254780610

254780610

RNA-pseudouridylate synthase protein, ribosomal large subunit D

GeneID in NCBI database:8209609Locus tag:CLIBASIA_02485
Protein GI in NCBI database:254780610Protein Accession:YP_003065023.1
Gene range:-(665465, 666487)Protein Length:340aa
Gene description:RNA-pseudouridylate synthase protein, ribosomal large subunit D
COG prediction:[J] Pseudouridylate synthases, 23S RNA-specific
KEGG prediction:rluD; RNA-pseudouridylate synthase protein, ribosomal large subunit D; K06180 ribosomal large subunit pseudouridine synthase D [EC:5.4.99.12]
SEED prediction:Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70)
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
TOPPRED3 TM-Helix
HMMTOP1 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
MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK
ccccccccccEEEEEEccccccccHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEcccccEEccccEEEEEccccccccccccccEEEEEEcccEEEEEEccccEEEccccccccccHHHHHHHHHHHHHccccccccEEEEEcccccccEEEEEEccHHHHHHHHHHHHHcccccEEEEEEEEEEEEEEccccEEEEcccccccccccEEEEEEccccccccccccEEEEccccccccccEEEEEEEEcccccHHHHHHHHHHcccEEccccccccccccccccccccHHHHccccHHHHHHHHEEEEccccccEEEEEccccHHHHHHHHHHccc
cccHHHHcccEEEEEEcHHHcccHHHHHHHHHHcHHccHHHHHHHHHcccEEEcccEccccccEEccccEEEEEcccccccccccccccccEEEEcccEEEEEcccccEEcccccccccHHHHHHHHHcccccccccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHccccccEEEEEEEEEEccccccccEEEcccccccccccEEEEEccccccccccEEEHHHHHHccccccccEEEEEEEEccccccEEEEEHHHcccccccccccccccccccccccHHHHHHHcccccHHHHHHHcccEccccccEEEEEcccHHHHHHHHHHHHcc
MQQTLDNCSSIKisllsdstaegrIDRWLATSLKEQFSRSYVKILILNGFISINgmvsknpnrkvvpgdsfliTVPAAQKlniaqenipldilyedddiivinkpaglvvhpapgnwtGTLVNALLYHChnnlssingvkrpgivhrldkdttgVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWgiplpdsgiinaplgrcksnRLRRavkgiddktadsaITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMahkgnpligdplygkgfktkANIVNNNAKSAILSLARQALHAhslsfshprnnqdmdfqvpipEDMLTVIRKLNEK
mqqtldncssikisllsdstaegRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSsingvkrpgIVHRLDKDTTGVMVVAKNDLahqklseqfvdhgkstRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAvkgiddktadsaITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSlsfshprnnqdMDFQVPIPEDMLTVIRKLNEK
MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK
************ISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNE*
********SSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK
MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNE*
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MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK
MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK
MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
254780608346 ribosomal large subunit pseudouridine synthase C [ 4e-27
>gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter asiaticus str. psy62] Length = 346 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: 92  ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVK--RPGIVHRLD 149
           +LYED  I V NKPAG+ V    G         + YH    L S    K  +P + HRLD
Sbjct: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151

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

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

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

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

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

IdentityAlignment graphLength Definition Round E-value
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
315121810340 RNA-pseudouridylate synthase protein, ribosomal large s 1 1e-158
190893167354 RNA-pseudouridylate synthase, ribosomal large subunit D 1 1e-110
86358939354 pseudouridylate synthase, ribosomal large subunit D pro 1 1e-109
241206033341 pseudouridine synthase, RluA family [Rhizobium legumino 1 1e-108
116253506341 ribosomal large subunit pseudouridine synthase D [Rhizo 1 1e-107
209550662341 pseudouridine synthase [Rhizobium leguminosarum bv. tri 1 1e-107
222086840343 pseudouridylate synthase [Agrobacterium radiobacter K84 1 1e-104
222149596342 ribosomal large subunit pseudouridine synthase RluD sub 1 1e-102
227823294352 putative ribosomal large subunit pseudouridine synthase 1 1e-101
15966478343 putative ribosomal large subunit pseudouridine synthase 1 1e-100
>gi|315121810|ref|YP_004062299.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 340 Back     alignment and organism information
 Score =  563 bits (1451), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 268/339 (79%), Positives = 299/339 (88%)

Query: 1   MQQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKN 60
           MQ   DNC  +KISLL+++ AEGRIDRWLA +LKE+FSRSYVK LILNG ISING+VS N
Sbjct: 1   MQTASDNCLPMKISLLANNEAEGRIDRWLAINLKEKFSRSYVKTLILNGAISINGVVSIN 60

