254780180

254780180

S-adenosylmethionine:tRNA ribosyltransferase-isomerase

GeneID in NCBI database:8209160Locus tag:CLIBASIA_00315
Protein GI in NCBI database:254780180Protein Accession:YP_003064593.1
Gene range:-(60341, 61423)Protein Length:360aa
Gene description:S-adenosylmethionine:tRNA ribosyltransferase-isomerase
COG prediction:[J] S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase)
KEGG prediction:queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC:5.-.-.-); K07568 S-adenosylmethionine:tRNA ribosyltransferase-isomerase [EC:5.-.-.-]
SEED prediction:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 5.-.-.-)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Queuosine-Archaeosine Biosynthesis;
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
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
cccccccccccHHHHcccccccccccEEEEEcccccccccccccHHHHHHHHcccccEEEEEccccEEEEEEEEEcccccccccEEEEEEEEEcccccEEEEEccccccccccEEEEccccccccEEEEEEEEccccEEEEEEccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHcccccEEcccccccccHHHHHHHHHcccEEEEEEEEccccccccEEEEccccccccEEEEEccHHHHHHHHHHHHccccEEEEcHHHHHHHHHHHccccEEccccccccEEEcccccEEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEcccEEEEEEcc
cccccccccccHHHHHccccccccccEEEEEcccccccHHHHcccHHHHHHHcccccEEEEccccEEEcEHcccccccccccccEEEEEEEEEcccccEEEEEccccccccccEEEEccccccccEEEEEEEEcccccEEEEEcccccHHHHHHHHHccccccccHHcccccccccHHHccEEEEccccccccccccccccHHHHHHHHHcccEEEEEEEEccccccccEEcccHHcccccHHHHHcHHHHHHHHHHHHHcccEEEEEEccccccHHHHHcccccEccccccccEEEccccEEEEEEEEEccccccHHHHHHHHHHHccHHHHHHHHHHHHHHccEEEEccccEEEEccc
mmvkefdfdlppsrialrpvfprdsarlmvvhpnlscplvisdhlvsdlpaflnsndaivfNNTKVITAQLNGVRFCHINRREKEISCtlhmrvspnswsvyarpskvikkgdilhFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQIslvgtiplppyiarkrpidardyvDYQTTYAKIqgsvaaptaglhFTSNLLSRLISIGIKVYFVTLHvgagtfmpvkvedtddhimhseigfidaptaQALNSvksrggrivsvgTTSLRLLetattedgiinpwsgftnifitpgyrfrAVDIlmsnfhlpkSTLLMLVSAFCGIEETKKMYQHAISHAyrfysygdtsllfqkr
mmvkefdfdlppsrialRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEIsctlhmrvspnswsvyaRPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISlvgtiplppyiarkrpiDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVksrggrivsvgttslrlletattedgiinpwsgfTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCH***REKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQK*
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
****EFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQK*
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MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR
MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQKR

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
315122778359 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-170
325293064374 S-adenosylmethionine tRNA ribosyltransferase [Agrobacte 1 1e-123
222148799352 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-122
327193336366 S-adenosylmethionine: tRNA ribosyltransferase-isomerase 1 1e-122
159184871366 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-121
227822132366 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-120
190891762373 S-adenosylmethionine: tRNA ribosyltransferase-isomerase 1 1e-120
86357735361 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-119
222085994360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-119
241204662361 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1 1e-118
>gi|315122778|ref|YP_004063267.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 359 Back     alignment and organism information
 Score =  602 bits (1553), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 285/359 (79%), Positives = 321/359 (89%)

Query: 1   MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIV 60
           MMVKEFDF LP SRIALRPV PRDSARLMVV+PNLSC  +ISD+ V DLP FLNSNDAIV
Sbjct: 1   MMVKEFDFHLPSSRIALRPVSPRDSARLMVVYPNLSCSQMISDYSVRDLPIFLNSNDAIV 60

Query: 61  FNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQ 120
           FNNTKVI AQL G R    N  E  ISCTLHMR+S NSWS Y RP K+I++GD ++FFSQ
Sbjct: 61  FNNTKVIAAQLRGRRLRRTNDSEHWISCTLHMRISSNSWSAYVRPGKIIRQGDTIYFFSQ 120

Query: 121 DGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDY 180
           DGQS+LEA VI+K +TGEILLVF +SG EL+RQI+L+GT+PLPPYIA+KRPID RDYVDY
Sbjct: 121 DGQSKLEANVIEKRDTGEILLVFPLSGTELDRQIALIGTMPLPPYIAKKRPIDERDYVDY 180

