254780406

254780406

putative ribosomal large subunit pseudouridine synthase B

GeneID in NCBI database:8209391Locus tag:CLIBASIA_01455
Protein GI in NCBI database:254780406Protein Accession:YP_003064819.1
Gene range:-(306801, 307865)Protein Length:354aa
Gene description:putative ribosomal large subunit pseudouridine synthase B
COG prediction:[J] 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases
KEGG prediction:putative ribosomal large subunit pseudouridine synthase B; K06178 ribosomal large subunit pseudouridine synthase B [EC:5.4.99.12]
SEED prediction:Ribosomal large subunit pseudouridine synthase B (EC 4.2.1.70)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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
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-------350----
MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK
cccccccccccccccHHHHHHHcccccHHHHHHHHHcccEEEccEEEcccccccccccEEEEccccccccccccEEEEEccccEEEcccccccccHHHHHHHHHcccEEEcccccccccEEEEEEccHHHHHHHHccHHcccEEEEEEEEccccHHHHHHHHHccEEcccccccEEEEEEcccccEEEEEEEEEEccHHHHHHHHHHcccEEEEEEEEEEccEEccccccccEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccHHHHHHHHHHHHccccHHHHHHHHHcccEEEccEEEEcccEEEccccEEEEcccEcccccccEEEEEEccccEEEEccccccccEEEcccccccccEEEEcEEcccccEEEEEEcccHHHHHccccccccEEEEEEEEEccccHHHHHHHHcccEEcccccccEEEEEEEcccccEEEEEEEEccccHHHHHHHHHHcccEEEEEEEEEccccccccccccEEEccHHHHHHHHcccccHcccccccccHccccccccccccHHccccccHHHHccccccccccccccccccccHHccccccEEEcccccccEccccccHHHccccccccccccccccccccc
mkdknivqenftpqRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNvmstdhievdgvplrkaERTRLWlyhkpiglvtthsdpdgrstvfdnlpSIFSRVISVgrldintegLLLLTNDgglarvlelpstqwlRVYRVRFHGQVDQDKLNLLKKGIVIQGIcygdmqvtldtqkgsnaWVTVGLREGKNREIKKVFEFFNWKVNRLIRisygpfqlgtllagstREVSKKILREQLGPHLLEEAqvnldapiyssetlvrdrpniisevpddftrmkknssqknglskqkklatpvhrrnlasnvWMAKGIhssflsdsgqreenhrrspsfpskrslrrtsakk
mkdknivqenftpqrvskVIARAGIASRREVERMIAQQRVKVNGILLERAavnvmstdhievdgvplrKAERTRLWLYHKPIglvtthsdpdgrSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGlregknreiKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIyssetlvrdrpniisevpddftrmkknssqknglskqkklatpvHRRNLASNVWMAKGIHSsflsdsgqreenhrrspsfpskrslrrtsakk
MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK
******************VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL*************************************************************************************************************
MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK****************TPVHRRNLASNVWMAKGIHSSF******************************
*********NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH**********************************************************************************************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK
MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK
MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target354 putative ribosomal large subunit pseudouridine synthase
315122182393 putative ribosomal large subunit pseudouridine synthase 1 1e-139
307320038 573 RNA-binding S4 domain protein [Sinorhizobium meliloti A 1 2e-96
116250666 701 ribosomal large subunit pseudouridine synthase B [Rhizo 1 2e-96
150395641 576 pseudouridine synthase [Sinorhizobium medicae WSM419] L 1 3e-96
15964554 573 hypothetical protein SMc00904 [Sinorhizobium meliloti 1 1 3e-96
227820997 607 pseudouridylate synthase, subunit B protein [Sinorhizob 1 5e-96
222085015 680 pseudouridylate synthase [Agrobacterium radiobacter K84 1 7e-96
15888032 669 ribosomal large subunit pseudouridine synthase B [Agrob 1 8e-96
209548084 689 RNA-binding S4 domain protein [Rhizobium leguminosarum 1 2e-95
241203270 698 RNA-binding S4 domain protein [Rhizobium leguminosarum 1 2e-95
>gi|315122182|ref|YP_004062671.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 393 Back     alignment and organism information
 Score =  498 bits (1281), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 248/361 (68%), Positives = 295/361 (81%), Gaps = 15/361 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +KD  IV E+  P+RVSKVIARAGIASRREVERMI Q+RVKVNG+ LERAAVNV+STD I
Sbjct: 8   LKDGQIVPEDLMPERVSKVIARAGIASRREVERMITQKRVKVNGVCLERAAVNVISTDCI 67