Query: 61  PNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGT 120
           P+RKVVPG+SF I VP  Q+LNIA ENIPLDILYEDDDIIVINK AGLVVHPAPGNWTGT
Sbjct: 61  PSRKVVPGESFFIDVPQLQQLNIAAENIPLDILYEDDDIIVINKQAGLVVHPAPGNWTGT 120

Query: 121 LVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTR 180
           LVNALL+HC+NNLS ING+KRPGIVHRLDKDTTG MVVAKND+AHQ+LSEQF DHG    
Sbjct: 121 LVNALLHHCNNNLSGINGIKRPGIVHRLDKDTTGTMVVAKNDIAHQRLSEQFADHGLHMG 180

Query: 181 LKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKN 240
           LKR+YYAMVWG+P PDSG INAPLGRCKSNRLRRAVK I+DKT D A+T YQT+EIYNKN
Sbjct: 181 LKRSYYAMVWGVPSPDSGTINAPLGRCKSNRLRRAVKRIEDKTGDRAVTRYQTVEIYNKN 240

Query: 241 SNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLA 300
           SNFA SLL+C LETGRTHQIRVHMAHKG P+IGDPLYGKGFKTK NIVN++ KSAILSLA
Sbjct: 241 SNFAASLLRCDLETGRTHQIRVHMAHKGYPIIGDPLYGKGFKTKENIVNHSTKSAILSLA 300

Query: 301 RQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNE 339
           RQALHA+SLSF+HP  N+DM+F+ PIPEDM  VI++L E
Sbjct: 301 RQALHAYSLSFTHPCKNKDMNFKTPIPEDMSNVIKELKE 339