Query: 181 QTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIM 240
           QTTYA IQGSVAAPTAGLHFTS+LLS+L+S+G+ VYF+TLHVGAGTFMPV+VEDTDDHIM
Sbjct: 181 QTTYASIQGSVAAPTAGLHFTSDLLSKLVSMGVAVYFITLHVGAGTFMPVRVEDTDDHIM 240

Query: 241 HSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPG 300
           HSEIGFIDA TAQ LN+VK RGGRIV+VGTTSLRLLETATTEDGII P SG+TNIFITPG
Sbjct: 241 HSEIGFIDAQTAQDLNAVKLRGGRIVAVGTTSLRLLETATTEDGIIMPLSGYTNIFITPG 300

Query: 301 YRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQK 359
           YRFRAVD+L+SNFHLPKSTLLMLVSAFCG+EETK MYQHAI+++YRFYSYGD SL+F+K
Sbjct: 301 YRFRAVDVLLSNFHLPKSTLLMLVSAFCGVEETKTMYQHAIANSYRFYSYGDASLIFKK 359



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325293064|ref|YP_004278928.1| S-adenosylmethionine tRNA ribosyltransferase [Agrobacterium sp. H13-3] Length = 374 Back     alignment and organism information
>gi|222148799|ref|YP_002549756.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Agrobacterium vitis S4] Length = 352 Back     alignment and organism information
>gi|327193336|gb|EGE60240.1| S-adenosylmethionine: tRNA ribosyltransferase-isomerase (Queuosine biosynthesis) protein [Rhizobium etli CNPAF512] Length = 366 Back     alignment and organism information
>gi|159184871|ref|NP_354665.2| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Agrobacterium tumefaciens str. C58] Length = 366 Back     alignment and organism information
>gi|227822132|ref|YP_002826103.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Sinorhizobium fredii NGR234] Length = 366 Back     alignment and organism information
>gi|190891762|ref|YP_001978304.1| S-adenosylmethionine: tRNA ribosyltransferase-isomerase (Queuosine biosynthesis) protein [Rhizobium etli CIAT 652] Length = 373 Back     alignment and organism information
>gi|86357735|ref|YP_469627.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Rhizobium etli CFN 42] Length = 361 Back     alignment and organism information
>gi|222085994|ref|YP_002544526.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Agrobacterium radiobacter K84] Length = 360 Back     alignment and organism information
>gi|241204662|ref|YP_002975758.1| S-adenosylmethionine:tRNA ribosyltransferase-isomerase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 361 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
PRK00147342 PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransf 1e-141
TIGR00113344 TIGR00113, queA, S-adenosylmethionine:tRNA ribosyltrans 2e-91
PRK01424366 PRK01424, PRK01424, S-adenosylmethionine:tRNA ribosyltr 4e-78
COG0809348 COG0809, QueA, S-adenosylmethionine:tRNA-ribosyltransfe 1e-119
pfam02547218 pfam02547, Queuosine_synth, Queuosine biosynthesis prot 5e-69
>gnl|CDD|178900 PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional Back     alignment and domain information
>gnl|CDD|161715 TIGR00113, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase Back     alignment and domain information
>gnl|CDD|134556 PRK01424, PRK01424, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional Back     alignment and domain information
>gnl|CDD|31151 COG0809, QueA, S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|145599 pfam02547, Queuosine_synth, Queuosine biosynthesis protein Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
PRK00147345 queA S-adenosylmethionine:tRNA ribosyltransferase-isome 100.0
COG0809348 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isome 100.0
TIGR00113364 queA S-adenosylmethionine:tRNA ribosyltransferase-isome 100.0
PRK01424366 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; 100.0
pfam02547218 Queuosine_synth Queuosine biosynthesis protein. Queuosi 100.0
TIGR00630956 uvra excinuclease ABC, A subunit; InterPro: IPR004602 A 95.48
TIGR03470318 HpnH hopanoid biosynthesis associated radical SAM prote 91.14
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional Back     alignment and domain information
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; InterPro: IPR003699 Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine Back     alignment and domain information
>PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional Back     alignment and domain information
>pfam02547 Queuosine_synth Queuosine biosynthesis protein Back     alignment and domain information
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems Back     alignment and domain information
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
1vky_A347 Crystal Structure Of S-Adenosylmethionine Trna Ribo 1e-113
1yy3_A346 Structure Of S-Adenosylmethionine:trna Ribosyltrans 1e-113
1wdi_A345 Crystal Structure Of Tt0907 From Thermus Thermophil 1e-102
>gi|52696131|pdb|1VKY|A Chain A, Crystal Structure Of S-Adenosylmethionine Trna Ribosyltransferase (Tm0574) From Thermotoga Maritima At 2.00 A Resolution Length = 347 Back     alignment and structure 
 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 140/357 (39%), Positives = 191/357 (53%), Gaps = 22/357 (6%)