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EVD VPLRKAERTRLWLYHKP+GLVTTHSDP GRSTVFDN+PSI SRV+SVGRLDINTEG
Sbjct: 68  EVDDVPLRKAERTRLWLYHKPVGLVTTHSDPTGRSTVFDNVPSIVSRVVSVGRLDINTEG 127

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDGGLAR+LELPSTQWLRVYRVR +GQ+DQ+KL+LLK+GIVI+GI Y  MQVT+D
Sbjct: 128 LLLLTNDGGLARILELPSTQWLRVYRVRAYGQIDQEKLDLLKEGIVIKGIHYRGMQVTID 187

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +QKG+N W+TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG LL G TREV+KK+
Sbjct: 188 SQKGANVWLTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGELLEGDTREVAKKV 247

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LREQLG +LL+EA+VNL+  +YSSET +RD   +  +  DD ++ K   S+ +G +K+K 
Sbjct: 248 LREQLGANLLKEARVNLEGLVYSSETPIRDHSKMKVK-SDDISKTKNKKSKVHGFNKKKH 306

Query: 301 LATPVHRRNLASNVWMAKGIHSSF------------LSDSG--QREENHRRSPSFPSKRS 346
           +  P+ RRN +SNVWMA+GIHSS             + D+G  +R+ +H+R+     K  
Sbjct: 307 VDFPIQRRNRSSNVWMAQGIHSSLPYEKQGEKDYQSMHDTGFKKRKYSHKRNKKLHKKSP 366