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|190893167|ref|YP_001979709.1| RNA-pseudouridylate synthase, ribosomal large subunit D [Rhizobium etli CIAT 652] Length = 354 Back     alignment and organism information
>gi|86358939|ref|YP_470831.1| pseudouridylate synthase, ribosomal large subunit D protein [Rhizobium etli CFN 42] Length = 354 Back     alignment and organism information
>gi|241206033|ref|YP_002977129.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 341 Back     alignment and organism information
>gi|116253506|ref|YP_769344.1| ribosomal large subunit pseudouridine synthase D [Rhizobium leguminosarum bv. viciae 3841] Length = 341 Back     alignment and organism information
>gi|209550662|ref|YP_002282579.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 341 Back     alignment and organism information
>gi|222086840|ref|YP_002545374.1| pseudouridylate synthase [Agrobacterium radiobacter K84] Length = 343 Back     alignment and organism information
>gi|222149596|ref|YP_002550553.1| ribosomal large subunit pseudouridine synthase RluD subfamily [Agrobacterium vitis S4] Length = 342 Back     alignment and organism information
>gi|227823294|ref|YP_002827266.1| putative ribosomal large subunit pseudouridine synthase D [Sinorhizobium fredii NGR234] Length = 352 Back     alignment and organism information
>gi|15966478|ref|NP_386831.1| putative ribosomal large subunit pseudouridine synthase protein [Sinorhizobium meliloti 1021] Length = 343 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
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, RluA fa 1e-86
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Prov 1e-68
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C 3e-29
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA-speci 5e-81
cd02869185 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/R 4e-54
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomera 1e-32
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; Prov 7e-27
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthas 3e-26
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu family 1e-20
KOG1919371 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthase 1e-32
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate syn 3e-12
pfam00849151 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthas 1e-31
cd02557213 cd02557, PseudoU_synth_ScRIB2, PseudoU_synth_ScRIB2_lik 8e-28
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_ 2e-20
cd02558246 cd02558, PSRA_1, PSRA_1: Pseudouridine synthase, a subg 2e-15
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain 2e-05
PRK11394217 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; 8e-04
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional 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|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|37130 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|31380 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase 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|30008 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family 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|29105 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
>gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 340 RNA-pseudouridylate synthase protein, ribosomal large s
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisional 100.0
TIGR00005337 rluA_subfam pseudouridine synthase, RluA family; InterP 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [Trans 100.0
KOG1919371 consensus 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of th 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
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
pfam00849151 PseudoU_synth_2 RNA pseudouridylate synthase. Members o 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases are res 100.0
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine sy 99.79
PRK11394207 23S rRNA pseudouridine synthase E; Provisional 99.65
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine sy 99.64
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine sy 99.6
TIGR00093185 TIGR00093 conserved hypothetical protein; InterPro: IPR 99.57
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of th 99.52
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridi 99.46
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase and 99.94
PRK10839231 16S rRNA pseudouridylate synthase A; Provisional 99.93
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 99.93
PRK10700291 23S rRNA pseudouridylate synthase B; Provisional 99.92
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The doma 99.11
TIGR01017217 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Rib 98.1
smart0036360 S4 S4 RNA-binding domain. 98.65
pfam0147948 S4 S4 domain. The S4 domain is a small domain consistin 98.55
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members of t 98.33
COG1188100 Ribosome-associated heat shock protein implicated in th 98.19
COG2302257 Uncharacterized conserved protein, contains S4-like dom 98.13
CHL00113201 rps4 ribosomal protein S4; Reviewed 98.04
PRK12565197 30S ribosomal protein S4; Provisional 98.0
PRK10348133 ribosome-associated heat shock protein Hsp15; Provision 98.0
COG0522205 RpsD Ribosomal protein S4 and related proteins [Transla 98.0
PRK05327201 rpsD 30S ribosomal protein S4; Validated 97.76
COG1189245 Predicted rRNA methylase [Translation, ribosomal struct 97.68
TIGR00478240 tly hemolysin A; InterPro: IPR004538 Hemolysins are exo 97.58
TIGR0298860 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014 95.67
pfam06353142 DUF1062 Protein of unknown function (DUF1062). This fam 95.53
PRK04051177 rps4p 30S ribosomal protein S4; Validated 95.34
PRK04313237 30S ribosomal protein S4e; Validated 95.21
TIGR01018170 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Rib 95.05
PTZ00223273 40S ribosomal protein S4; Provisional 95.02
PTZ00118262 40S ribosomal protein S4; Provisional 94.96
COG250173 S4-like RNA binding protein [Replication, recombination 94.86
PRK1150770 hypothetical protein; Provisional 94.6
PTZ00155188 40S ribosomal protein S9; Provisional 93.6
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridi 97.38
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 97.26
PRK00989235 truB tRNA pseudouridine synthase B; Provisional 97.22
PRK00130289 truB tRNA pseudouridine synthase B; Provisional 97.11
PRK04099272 truB tRNA pseudouridine synthase B; Provisional 97.11
PRK02484293 truB tRNA pseudouridine synthase B; Provisional 97.09
PRK01851310 truB tRNA pseudouridine synthase B; Provisional 97.07
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: P 96.95
PRK01528293 truB tRNA pseudouridine synthase B; Provisional 96.93
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: P 96.88
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 96.86
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 96.85
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 96.81
PRK01550307 truB tRNA pseudouridine synthase B; Provisional 96.77
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 96.74
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewed 96.67
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridin 96.63
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridin 96.61
COG0130271 TruB Pseudouridine synthase [Translation, ribosomal str 96.57
PRK05033314 truB tRNA pseudouridine synthase B; Provisional 96.52
PRK02755291 truB tRNA pseudouridine synthase B; Provisional 96.02
TIGR00431236 TruB tRNA pseudouridine synthase B; InterPro: IPR014780 95.25
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthases ca 93.09
KOG2559318 consensus 93.01
>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
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional 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
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family 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
>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
>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
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>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
>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
>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
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>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
>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
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>pfam01479 S4 S4 domain Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein 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
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>PRK12565 30S ribosomal protein S4; Provisional Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional 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
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] 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
>pfam06353 DUF1062 Protein of unknown function (DUF1062) Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4; Validated Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms 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
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK11507 hypothetical protein; Provisional Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00989 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
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 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
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 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
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional 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
>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
>KOG2559 consensus 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
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 1e-40
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 7e-38
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 7e-16
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 1e-12
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 5e-14
1i94_D208 Crystal Structures Of The Small Ribosomal Subunit W 2e-07
1fjg_D209 Structure Of The Thermus Thermophilus 30s Ribosomal 2e-07
1fka_D209 Structure Of Functionally Activated Small Ribosomal 2e-07
1vio_A243 Crystal Structure Of Pseudouridylate Synthase Lengt 2e-06
1qd7_C159 Partial Model For 30s Ribosomal Subunit Length = 15 1e-04
1ksk_A234 Structure Of Rsua Length = 234 5e-04
3dh3_A290 Crystal Structure Of Rluf In Complex With A 22 Nucl 7e-04
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 3e-06
>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 =  171 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 118/324 (36%), Positives = 166/324 (51%), Gaps = 20/324 (6%)

Query: 15  LLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74
            +S++    R+D+ LA    + +SRS +K  IL+  + +NG V   P  KV+ G+   I 
Sbjct: 9   TVSENQLGQRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAIN 67

Query: 75  VPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLS 134
               ++     ++IPLDI+YED+DII+INKP  LVVHP  GN  GT++NA      +   
Sbjct: 68  AEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNA----LLHYYP 123

Query: 135 SINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPL 194
            I  V R GIVHRLDKDTTG+MVVAK   A  +L E       +   +      +     
Sbjct: 124 PIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGT 183