Query: 1   MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIV 60
           M V EFD++LPP  IA  PV PRD++RLMV+H        I   +  ++  +L   D +V
Sbjct: 13  MKVSEFDYELPPELIAQEPVEPRDASRLMVLHRKTQ---RIEHRIFREIIEYLEPGDLLV 69

Query: 61  FNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQ 120
            N +KVI A+L   +     +    I   L  R+    W    RP + +KKG  L     
Sbjct: 70  LNVSKVIPARLYARK-----KTGASIEILLIERLEEGIWKCLVRPGQKVKKGTELVI--- 121

Query: 121 DGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDY 180
                L A  + +   G  +L F      L  +    G  PLPPYI      +      Y
Sbjct: 122 --DEDLSAVCLGRGEDGTRILKFQPQDDRLIFEK---GRTPLPPYIK-----NEVPLERY 171

Query: 181 QTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIM 240
           QT YAK +GSVAAPTAGLHFT  L+ +L   G++   V LHVG GTF PVKVE+ + H M
Sbjct: 172 QTVYAKEEGSVAAPTAGLHFTPELIEKLKKKGVQFAEVVLHVGIGTFRPVKVEEVEKHKM 231

Query: 241 HSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPG 300
           H E   +   T + L   + RG RIV+VGTT++R LET          + G T++FI P 
Sbjct: 232 HEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLP-EQEEYVGKTDLFIYPP 290

Query: 301 YRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLF 357
           + F+ VD L++NFHLP+STLLMLV+AF G +   + Y+ A+   YRF+S+GD  L+ 
Sbjct: 291 FEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL 347
>gi|93278505|pdb|1YY3|A Chain A, Structure Of S-Adenosylmethionine:trna Ribosyltransferase- Isomerase (Quea) Length = 346 Back     alignment and structure
gi|56966767|pdb|1WDI|A Chain A, Crystal Structure Of Tt0907 From Thermus Thermophilus Hb8 Length = 345 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
1yy3_A346 S-adenosylmethionine:tRNA ribosyltransferase- isomerase 3e-95
1vky_A347 S-adenosylmethionine:tRNA ribosyltransferase- isomerase 1e-91
1wdi_A345 Hypothetical protein TT0907; structural genomics, riken 1e-91
>1yy3_A S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis} Length = 346 Back     alignment and structure
 Score =  343 bits (882), Expect = 3e-95
 Identities = 149/357 (41%), Positives = 210/357 (58%), Gaps = 17/357 (4%)

Query: 1   MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIV 60
             V  FDF+LP   IA  P+  RD++RLMV+  +      ++D     + +F N  D +V
Sbjct: 5   SKVDLFDFELPERLIAQVPLEQRDASRLMVLDKHTG---ELTDSSFKHIISFFNEGDCLV 61

Query: 61  FNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQ 120
            NNT+V+ A+L G +     + E      L  + + + W   A+P+K +KKG ++ F   
Sbjct: 62  LNNTRVLPARLFGTKEDTGAKVE----LLLLKQETGDKWETLAKPAKRVKKGTVVTF--- 114

Query: 121 DGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDY 180
            G  RL+A   ++   G   + F   GI  E  +  +G +PLPPYI  +      D   Y
Sbjct: 115 -GDGRLKAICTEELEHGGRKMEFQYDGIFYEV-LESLGEMPLPPYIKEQLD----DKERY 168

Query: 181 QTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIM 240
           QT Y+K  GS AAPTAGLHFT  +L +L   G+++ F+TLHVG GTF PV  ++ ++H M
Sbjct: 169 QTVYSKEIGSAAAPTAGLHFTEEILQQLKDKGVQIEFITLHVGLGTFRPVSADEVEEHNM 228

Query: 241 HSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLET-ATTEDGIINPWSGFTNIFITP 299
           H+E   +   TA ALN V+  GGRI+SVGTTS R LET A   DG     SG+T+IFI P
Sbjct: 229 HAEFYQMSEETAAALNKVRENGGRIISVGTTSTRTLETIAGEHDGQFKASSGWTSIFIYP 288