Query: 347 L 347
           L
Sbjct: 367 L 367


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|307320038|ref|ZP_07599459.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83] Length = 573 Back     alignment and organism information
>gi|116250666|ref|YP_766504.1| ribosomal large subunit pseudouridine synthase B [Rhizobium leguminosarum bv. viciae 3841] Length = 701 Back     alignment and organism information
>gi|150395641|ref|YP_001326108.1| pseudouridine synthase [Sinorhizobium medicae WSM419] Length = 576 Back     alignment and organism information
>gi|15964554|ref|NP_384907.1| hypothetical protein SMc00904 [Sinorhizobium meliloti 1021] Length = 573 Back     alignment and organism information
>gi|227820997|ref|YP_002824967.1| pseudouridylate synthase, subunit B protein [Sinorhizobium fredii NGR234] Length = 607 Back     alignment and organism information
>gi|222085015|ref|YP_002543544.1| pseudouridylate synthase [Agrobacterium radiobacter K84] Length = 680 Back     alignment and organism information
>gi|15888032|ref|NP_353713.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium tumefaciens str. C58] Length = 669 Back     alignment and organism information
>gi|209548084|ref|YP_002280001.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 689 Back     alignment and organism information
>gi|241203270|ref|YP_002974366.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 698 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
Target354 putative ribosomal large subunit pseudouridine synthase
cd02556167 cd02556, PseudoU_synth_RluB, PseudoU_synth_RluB: Pseudo 6e-52
cd02870146 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthas 1e-29
cd02553167 cd02553, PseudoU_synth_RsuA, PseudoU_synth_RsuA: Pseudo 4e-24
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_ 1e-15
cd02566168 cd02566, PseudoU_synth_RluE, PseudoU_synth_RluE: Pseudo 2e-15
cd02554164 cd02554, PseudoU_synth_RluF, PseudoU_synth_RluF_like: P 1e-14
PRK11394217 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; 3e-14
cd02555177 cd02555, PSSA_1, PSSA_1: Pseudouridine synthase, a subg 3e-11
PRK10700289 PRK10700, PRK10700, 23S rRNA pseudouridylate synthase B 3e-41
PRK10475290 PRK10475, PRK10475, 23S rRNA pseudouridine synthase F; 2e-13
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate syn 3e-58
TIGR00093128 TIGR00093, TIGR00093, pseudouridine synthase 2e-23
PRK10839232 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A 7e-12
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA-speci 8e-06
pfam00849151 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthas 9e-07
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain 2e-05
smart0036360 smart00363, S4, S4 RNA-binding domain 4e-05
pfam0147948 pfam01479, S4, S4 domain 0.002
>gnl|CDD|30013 cd02556, PseudoU_synth_RluB, PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like 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|30010 cd02553, PseudoU_synth_RsuA, PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA 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|30017 cd02566, PseudoU_synth_RluE, PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>gnl|CDD|30011 cd02554, PseudoU_synth_RluF, PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>gnl|CDD|30012 cd02555, PSSA_1, PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>gnl|CDD|182659 PRK10700, PRK10700, 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>gnl|CDD|182487 PRK10475, PRK10475, 23S rRNA pseudouridine synthase F; Provisional 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|161704 TIGR00093, TIGR00093, pseudouridine synthase Back     alignment and domain information
>gnl|CDD|182770 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A; 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|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase 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|128657 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information
>gnl|CDD|144902 pfam01479, S4, S4 domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 354 putative ribosomal large subunit pseudouridine synthase
PRK10700291 23S rRNA pseudouridylate synthase B; Provisional 100.0
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 100.0
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase and 100.0
PRK10839231 16S rRNA pseudouridylate synthase A; Provisional 100.0
PRK11394207 23S rRNA pseudouridine synthase E; Provisional 100.0
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine sy 100.0
TIGR00093185 TIGR00093 conserved hypothetical protein; InterPro: IPR 100.0
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine sy 100.0
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of th 100.0
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridi 100.0
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine sy 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases are res 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseud 99.97
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudou 99.77
PRK11112257 tRNA pseudouridine synthase C; Provisional 99.76
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisional 99.75
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseu 99.73
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseud 99.67
TIGR01621222 RluA-like pseudouridine synthase Rlu family protein, TI 99.37
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewed 98.18
PRK04099272 truB tRNA pseudouridine synthase B; Provisional 98.13
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: P 98.07
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 98.07
PRK00989235 truB tRNA pseudouridine synthase B; Provisional 98.01
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 97.97
PRK01851310 truB tRNA pseudouridine synthase B; Provisional 97.97
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: P 97.95
PRK05033314 truB tRNA pseudouridine synthase B; Provisional 97.93
PRK00130289 truB tRNA pseudouridine synthase B; Provisional 97.92
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 97.88
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridin 97.85
PRK01528293 truB tRNA pseudouridine synthase B; Provisional 97.8
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 97.79
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridi 97.78
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 97.64
PRK02484293 truB tRNA pseudouridine synthase B; Provisional 97.58
PRK01550307 truB tRNA pseudouridine synthase B; Provisional 97.56
PRK02755291 truB tRNA pseudouridine synthase B; Provisional 97.56
COG0130271 TruB Pseudouridine synthase [Translation, ribosomal str 96.9
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridin 96.83
TIGR00425326 CBF5 rRNA pseudouridine synthase, putative; InterPro: I 96.2
TIGR00005337 rluA_subfam pseudouridine synthase, RluA family; InterP 99.97
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisional 99.97
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [Trans 99.97
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 99.96
KOG1919371 consensus 99.73
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of th 99.9
pfam00849151 PseudoU_synth_2 RNA pseudouridylate synthase. Members o 99.8
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthases ca 97.05
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The doma 99.07
smart0036360 S4 S4 RNA-binding domain. 99.01
pfam0147948 S4 S4 domain. The S4 domain is a small domain consistin 98.85
COG1188100 Ribosome-associated heat shock protein implicated in th 98.48
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members of t 98.46
COG1189245 Predicted rRNA methylase [Translation, ribosomal struct 98.45
TIGR01017217 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Rib 98.36
COG0522205 RpsD Ribosomal protein S4 and related proteins [Transla 98.29
COG2302257 Uncharacterized conserved protein, contains S4-like dom 98.22
PRK12565197 30S ribosomal protein S4; Provisional 98.16
PRK10348133 ribosome-associated heat shock protein Hsp15; Provision 98.14
CHL00113201 rps4 ribosomal protein S4; Reviewed 98.09
TIGR00478240 tly hemolysin A; InterPro: IPR004538 Hemolysins are exo 98.03
PRK05327201 rpsD 30S ribosomal protein S4; Validated 98.0
PRK1150770 hypothetical protein; Provisional 97.81
PRK13354405 tyrosyl-tRNA synthetase; Provisional 97.53
COG250173 S4-like RNA binding protein [Replication, recombination 97.37
PRK05912402 tyrosyl-tRNA synthetase; Validated 97.36
PRK04051177 rps4p 30S ribosomal protein S4; Validated 97.03
TIGR0298860 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014 96.92
PTZ00155188 40S ribosomal protein S9; Provisional 96.72
TIGR01018170 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Rib 95.66
PRK04313237 30S ribosomal protein S4e; Validated 94.94
PTZ00223273 40S ribosomal protein S4; Provisional 94.84
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosomal str 93.9
PTZ00118262 40S ribosomal protein S4; Provisional 95.95
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional 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
>PRK11394 23S rRNA pseudouridine synthase E; Provisional 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
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA 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
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE 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
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>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
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family 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
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PRK04099 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
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 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
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 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
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 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
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative; InterPro: IPR004802 This family contains the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase 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
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional 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
>pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase 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
>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
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] 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
>COG0522 RpsD Ribosomal protein S4 and related proteins [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
>PRK12565 30S ribosomal protein S4; Provisional Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed 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
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>PRK11507 hypothetical protein; Provisional Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4; Validated 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
>PTZ00155 40S ribosomal protein S9; Provisional 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
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; 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
Target354 putative ribosomal large subunit pseudouridine synthase
3dh3_A290 Crystal Structure Of Rluf In Complex With A 22 Nucl 5e-43
1ksk_A234 Structure Of Rsua Length = 234 7e-40
1vio_A243 Crystal Structure Of Pseudouridylate Synthase Lengt 8e-38
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 3e-08
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 1e-06
2oml_A189 Crystal Structure Of E. Coli Pseudouridine Synthase 5e-17
2olw_A217 Crystal Structure Of E. Coli Pseudouridine Synthase 1e-16
2gml_A237 Crystal Structure Of Catalytic Domain Of E.Coli Rlu 5e-17
1fjg_D209 Structure Of The Thermus Thermophilus 30s Ribosomal 2e-05
1fka_D209 Structure Of Functionally Activated Small Ribosomal 2e-05
1i94_D208 Crystal Structures Of The Small Ribosomal Subunit W 2e-05
1qd7_C159 Partial Model For 30s Ribosomal Subunit Length = 15 0.002
1vs5_D206 Crystal Structure Of The Bacterial Ribosome From Es 0.003
1p6g_D205 Real Space Refined Coordinates Of The 30s Subunit F 0.003
2gy9_D204 Structure Of The 30s Subunit Of A Pre-Translocation 0.003
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
 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 117/292 (40%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|20664188|pdb|1KSK|A Chain A, Structure Of Rsua Length = 234 Back     alignment and structure
>gi|40890007|pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase Length = 243 Back     alignment and structure
>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
>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|145580106|pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue Length = 189 Back     alignment and structure
gi|145580080|pdb|2OLW|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue Length = 217 Back     alignment and structure
>gi|112490799|pdb|2GML|A Chain A, Crystal Structure Of Catalytic Domain Of E.Coli Rluf Length = 237 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|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|6137687|pdb|1QD7|C Chain C, Partial Model For 30s Ribosomal Subunit Length = 159 Back     alignment and structure
gi|116666551|pdb|1VS5|D Chain D, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 206 Back     alignment and structure
>gi|33357881|pdb|1P6G|D Chain D, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 205 Back     alignment and structure
>gi|116667413|pdb|2GY9|D Chain D, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 204 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target354 putative ribosomal large subunit pseudouridine synthase
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; RSUA, 2e-40
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; prote 3e-39
1vio_A243 Ribosomal small subunit pseudouridine synthase A; struc 6e-27
2gml_A237 Ribosomal large subunit pseudouridine synthase F; RLUF, 1e-29
2olw_A217 Ribosomal large subunit pseudouridine synthase E; bifur 3e-29
2oml_A189 Ribosomal large subunit pseudouridine synthase E; bifur 8e-28
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 1e-07
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; RNA b 4e-06
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 0.001
>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
 Score =  161 bits (409), Expect = 2e-40
 Identities = 58/226 (25%), Positives = 100/226 (44%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 5   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 65  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +              +  +   V + + 
Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPA--VLEVITPTQVRLTIS 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   L  G  R ++++
Sbjct: 183 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 228