Query: 195 PDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLET 254
            D  I   P  R                    A+THY+ +E +  +     + L+  LET
Sbjct: 184 VDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHFRVH-----TRLRLRLET 229

Query: 255 GRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHP 314
           GRTHQIRVHMAH  +PL+GDP+YG G        +    S +    RQALHA  L   HP
Sbjct: 230 GRTHQIRVHMAHITHPLVGDPVYG-GRPRPPKGASEAFISTLRKFDRQALHATMLRLYHP 288

Query: 315 RNNQDMDFQVPIPEDMLTVIRKLN 338
            +  +M++  PIP+DM+ +I  + 
Sbjct: 289 ISGIEMEWHAPIPQDMVELIEVMR 312


>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|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|38492837|pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 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|40890007|pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase Length = 243 Back     alignment and structure
>gi|6137687|pdb|1QD7|C Chain C, Partial Model For 30s Ribosomal Subunit Length = 159 Back     alignment and structure
>gi|20664188|pdb|1KSK|A Chain A, Structure Of Rsua Length = 234 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|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

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; RNA b 7e-50
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; pseud 1e-40
2i82_A217 Ribosomal large subunit pseudouridine synthase A; lyase 7e-33
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; RSUA, 5e-19
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; prote 4e-11
1vio_A243 Ribosomal small subunit pseudouridine synthase A; struc 6e-09
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 1e-13
2oml_A189 Ribosomal large subunit pseudouridine synthase E; bifur 5e-11
2olw_A217 Ribosomal large subunit pseudouridine synthase E; bifur 5e-09
2gml_A237 Ribosomal large subunit pseudouridine synthase F; RLUF, 5e-06
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 2e-06
>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 =  192 bits (489), Expect = 7e-50
 Identities = 120/328 (36%), Positives = 172/328 (52%), Gaps = 21/328 (6%)

Query: 11  IKISLLSDSTAEG-RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGD 69
           ++++        G R+D+ LA    + +SRS +K  IL+  + +NG V   P  KV+ G+
Sbjct: 4   VQLTATVSENQLGQRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGE 62

Query: 70  SFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHC 129
              I     ++     ++IPLDI+YED+DII+INKP  LVVHP  GN  GT++N      
Sbjct: 63  QVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN----AL 118

Query: 130 HNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMV 189
            +    I  V R GIVHRLDKDTTG+MVVAK   A  +L E               Y  V
Sbjct: 119 LHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE-----ITREYEAV 173

Query: 190 WGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249
               +   G ++ P+ R  + R   AV          A+THY+ +E +  +     + L+
Sbjct: 174 AIGHMTAGGTVDEPISRHPTKRTHMAV----HPMGKPAVTHYRIMEHFRVH-----TRLR 224

Query: 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSL 309
             LETGRTHQIRVHMAH  +PL+GDP+YG   +      +    S +    RQALHA  L
Sbjct: 225 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGA-SEAFISTLRKFDRQALHATML 283

Query: 310 SFSHPRNNQDMDFQVPIPEDMLTVIRKL 337
              HP +  +M++  PIP+DM+ +I  +
Sbjct: 284 RLYHPISGIEMEWHAPIPQDMVELIEVM 311


>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
>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
>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} Length = 290 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 Length = 243 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
>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 Length = 133 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
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 100.0
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, 99.84
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 99.57
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NE 94.17
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 98.51
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 98.41
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-binding, m 98.11
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, unique t 98.09
3ofo_D205 30S ribosomal protein S4; protein biosynthesis, ribosom 97.89
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spinach 97.87
3hp7_A291 Hemolysin, putative; structural genomics, APC64019, PSI 97.56
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protein IMP 97.49
3jyv_D158 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 97.2
1s1h_D179 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal 96.9
2jan_A 432 Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacy 92.23
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex, T s 97.41
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, pseudo 97.17
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA modi 97.15
2apo_A357 Probable tRNA pseudouridine synthase B; protein-protein 96.32
2aus_C334 Pseudouridine synthase; isomerase, structural protein, 96.32
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthet 94.6
>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=556.10  Aligned_cols=307  Identities=40%  Similarity=0.643  Sum_probs=262.3

Q ss_pred             EEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHH
Q ss_conf             99957113687578999987176889899999998599049989932867580489889997056011110233222221
Q gi|254780610|r   13 ISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDI   92 (340)
Q Consensus        13 ~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~I   92 (340)
                      +.+|+++++|+|||+||++.|+ ++||++++++|++|.|+|||+++++++++|..||.|.+..+........+...+++|
T Consensus         7 t~tV~~~~~G~RLD~~L~~~~~-~~sr~~i~k~i~~g~V~vNg~~~~k~~~~l~~gD~I~i~~~~~~~~~~~~~~~~~~i   85 (325)
T 1v9f_A            7 TATVSENQLGQRLDQALAEMFP-DYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDI   85 (325)
T ss_dssp             ----------------------------------------------------------------------CCCCCCCCCE
T ss_pred             EEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCCCCCCE
T ss_conf             9998977588679999998668-779999999998699899999937854165699999982676665446755688607


