+++|||||++||||||+|
T Consensus        73 ----~~~~~~~~~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~A  148 (325)
T 1v9f_A           73 ----EARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVA  148 (325)
T ss_dssp             -------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEE
T ss_pred             ----CCCCCCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEE
T ss_conf             ----2233334454112510110578707888654898777888632321134443333342146532588986514664


Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCC
Q ss_conf             23101222102333322111200013456541000000012234655432111335555555303430101343202442
Q gi|254780608|r  162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC  241 (346)
Q Consensus       162 K~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~s  241 (346)
                      ||..+++.|+.+|+.+.+.|+|+|+|.|.+....+.+..+........      .......++.|.|+|.+..... .+|
T Consensus       149 k~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~a~~~~~~~~~~~-~~s  221 (325)
T 1v9f_A          149 KTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRT------HMAVHPMGKPAVTHYRIMEHFR-VHT  221 (325)
T ss_dssp             SSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT------CEEECTTSBCCEEEEEEEEECS-SEE
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC------EEEECCCCCEEEEEEEEEEECC-CCE
T ss_conf             025889999987501210124234301354745662355335766653------0587688715789989865338-845


Q ss_pred             EEEEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCH--------HCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCC
Q ss_conf             04578612378999999996398000464446652210--------001344624131100043758896-499983997
Q gi|254780608|r  242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP  312 (346)
Q Consensus       242 lv~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~--------~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP  312 (346)
                      +++|+|.|||+||||+||+++||||+||.+||......        .......+++|||+.++|+||.++ .+.|+||+|
T Consensus       222 l~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P  301 (325)
T 1v9f_A          222 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP  301 (325)
T ss_dssp             EEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC
T ss_pred             EEEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH
T ss_conf             79999778831799999998399766877789855454433166777651586434653705857789998899991797


Q ss_pred             HHHHHHHHHHCCCCCC
Q ss_conf             8999999980898752
Q gi|254780608|r  313 AHMVKTWDSLGFKYDR  328 (346)
Q Consensus       313 ~~f~~~l~~l~~~~d~  328 (346)
                      ++|..+|+.|+++.+.
T Consensus       302 ~~f~~~l~~l~~~~~~  317 (325)
T 1v9f_A          302 QDMVELIEVMRADFEE  317 (325)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999997307765



>1v9k_A (A:) Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} Back     alignment and structure
>2i82_A (A:) Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>2gml_A (A:) Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>3dh3_A (A:64-290) Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1ksk_A (A:59-234) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} Back     alignment and structure
>1vio_A (A:58-243) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} Back     alignment and structure
>2oml_A (A:) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>1dm9_A (A:) Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} Back     alignment and structure
>2olw_A (A:1-102,A:201-217) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>2olw_A (A:103-200) Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>2k6p_A (A:) Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>3dh3_A (A:1-63) Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1p9k_A (A:) ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} Back     alignment and structure
>1ksk_A (A:1-58) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} Back     alignment and structure
>1vio_A (A:1-57) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} Back     alignment and structure