>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
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Length = 237 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
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189 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 Length = 79 Back     alignment and structure
>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
>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
Target354 putative ribosomal large subunit pseudouridine synthase
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; prote 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; RSUA, 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; struc 100.0
2gml_A237 Ribosomal large subunit pseudouridine synthase F; RLUF, 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; bifur 100.0
2oml_A189 Ribosomal large subunit pseudouridine synthase E; bifur 100.0
2aus_C334 Pseudouridine synthase; isomerase, structural protein, 98.27
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, pseudo 98.05
2apo_A357 Probable tRNA pseudouridine synthase B; protein-protein 98.04
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex, T s 98.04
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA modi 97.82
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; RNA b 99.97
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; pseud 99.74
2i82_A217 Ribosomal large subunit pseudouridine synthase A; lyase 99.71
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 99.4
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 98.82
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 98.77
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-binding, m 98.35
3hp7_A291 Hemolysin, putative; structural genomics, APC64019, PSI 98.35
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, unique t 98.26
3ofo_D205 30S ribosomal protein S4; protein biosynthesis, ribosom 98.09
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spinach 98.07
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protein IMP 97.86
3jyv_D158 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 97.55
1s1h_D179 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal 97.42
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacy 96.92
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NE 95.9
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthet 97.15
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; trunc 96.38
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Ge 96.34
>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
Probab=100.00  E-value=0  Score=459.78  Aligned_cols=231  Identities=27%  Similarity=0.402  Sum_probs=210.9