Q ss_pred             CCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             01440278996240111045678754210022222210244334444364324444332324057212035788889999
Q gi|254780610|r   93 LYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQF  172 (340)
Q Consensus        93 lyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f  172 (340)
                      ||||++|+|||||+||+|||+++...+|+.+.+..++...    ....++++||||||+||||||||||+.+++.|+++|
T Consensus        86 lyed~~~ivvnKP~Gl~~~p~~~~~~~tl~~~~~~~~~~~----~~~~~~~~vHRLDr~TSGlll~Ak~~~~~~~l~~~f  161 (325)
T 1v9f_A           86 VYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESL  161 (325)
T ss_dssp             EEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG----GGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHH
T ss_pred             EEEECCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHH----CCCCCCEEECCCCCCCCCEEEEEECCHHHHHHHHHH
T ss_conf             9960889999899987258999988874999999863431----377652166578988742699740005789998876


Q ss_pred             HHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEE
Q ss_conf             97211322133445432024332332110013434443322123444555553000012221011256677500123443
Q gi|254780610|r  173 VDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHL  252 (340)
Q Consensus       173 ~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~  252 (340)
                      .    ++.|.|+|+|+|.|.++. .+.+..++..+......+.+    .+.|++|.|+|++++..     ..+|||+|+|
T Consensus       162 ~----~~~v~K~Y~A~v~G~~~~-~~~~~~~~~~~~~~~~~~~v----~~~gk~a~T~~~~~~~~-----~~~slv~~~~  227 (325)
T 1v9f_A          162 Q----RREITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMAV----HPMGKPAVTHYRIMEHF-----RVHTRLRLRL  227 (325)
T ss_dssp             H----TTCSEEEEEEEEESCCCC-CEEEECCEEECSSCTTCEEE----CTTSBCCEEEEEEEEEC-----SSEEEEEEEE
T ss_pred             H----HCEEEEEEEEEEECCCCC-CCCEECCCCCCCCCCCEEEE----CCCCEEEEEEEEEEEEC-----CCCEEEEEEE
T ss_conf             4----070205899999764276-65050443237777627997----88980358999974423-----8844689997


Q ss_pred             CHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHHHHH
Q ss_conf             11589999999987097860415447755444334570135544079804432100042468897689998499789999
Q gi|254780610|r  253 ETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLT  332 (340)
Q Consensus       253 ~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~~~~  332 (340)
                      +||||||||+||+++||||+||.+||+....... ..........+++||||||++|+|+||.||+.++|+||+|+||++
T Consensus       228 ~TGRtHQIRvHla~lG~PIlGD~~YG~~~~~~~~-~~~~~~~~~~~~~r~~LHA~~L~f~hP~t~~~~~~~aplP~df~~  306 (325)
T 1v9f_A          228 ETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG-ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVE  306 (325)
T ss_dssp             SCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT-CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCCHHHHH
T ss_pred             CCCCCHHHHHHHHHCCCCEECCCCCCCCCCCCCC-CHHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCHHHHHH
T ss_conf             8888679999999859937586134876556543-205667665058641253480696669999889999179799999


Q ss_pred             HHHHHHC
Q ss_conf             9998851
Q gi|254780610|r  333 VIRKLNE  339 (340)
Q Consensus       333 ~l~~L~~  339 (340)
                      +|+.|+.
T Consensus       307 ~l~~L~~  313 (325)
T 1v9f_A          307 LIEVMRA  313 (325)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
T ss_conf             9999741



>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
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Back     alignment and structure
>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
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} 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
>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
>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
>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
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* 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 340 RNA-pseudouridylate synthase protein, ribosomal large s
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridine sy 2e-47
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridine sy 1e-41
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-termina 3e-05
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-termina 2e-04
d1vioa1174 d.265.1.3 (A:58-231) Ribosomal small subunit pseudourid 3e-04
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250 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]
 Score =  183 bits (464), Expect = 2e-47
 Identities = 104/253 (41%), Positives = 141/253 (55%), Gaps = 19/253 (7%)

Query: 86  ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145
           ++IPLDI+YED+DII+INKP  LVVHP  GN  GT++NALL++       I  V R GIV
Sbjct: 4   QDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY----PPIADVPRAGIV 59

Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205
           HRLDKDTTG+MVVAK   A  +L E               Y  V    +   G ++ P+ 
Sbjct: 60  HRLDKDTTGLMVVAKTVPAQTRLVESLQRRE-----ITREYEAVAIGHMTAGGTVDEPIS 114

Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
           R  + R   AV          A+THY+ +E +  +     + L+  LETGRTHQIRVHMA
Sbjct: 115 RHPTKRTHMAV----HPMGKPAVTHYRIMEHFRVH-----TRLRLRLETGRTHQIRVHMA 165

Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP 325
           H  +PL+GDP+YG   +      +    S +    RQALHA  L   HP +  +M++  P
Sbjct: 166 HITHPLVGDPVYGGRPRPPKGA-SEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAP 224

Query: 326 IPEDMLTVIRKLN 338
           IP+DM+ +I  + 
Sbjct: 225 IPQDMVELIEVMR 237


>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58 Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Length = 59 Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Length = 174 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
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 99.95
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase RsuA 99.89
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Escheric 98.81
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Haemophi 98.77
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 562] 98.55
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId: 562 98.34
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus [TaxI 98.15
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562]} 98.12
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 274] 98.08
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {The 96.37
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bac 94.99
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [TaxId 97.4
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcus fur 97.22
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritima [Ta 97.09
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tuberculo 96.96
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanococcus 96.78
>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=446.56  Aligned_cols=237  Identities=44%  Similarity=0.705  Sum_probs=199.1

Q ss_pred             HHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH
Q ss_conf             23322222101440278996240111045678754210022222210244334444364324444332324057212035
Q gi|254780610|r   84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDL  163 (340)
Q Consensus        84 ~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~  163 (340)
                      .|++++++|||||++|+|||||+||+|||++++..+|+++.+..++...    ....++++||||||+||||||||||+.
T Consensus         2 ~P~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~----~~~~~~~~vHRLDr~TSGlll~Ak~~~   77 (250)
T d1v9fa_           2 EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVP   77 (250)
T ss_dssp             CCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG----GGSGGGGBCCCCCTTCEEEEEEESSHH
T ss_pred             CCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHC----CCCCCEEEEEECCCCCCCEEEEECCCH
T ss_conf             8888997789978999999999998780799999845999999973650----488742577514888765178851527


Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCC
Q ss_conf             78888999997211322133445432024332332110013434443322123444555553000012221011256677
Q gi|254780610|r  164 AHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNF  243 (340)
Q Consensus       164 a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~  243 (340)
                      +++.|+++|.    ++.|.|+|+|+|.|.++. .+.++.|+.........+.+    .+.|++|.|+|++++..     .
T Consensus        78 a~~~l~~~f~----~~~v~K~Y~a~~~g~~~~-~~~~~~~~~~~~~~~~~~~~----~~~gk~a~T~~~~l~~~-----~  143 (250)
T d1v9fa_          78 AQTRLVESLQ----RREITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMAV----HPMGKPAVTHYRIMEHF-----R  143 (250)
T ss_dssp             HHHHHHHHHH----TTCSEEEEEEEEESCCCC-CEEEECCEEECSSCTTCEEE----CTTSBCCEEEEEEEEEC-----S
T ss_pred             HHHHHHHHHC----CCEEEEEEEEEECCCCCC-CCCCCCCCCCCCCCCCEEEE----CCCCEECCCCCHHHHCC-----C
T ss_conf             8886323304----545767744321135464-56623553357766630687----78983444101134405-----6


Q ss_pred             CCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEE
Q ss_conf             50012344311589999999987097860415447755444334570135544079804432100042468897689998
Q gi|254780610|r  244 AVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQ  323 (340)
Q Consensus       244 ~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~  323 (340)
                      .+||++|+|+||||||||+||+++||||+||.+||+....... ..........+++||+|||++|+|.||.||+.++|+
T Consensus       144 ~~slv~~~~~TGR~HQIRvHla~lG~PIlGD~~YG~~~~~~~~-~~~~~~~~~~~~~r~~LHA~~L~f~hP~t~~~~~~~  222 (250)
T d1v9fa_         144 VHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG-ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWH  222 (250)
T ss_dssp             SEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT-CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEE
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCCCCCCC-CCHHHHHHHHCCCHHHHHCCCCCCCCCCCCCEEEEE
T ss_conf             7426887863663279999999859830011157621135444-558788877425264564071153268999869998


Q ss_pred             CCCCHHHHHHHHHHHC
Q ss_conf             4997899999998851
Q gi|254780610|r  324 VPIPEDMLTVIRKLNE  339 (340)
Q Consensus       324 aplP~~~~~~l~~L~~  339 (340)
                      ||+|+||.++|+.|+.
T Consensus       223 aplP~df~~~l~~L~~  238 (250)
T d1v9fa_         223 APIPQDMVELIEVMRA  238 (250)
T ss_dssp             CCCCHHHHHHHHHHHH
T ss_pred             ECCCHHHHHHHHHHHH
T ss_conf             0790999999999751