Query: 300 GYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLL 356
           GY F+A+D +++NFHLPKS+L+MLVSA  G E   + Y HA+   YRF+S+GD  L+
Sbjct: 289 GYEFKAIDGMITNFHLPKSSLIMLVSALAGRENILRAYNHAVEEEYRFFSFGDAMLI 345
>1vky_A S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima} SCOP: e.53.1.1 Length = 347 Back     alignment and structure
>1wdi_A Hypothetical protein TT0907; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; HET: CIT; 2.10A {Thermus thermophilus} SCOP: e.53.1.1 Length = 345 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
1vky_A347 S-adenosylmethionine:tRNA ribosyltransferase- isomerase 100.0
1yy3_A346 S-adenosylmethionine:tRNA ribosyltransferase- isomerase 100.0
1wdi_A345 Hypothetical protein TT0907; structural genomics, riken 100.0
>1vky_A S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima} SCOP: e.53.1.1 Back     alignment and structure
Probab=100.00  E-value=0  Score=1022.95  Aligned_cols=335  Identities=42%  Similarity=0.683  Sum_probs=317.8

Q ss_pred             CCCCCCCCCCCHHHHCCCCCCCCCCCEEEEECCCCCCCCEEEEEEHHHHHHHCCCCCEEEEECCCEEEEEEEEEEECCCC
Q ss_conf             98633588889778616998781203135663788875315310143478726988799994795688899876404677
Q gi|254780180|r    1 MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHIN   80 (360)
Q Consensus         1 M~lsdfDy~LP~elIAq~P~~~Rd~SRLLV~~r~~~~~~~i~h~~F~dl~~~L~~gDLLV~NnTKVipARL~g~k~~~~~   80 (360)
                      |+||||||+||+|||||+|+++||+|||||++++++   .|.|+.|+||++||+||||||||||||+||||+|+|     
T Consensus        13 Mklsdfdy~LP~elIAq~P~~~Rd~SRLLVl~~~~~---~i~h~~F~dl~~~L~~gDlLV~NdTkVipARL~g~k-----   84 (347)
T 1vky_A           13 MKVSEFDYELPPELIAQEPVEPRDASRLMVLHRKTQ---RIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARK-----   84 (347)
T ss_dssp             ---CTTCCCCCGGGBCSSCCSSGGGSEEEEEETTTT---EEEEEEGGGGGGGCCTTCEEEEEEEECCSCEEEEBC-----
T ss_pred             EEHHHCCCCCCHHHHCCCCCCCCCCCEEEEEECCCC---CEEEEEHHHHHHHCCCCCEEEEECCEEEEEEEEEEE-----
T ss_conf             588783989895996689999965144889988999---077756765686479998999979989887998774-----


Q ss_pred             CCCCEEEEEEECCCCCCCHHHHHHCCCCCCCCCEEEECCCCCCCCEEEEEEECCCCCCEEEEECCCCCCHHHHHHHHHCC
Q ss_conf             77650589981124866101122115643698579970578874069999603557724999726786300025442035
Q gi|254780180|r   81 RREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQSRLEATVIDKWNTGEILLVFSISGIELERQISLVGTI  160 (360)
Q Consensus        81 ~~g~~ieill~~~~~~~~w~~l~kp~kklk~G~~l~~~~~~~~~~l~~~vi~~~~~g~~~i~f~~~~~~~~~~L~~~G~i  160 (360)
                      .+|++||++++++.+++.|.|++||+||+|+|+++.+.+     .+.++++++.+.+.+.+.|+.+   .+++|+++|+|
T Consensus        85 ~tgg~vEill~~~~~~~~w~~likp~kk~k~g~~l~~~~-----~~~~~v~~~~~~~~~~~~~~~~---~~~~l~~~G~~  156 (347)
T 1vky_A           85 KTGASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDE-----DLSAVCLGRGEDGTRILKFQPQ---DDRLIFEKGRT  156 (347)
T ss_dssp             ---CCEEEEEEEEEETTEEEEEEESCTTCCTTCEEEEET-----TEEEEEEEECTTSCEEEEEESC---CHHHHHHHC--
T ss_pred             CCCCEEEEEEEEECCCCEEEEEEECCCCCCCCCEEEECC-----CCEEEEEEEECCCCEEEECCCC---HHHHHHHCCCC
T ss_conf             379709999977528983999974076789998899605-----6348999971476078851774---26899977999