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCC--CEEEEECCCCCEEEECC
Q ss_conf             7734478899988687789999999869869999992406878079997999998922556--43896027875156314
Q gi|254780406|r   11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--RTRLWLYHKPIGLVTTH   88 (354)
Q Consensus        11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~--~~~~~~~~KP~g~~~~~   88 (354)
                      ++++|||||||++|+||||+|++||++|+|+|||++|+ ++++|.++|.|.|||+++.+.+  ...||++|||.+++|+.
T Consensus         4 ~~~iRL~K~La~~g~~SRr~ae~lI~~GrV~VNGkvv~-~~~kV~~~D~I~vdg~~~~~~~~~~~~~i~~~kp~~~~~~~   82 (290)
T 3dh3_A            4 DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTT   82 (290)
T ss_dssp             CCCEEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEEECCCCGGGCCEEEEEECTTCBCCC
T ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHCCEEEECCEECC-CCCCCCCCCEEEECCEECCCCCCCCEEEEEECCCCCEECCC
T ss_conf             88725999998778842999999997796998999957-98897999989999998444356525999707987423354


Q ss_pred             CCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43333644210110234320026655433232022236764100012344574047752112455646788874000008
Q gi|254780406|r   89 SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ  168 (354)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~  168 (354)
                      .+.. ..+++++ .....+|++|||||+||||||||||||+|+++|+||+++|+++|+|+|.++++++.+..|..|+.++
T Consensus        83 ~~~~-~~~~~~l-~~~~~rl~~VGRLD~dTsGLLLlTnDg~l~~~L~~p~~~i~k~Y~v~v~g~i~~~~l~~l~~Gv~~~  160 (290)
T 3dh3_A           83 EDGE-RDNIVDF-VNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL  160 (290)
T ss_dssp             CSSC-TTBHHHH-HTCSSCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGCCCEEEEEEESSCCCHHHHHHHHTCCBCS
T ss_pred             CCCC-CCCHHHH-CCCCCCEEECCCCCCCCCCEEEEECCCHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHCCCEEE
T ss_conf             5677-7754441-1355523561346888875499955958999986022267626899993679999999997387531


Q ss_pred             CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHH
Q ss_conf             76750343036402688079999995184289999999839868688975870545187554748867999998753210
Q gi|254780406|r  169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH  248 (354)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~~~~  248 (354)
                      ++.+.++.+..    ..++|++|+|.||+|||||+||+++||+|++|+||+||+|+|++|++|+||+|+++||.+|+...
T Consensus       161 ~~~~~~~~~~~----~~~~~l~i~l~eGr~rqIRr~~~~iG~~V~~L~R~~~G~~~l~~L~~G~~r~l~~~ei~~l~~~~  236 (290)
T 3dh3_A          161 GTVTKKCKVKK----EAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLI  236 (290)
T ss_dssp             SSBCCCCEEEE----CSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTC
T ss_pred             EEEEEEEEEEE----CCCCEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHH
T ss_conf             15732124552----36715899925886799999999869979798999989987389899774899999999999876