>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} 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
>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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 340 RNA-pseudouridylate synthase protein, ribosomal la
1v9k_A_228 (A:) Ribosomal large subunit pseudouridine synthas 7e-46
2i82_A_217 (A:) Ribosomal large subunit pseudouridine synthas 8e-40
2gml_A_237 (A:) Ribosomal large subunit pseudouridine synthas 9e-36
3dh3_A_64-290227 (A:64-290) Ribosomal large subunit pseudouridine s 7e-34
1vio_A_58-243186 (A:58-243) Ribosomal small subunit pseudouridine s 1e-29
1ksk_A_59-234176 (A:59-234) Ribosomal small subunit pseudouridine s 4e-27
1v9f_A_325 (A:) Ribosomal large subunit pseudouridine synthas 1e-41
2oml_A_189 (A:) Ribosomal large subunit pseudouridine synthas 2e-31
2olw_A_1-102_201-217119 (A:1-102,A:201-217) Ribosomal large subunit pseudo 1e-19
1dm9_A_133 (A:) Hypothetical 15.5 KD protein in MRCA-PCKA int 4e-17
2olw_A_103-20098 (A:103-200) Ribosomal large subunit pseudouridine 7e-18
2k6p_A_92 (A:) Uncharacterized protein HP_1423; alpha-L moti 9e-16
1ksk_A_1-5858 (A:1-58) Ribosomal small subunit pseudouridine syn 1e-05
1p9k_A_79 (A:) ORF, hypothetical protein; alfal motif, RNA-b 4e-05
1vio_A_1-5757 (A:1-57) Ribosomal small subunit pseudouridine syn 1e-04
3dh3_A_1-6363 (A:1-63) Ribosomal large subunit pseudouridine syn 2e-04
>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 =  179 bits (453), Expect = 7e-46
 Identities = 73/251 (29%), Positives = 104/251 (41%), Gaps = 25/251 (9%)

Query: 90  LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149
             I YEDD I+V+NKP+G  VH   G   G +                      +VHRLD
Sbjct: 2   DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEAR--------FLELVHRLD 53

Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209
           +DT+GV++VAK   A + L EQ  + G        Y A+V G        + APL +   
Sbjct: 54  RDTSGVLLVAKKRSALRSLHEQLREKGXQKD----YLALVRGQWQSHVKSVQAPLLKNIL 109

Query: 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGN 269
               R V     +    + T ++  E Y   +       +C   TGRTHQIRVH  + G+
Sbjct: 110 QSGERIV--RVSQEGKPSETRFKVEERYAFATLV-----RCSPVTGRTHQIRVHTQYAGH 162

Query: 270 PLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED 329
           P+  D  YG     +          A   L R  LHA +L F+HP   +    + P  E 
Sbjct: 163 PIAFDDRYGDREFDRQL------TEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEG 216

Query: 330 MLTVIRKLNEK 340
           +   ++K    
Sbjct: 217 LKRCLQKXRNA 227


>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
>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
>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
>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
>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
>2k6p_A (A:) Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}Length = 92 Back     alignment and structure
>1ksk_A (A:1-58) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli}Length = 58 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}Length = 79 Back     alignment and structure
>1vio_A (A:1-57) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae}Length = 57 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
Target340 RNA-pseudouridylate synthase protein, ribosomal large s
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
2olw_A_1-102_201-217119 Ribosomal large subunit pseudouridine synthase E; 99.89
1dm9_A_133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 99.88
2olw_A_103-20098 Ribosomal large subunit pseudouridine synthase E; 99.81
2k6p_A_92 Uncharacterized protein HP_1423; alpha-L motif, RN 99.79
3kbg_A_1-8181 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 95.03
3dh3_A_1-6363 Ribosomal large subunit pseudouridine synthase F; 99.03
1p9k_A_79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.92
1ksk_A_1-5858 Ribosomal small subunit pseudouridine synthase A; 98.86
1vio_A_1-5757 Ribosomal small subunit pseudouridine synthase A; 98.82
2vqe_D_100-19394 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.42
3hp7_A_1-6565 Hemolysin, putative; structural genomics, APC64019 98.36
1h3f_A_350-43283 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 98.15
3i1m_D_97-19094 30S ribosomal protein S4; ribosome structure, prot 98.14
3bbn_D_82-201120 Ribosomal protein S4; small ribosomal subunit, spi 98.1
1s1h_D_81-17999 40S ribosomal protein S9-A; 80S ribosome, 40S ribo 97.98
2cqj_A_71 BRMS2, U3 small nucleolar ribonucleoprotein protei 97.8
2jan_A_345-43288 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 96.76
1jil_A_247-420174 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; 94.27
2ts1_A_246-419174 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 93.09
2aus_C_31-245215 Pseudouridine synthase; isomerase, structural prot 96.94
2apo_A_51-266216 Probable tRNA pseudouridine synthase B; protein-pr 96.87
1sgv_A_1-60_206-23287 TRNA pseudouridine synthase B; hinged motion, tRNA 94.64
1k8w_A_1-79_225-253108 TRNA pseudouridine synthase B; protein-RNA complex 94.41
1r3e_A_1-57_190-22492 TRNA pseudouridine synthase B; RNA modification, p 94.13
1c05_A_77-15983 Ribosomal protein S4 delta 41; two subdomains, uni 92.86
>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=463.50  Aligned_cols=311  Identities=38%  Similarity=0.580  Sum_probs=256.2