Q ss_pred             CCCHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             78522212345652114331013456757400555688789999999997215530378731656657887410135667
Q gi|254780180|r  161 PLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIM  240 (360)
Q Consensus       161 PLPPYI~r~r~~~~~D~~~YQTVyA~~~GSVAAPTAGLHFt~~ll~~L~~kGi~~~~iTLHVG~GTF~Pi~~~~i~~h~m  240 (360)
                      ||||||+|  +   .|.+|||||||+++|||||||||||||++||++|++|||++++||||||+|||+||++|+|++|+|
T Consensus       157 PLPPYI~r--~---~d~erYQTVyAk~~GSVAAPTAGLHFT~~ll~~L~~kGv~~~~vTLHVG~GTF~Pv~~e~i~~H~m  231 (347)
T 1vky_A          157 PLPPYIKN--E---VPLERYQTVYAKEEGSVAAPTAGLHFTPELIEKLKKKGVQFAEVVLHVGIGTFRPVKVEEVEKHKM  231 (347)
T ss_dssp             ----------------------------------CGGGGCCHHHHHHHHHHTCEEEEEEEEC------------------
T ss_pred             CCCCEEEC--C---CCHHHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             99961745--6---418878788714898553677878779999999998499267789986467546764443455788


Q ss_pred             CCHHEEECHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCEEEEEEEECCCCCHHHH
Q ss_conf             70007785999999998753798099962878998999985289846888722366574096114312552775545789
Q gi|254780180|r  241 HSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTL  320 (360)
Q Consensus       241 H~E~~~i~~~~~~~I~~ak~~g~rIiAVGTT~~R~LEs~~~~~~~~~~~~g~T~lfI~Pg~~f~~vd~LiTNFH~P~Stl  320 (360)
                      |+|||+||++|+++||+||++|+|||||||||||||||++. +|.+++++|||||||+|||+|++||+||||||+|||||
T Consensus       232 H~E~~~I~~~ta~~I~~ak~~g~RIiAVGTT~~RaLEs~~~-~~~~~~~~G~T~lfI~Pgy~fkvvD~LiTNFHlPkSTL  310 (347)
T 1vky_A          232 HEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIAR-LPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTL  310 (347)
T ss_dssp             CCCEEEECHHHHHHHHHHHHHTCCEEEESHHHHHHHHHHTT-SCCCSSEEECCCCCCCSSCCCSSCSEEEEECCCTTCHH
T ss_pred             CCEEEEECHHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHH-HCCCCCCCCCCCEEECCCCCCCEECEEEECCCCCCCHH
T ss_conf             65589937999999999997189489995418999999875-13677778861559789998728276343573783589


Q ss_pred             HHHHHHHHCHHHHHHHHHHHHHCCCEEECCCCHHHCC
Q ss_conf             9999987198999999999998698261101022233
Q gi|254780180|r  321 LMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLF  357 (360)
Q Consensus       321 l~Lv~Af~G~~~~~~~Y~~Ai~~~yrF~syGDamLi~  357 (360)
                      |||||||+|+++++++|++||+++||||||||||||+
T Consensus       311 l~LvsAf~G~~~~~~aY~~Ai~~~YrF~SyGDamLil  347 (347)
T 1vky_A          311 LMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL  347 (347)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHTTCCBSTTSCEEEEC
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHCCCCEECCCHHHEEC
T ss_conf             9999985896999999999998799601502230109
>1yy3_A S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis} Back     alignment and structure
>1wdi_A Hypothetical protein TT0907; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; HET: CIT; 2.10A {Thermus thermophilus} SCOP: e.53.1.1 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

Original result of RPS-BLAST against SCOP70(version1.75) database

IdentityAlignment graphLength Definition E-value
Target 360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
d1wdia_344 e.53.1.1 (A:) Queuosine biosynthesis protein queA {Ther 3e-91
d1vkya_332 e.53.1.1 (A:) Queuosine biosynthesis protein queA {Ther 3e-87
>d1wdia_ e.53.1.1 (A:) Queuosine biosynthesis protein queA {Thermus thermophilus [TaxId: 274]} Length = 344 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: QueA-like
superfamily: QueA-like
family: QueA-like
domain: Queuosine biosynthesis protein queA
species: Thermus thermophilus [TaxId: 274]

 Score =  329 bits (844), Expect = 3e-91
 Identities = 149/355 (41%), Positives = 196/355 (55%), Gaps = 19/355 (5%)