>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {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
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} 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
>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
>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
>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
>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
>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
>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
>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
>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
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} 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
>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
>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
>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
>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Back     alignment and structure
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_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 354 putative ribosomal large subunit pseudouridine synthase
d1kska4172 d.265.1.3 (A:60-231) Ribosomal small subunit pseudourid 7e-28
d1vioa1174 d.265.1.3 (A:58-231) Ribosomal small subunit pseudourid 7e-25
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-termina 2e-09
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-termina 3e-09
d1p9ka_79 d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia co 4e-06
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Length = 172 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 small subunit pseudouridine 516 synthase RsuA
species: Escherichia coli [TaxId: 562]
 Score =  118 bits (296), Expect = 7e-28
 Identities = 41/167 (24%), Positives = 74/167 (44%), Gaps = 3/167 (1%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 2   RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   +T  +
Sbjct: 62  ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLT--I 119

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            EG+  ++K++F      V  L R   G   L   L  G  R ++++
Sbjct: 120 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 166


>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
>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
>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
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Length = 79 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target354 putative ribosomal large subunit pseudouridine synthase
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase RsuA 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase RsuA 100.0
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, RluD 99.73
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcus fur 98.25
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritima [Ta 98.2
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanococcus 98.09
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [TaxId 98.07
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tuberculo 97.67
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, RluC 99.74
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Escheric 99.51
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Haemophi 99.47
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId: 562 99.4
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 562] 98.74
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 274] 98.34
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562]} 98.19
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus [TaxI 98.11
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {The 97.63
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bac 97.51
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {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 small subunit pseudouridine 516 synthase RsuA
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=310.78  Aligned_cols=171  Identities=24%  Similarity=0.402  Sum_probs=150.0

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      ++||++|||+|++||..|+.++.++.........++++|||||+||||||||||||+|+++|+||.++++++|.|+|+++
T Consensus         1 p~yi~lNKP~G~l~s~~~~~~~~~~~~l~~~~~~~l~~vgRLD~~tsGLlL~tndg~~~~~l~~~~~~i~k~Y~v~v~~~   80 (172)
T d1kska4           1 PRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP   80 (172)
T ss_dssp             CCEEEEEECTTCBSSSSCSSSCBGGGGCCCTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSC
T ss_pred             CEEEEEECCCCEEECCCCCCCCCEEEECCCCCCCCEEEEECCCCCCCCCEEEECCCCEEEEECCCCCCCCEEEEEEEECC
T ss_conf             98999989997897973989993788657523676789613786003639990456415431122324627999998226


Q ss_pred             CCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCC
Q ss_conf             5646788874000008767503430364026880799999951842899999998398686889758705451-875547
Q gi|254780406|r  153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG  231 (354)
Q Consensus       153 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G  231 (354)
                      ++.+.+.+++.|+.+++.......+.+...  ..+|++|+|.||||||||+||+++|++|.+|+||+||+|+| ++|++|
T Consensus        81 i~~~~~~~l~~gv~i~~~~~~~~~~~v~~~--~~~~l~i~l~~Gr~~qIR~~~~~lg~~V~~L~Rv~~G~~~L~~~L~~G  158 (172)
T d1kska4          81 VADDTAEQFAKGVQLHNEKDLTKPAVLEVI--TPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPG  158 (172)
T ss_dssp             CCTTHHHHHHHCCCCTTCSSCCCCCEEEEE--ETTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTT
T ss_pred             CCHHHHHHHHCCEEECCCCCCCCCEEEEEC--CCCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCC
T ss_conf             897898886365577685111152588514--675999999448538999999975988949999998368048988998


Q ss_pred             CEEECCHHHHHHHH
Q ss_conf             48867999998753
Q gi|254780406|r  232 STREVSKKILREQL  245 (354)
Q Consensus       232 ~~r~l~~~e~~~l~  245 (354)
                      +||+|+++||..|+
T Consensus       159 ~~r~L~~~Ei~~l~  172 (172)
T d1kska4         159 EYRPLTEEEIASVV  172 (172)
T ss_dssp             CEEECCHHHHTTCC
T ss_pred             CEEECCHHHHHHHC
T ss_conf             75899999999659