Q ss_pred             CCEEE-EEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHH
Q ss_conf             62499-99571136875789999871768898999999985990499899328675804898899970560111102332
Q gi|254780610|r    9 SSIKI-SLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQEN   87 (340)
Q Consensus         9 ~~~~~-~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~   87 (340)
                      +-|++ ++|+++++|+|||+||++.++ ++||+.++++|++|.|+|||+++..+++.+..++.+.............+..
T Consensus         2 ~~~~~~~~v~~~~~g~rl~~~L~~~~~-~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (325)
T 1v9f_A            2 QRVQLTATVSENQLGQRLDQALAEMFP-DYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQD   80 (325)
T ss_dssp             ---------------------------------------------------------------------------CCCCC
T ss_pred             CEEEEEEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCC
T ss_conf             748999998976488669999998668-6799999999986998999999178320625898997325433222333344


Q ss_pred             HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             22221014402789962401110456787542100222222102443344443643244443323240572120357888
Q gi|254780610|r   88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQK  167 (340)
Q Consensus        88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~  167 (340)
                      .++.|||||++++|+|||+|++|||+++...+|+...+.......    .....+++|||||++|||+||+|||..+++.
T Consensus        81 ~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~  156 (325)
T 1v9f_A           81 IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTR  156 (325)
T ss_dssp             CCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG----GGSGGGGBCCCCCTTCEEEEEEESSHHHHHH
T ss_pred             CCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCC----CCCCCEEEEECCCCCCCCCEEEECCHHHHHH
T ss_conf             541125101105787078886548987778886323211344433----3334214653258898651466402588999


Q ss_pred             HHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCE
Q ss_conf             89999972113221334454320243323321100134344433221234445555530000122210112566775001
Q gi|254780610|r  168 LSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSL  247 (340)
Q Consensus       168 l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~sl  247 (340)
                      |.++|.    .+.+.|+|+|+|.|.+..+.+.+..+........     .......+++|.|+|.+...     ...+|+
T Consensus       157 l~~~~~----~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~a~~~~~~~~~-----~~~~sl  222 (325)
T 1v9f_A          157 LVESLQ----RREITREYEAVAIGHMTAGGTVDEPISRHPTKRT-----HMAVHPMGKPAVTHYRIMEH-----FRVHTR  222 (325)
T ss_dssp             HHHHHH----TTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT-----CEEECTTSBCCEEEEEEEEE-----CSSEEE
T ss_pred             HHHHHH----CCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC-----EEEECCCCCEEEEEEEEEEE-----CCCCEE
T ss_conf             998750----1210124234301354745662355335766653-----05876887157899898653-----388457


Q ss_pred             EEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCC
Q ss_conf             23443115899999999870978604154477554443345701355440798044321000424688976899984997
Q gi|254780610|r  248 LKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIP  327 (340)
Q Consensus       248 v~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP  327 (340)
                      ++|+|.|||+||||+|||++|||||||.+||........ .............+++|||+.|+|.||.+++.++|+||+|
T Consensus       223 ~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~-l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P  301 (325)
T 1v9f_A          223 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG-ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP  301 (325)
T ss_dssp             EEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT-CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC
T ss_pred             EEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH
T ss_conf             999977883179999999839976687778985545443-3166777651586434653705857789998899991797


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             899999998851
Q gi|254780610|r  328 EDMLTVIRKLNE  339 (340)
Q Consensus       328 ~~~~~~l~~L~~  339 (340)
                      ++|..+|++|+.
T Consensus       302 ~~f~~~l~~l~~  313 (325)
T 1v9f_A          302 QDMVELIEVMRA  313 (325)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999730



>1v9k_A (A:) Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} Back     alignment and structure