>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {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
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {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
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {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
>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
>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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 354 putative ribosomal large subunit pseudouridine syn
3dh3_A_64-290227 (A:64-290) Ribosomal large subunit pseudouridine s 1e-22
2gml_A_237 (A:) Ribosomal large subunit pseudouridine synthas 4e-22
1v9k_A_228 (A:) Ribosomal large subunit pseudouridine synthas 5e-20
1ksk_A_59-234176 (A:59-234) Ribosomal small subunit pseudouridine s 2e-22
1vio_A_58-243186 (A:58-243) Ribosomal small subunit pseudouridine s 3e-20
2oml_A_189 (A:) Ribosomal large subunit pseudouridine synthas 1e-16
2i82_A_217 (A:) Ribosomal large subunit pseudouridine synthas 4e-15
1v9f_A_325 (A:) Ribosomal large subunit pseudouridine synthas 6e-18
2olw_A_1-102_201-217119 (A:1-102,A:201-217) Ribosomal large subunit pseudo 7e-17
1dm9_A_133 (A:) Hypothetical 15.5 KD protein in MRCA-PCKA int 3e-13
1vio_A_1-5757 (A:1-57) Ribosomal small subunit pseudouridine syn 3e-09
1ksk_A_1-5858 (A:1-58) Ribosomal small subunit pseudouridine syn 7e-09
3dh3_A_1-6363 (A:1-63) Ribosomal large subunit pseudouridine syn 3e-08
1p9k_A_79 (A:) ORF, hypothetical protein; alfal motif, RNA-b 4e-07
2jan_A_345-43288 (A:345-432) Tyrosyl-tRNA synthetase; protein biosy 2e-06
3hp7_A_1-6565 (A:1-65) Hemolysin, putative; structural genomics, 6e-05
2olw_A_103-20098 (A:103-200) Ribosomal large subunit pseudouridine 1e-05
>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
 Score =  101 bits (252), Expect = 1e-22
 Identities = 45/234 (19%), Positives = 92/234 (39%), Gaps = 15/234 (6%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE   L   +KP+G+V+  ++   R  + D +     RV  +GRLD +++GL+ LTN G 
Sbjct: 1   AEDLVLIALNKPVGIVS-TTEDGERDNIVDFVNHSK-RVFPIGRLDKDSQGLIFLTNHGD 58

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     + ++ +  +  G+ I G      +     +K +    
Sbjct: 59  LVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCK----VKKEAPFVF 114

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
            + L +G NR+I+++ E F ++V +L R       L  +  G  R+++      L + + 
Sbjct: 115 RITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 174

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
               E        P              + ++     +  + +S     +   +
Sbjct: 175 NSSSEVKPKAKAKPKT------AGIKRPVVKMEKTAEKGGRPASNGKRFTSPGR 222


>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
>1v9k_A (A:) Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli}Length = 228 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
>1vio_A (A:58-243) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae}Length = 186 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
>2i82_A (A:) Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}Length = 217 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: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
>1vio_A (A:1-57) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae}Length = 57 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
>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
>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
>2jan_A (A:345-432) Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}Length = 88 Back     alignment and structure
>3hp7_A (A:1-65) Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311}Length = 65 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

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target354 putative ribosomal large subunit pseudouridine synthase
1v9f_A_325 Ribosomal large subunit pseudouridine synthase D; 100.0
2gml_A_237 Ribosomal large subunit pseudouridine synthase F; 100.0
1ksk_A_59-234176 Ribosomal small subunit pseudouridine synthase A; 100.0
3dh3_A_64-290227 Ribosomal large subunit pseudouridine synthase F; 99.97
2oml_A_189 Ribosomal large subunit pseudouridine synthase E; 99.97
1vio_A_58-243186 Ribosomal small subunit pseudouridine synthase A; 99.97
1v9k_A_228 Ribosomal large subunit pseudouridine synthase C; 99.91
2i82_A_217 Ribosomal large subunit pseudouridine synthase A; 99.88
2aus_C_31-245215 Pseudouridine synthase; isomerase, structural prot 98.24
2apo_A_51-266216 Probable tRNA pseudouridine synthase B; protein-pr 97.93
2olw_A_1-102_201-217119 Ribosomal large subunit pseudouridine synthase E; 99.79
1dm9_A_133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 99.77
2olw_A_103-20098 Ribosomal large subunit pseudouridine synthase E; 99.53
1k8w_A_80-224145 TRNA pseudouridine synthase B; protein-RNA complex 90.68
1vio_A_1-5757 Ribosomal small subunit pseudouridine synthase A; 99.5
1ksk_A_1-5858 Ribosomal small subunit pseudouridine synthase A; 99.49
3dh3_A_1-6363 Ribosomal large subunit pseudouridine synthase F; 99.43
1p9k_A_79 ORF, hypothetical protein; alfal motif, RNA-bindin 99.22
3hp7_A_1-6565 Hemolysin, putative; structural genomics, APC64019 99.17
2k6p_A_92 Uncharacterized protein HP_1423; alpha-L motif, RN 99.06
2vqe_D_100-19394 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.83
2cqj_A_71 BRMS2, U3 small nucleolar ribonucleoprotein protei 98.51
1h3f_A_350-43283 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 98.46
3i1m_D_97-19094 30S ribosomal protein S4; ribosome structure, prot 98.39
2jan_A_345-43288 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 98.35
3bbn_D_82-201120 Ribosomal protein S4; small ribosomal subunit, spi 98.3
1s1h_D_81-17999 40S ribosomal protein S9-A; 80S ribosome, 40S ribo 98.09
1jil_A_247-420174 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; 97.38
2ts1_A_246-419174 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 96.97
3kbg_A_1-8181 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 95.98
1c05_A_77-15983 Ribosomal protein S4 delta 41; two subdomains, uni 91.52
>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=7.8e-41  Score=276.59  Aligned_cols=244  Identities=17%  Similarity=0.103  Sum_probs=203.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE-------------
Q ss_conf             986534466677344788999886-877899999998698699999924068780799979999989-------------
Q gi|254780406|r    1 MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-------------   66 (354)
Q Consensus         1 ~~~~~~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~-------------   66 (354)
                      |+....+.++..++||++||+..+ .|||++++++|++|+|+|||+.+..+...+...+.+.+....             
T Consensus         4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (325)
T 1v9f_A            4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPL   83 (325)
T ss_dssp             ------------------------------------------------------------------------CCCCCCCC
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCCCCC
T ss_conf             89999989764886699999986686799999999986998999999178320625898997325433222333344541


Q ss_pred             CCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC------CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--C
Q ss_conf             2255643896027875156314433336442101102------3432002665543323202223676410001234--4
Q gi|254780406|r   67 LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--S  138 (354)
Q Consensus        67 i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~  138 (354)
                      ...+++..|+++|||.|+.|+..+.....++...+..      ....+++|||||++||||||||++++++++|..+  .
T Consensus        84 ~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~  163 (325)
T 1v9f_A           84 DIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQR  163 (325)
T ss_dssp             CEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHT
T ss_pred             CEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHC
T ss_conf             12510110578707888654898777888632321134443333342146532588986514664025889999987501


Q ss_pred             CCCEEEEEEEECCCCCHHHHHHHHHHHHCC---------CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC
Q ss_conf             574047752112455646788874000008---------76750343036402688079999995184289999999839
Q gi|254780406|r  139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN  209 (354)
Q Consensus       139 ~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~---------~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g  209 (354)
                      ..+.|+|++.|.|.+..+............         .+......+.+.......+++++.+.|||+||||+||+++|
T Consensus       164 ~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~sl~~~~~~TGR~HQIR~hla~~G  243 (325)
T 1v9f_A          164 REITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHIT  243 (325)
T ss_dssp             TCSEEEEEEEEESCCCCCEEEECCEEECSSCTTCEEECTTSBCCEEEEEEEEECSSEEEEEEEESCCCTTHHHHHHHHTT
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHC
T ss_conf             21012423430135474566235533576665305876887157899898653388457999977883179999999839


Q ss_pred             CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHH
Q ss_conf             86868897587054518755474886799999875
Q gi|254780406|r  210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ  244 (354)
Q Consensus       210 ~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l  244 (354)
                      ++|+.+++.++|++.+++|+.|+|++++..+...|
T Consensus       244 ~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~L  278 (325)
T 1v9f_A          244 HPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQAL  278 (325)
T ss_dssp             CCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSE
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHH
T ss_conf             97668777898554544331667776515864346



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