Query: 5   EFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNT 64
            +D+ LPP +IA   V PRD ARLMVV+     P  ++   V DLP FL   D +VFN +
Sbjct: 5   AYDYHLPPEQIAQEGVEPRDMARLMVVYRE--GPFRVAHKRVRDLPEFLRPGDVLVFNES 62

Query: 65  KVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQS 124
           KVI A+L   +         ++   L    SP  W     P++    G  L   S    +
Sbjct: 63  KVIPARLLARKPTG-----GKVEILLVRERSPGLWEALLGPARKAPPGTRLLLLSPKDLA 117

Query: 125 R---LEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARDYVDYQ 181
               L+A V+     G  LL F    +    ++     +PLPPYI  K P        YQ
Sbjct: 118 PVPGLQAEVVAVEEDGVRLLRFQGDLVAHLEEVG---EVPLPPYIKAKIP-----MERYQ 169

Query: 182 TTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMH 241
           T YA+  GSVAAPTAGLHFT  LL RL  +G+++ F+TLHVG GTF PVK  D + H MH
Sbjct: 170 TVYARRPGSVAAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRPVK-GDPEKHEMH 228

Query: 242 SEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGY 301
           +E   I    A+A+N  K+ G R+V+VGTT +R LE+A  E   +    G T +FI P Y
Sbjct: 229 AEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLFIRPPY 288

Query: 302 RFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLL 356
            F+ VD L +NFHLP+STLLMLV+AF G E T + Y+ A++  YRFYS GD  L+
Sbjct: 289 TFKVVDALFTNFHLPRSTLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLI 343
>d1vkya_ e.53.1.1 (A:) Queuosine biosynthesis protein queA {Thermotoga maritima [TaxId: 2336]} Length = 332 Back     information, alignment and structure

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

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
d1wdia_344 Queuosine biosynthesis protein queA {Thermus thermophil 100.0
d1vkya_332 Queuosine biosynthesis protein queA {Thermotoga maritim 100.0
>d1wdia_ e.53.1.1 (A:) Queuosine biosynthesis protein queA {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: QueA-like
superfamily: QueA-like
family: QueA-like
domain: Queuosine biosynthesis protein queA
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=0  Score=1021.26  Aligned_cols=340  Identities=44%  Similarity=0.677  Sum_probs=318.5

Q ss_pred             CCCCCCCCCCHHHHCCCCCCCCCCCEEEEECCCCCCCCEEEEEEHHHHHHHCCCCCEEEEECCCEEEEEEEEEEECCCCC
Q ss_conf             86335888897786169987812031356637888753153101434787269887999947956888998764046777
Q gi|254780180|r    2 MVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHINR   81 (360)
Q Consensus         2 ~lsdfDy~LP~elIAq~P~~~Rd~SRLLV~~r~~~~~~~i~h~~F~dl~~~L~~gDLLV~NnTKVipARL~g~k~~~~~~   81 (360)
                      -||||||+||++||||+|+++||+|||||++++++.  +|+|+.|+||++||+||||||||||||+||||+|+|     .
T Consensus         2 ~LsdfDy~LP~elIAq~P~~~Rd~SRLLVl~r~~~~--~I~h~~F~dl~~~L~~gDlLV~NnTkVipARL~g~k-----~   74 (344)
T d1wdia_           2 GLEAYDYHLPPEQIAQEGVEPRDMARLMVVYREGPF--RVAHKRVRDLPEFLRPGDVLVFNESKVIPARLLARK-----P   74 (344)
T ss_dssp             GGGGGCCCCCGGGBCSSCCSSGGGSEEEEECSSSSC--CEEEEEGGGHHHHCCTTCEEEEEEEEECCEEEEEEC-----T
T ss_pred             CHHHCCCCCCHHHHCCCCCCCCCCCEEEEEECCCCC--EEEECCHHHHHHHCCCCCEEEEECCEEEEEEEEEEE-----C
T ss_conf             734549997959976899999621128999889998--576332623676479998999989989778999781-----6


Q ss_pred             CCCEEEEEEECCCCCCCHHHHHHCCCCCCCCCEEEECCCCCC---CCEEEEEEECCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             765058998112486610112211564369857997057887---40699996035577249997267863000254420
Q gi|254780180|r   82 REKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQ---SRLEATVIDKWNTGEILLVFSISGIELERQISLVG  158 (360)
Q Consensus        82 ~g~~ieill~~~~~~~~w~~l~kp~kklk~G~~l~~~~~~~~---~~l~~~vi~~~~~g~~~i~f~~~~~~~~~~L~~~G  158 (360)
                      +|++||+++++..+++.|.|++||+||+++|+++.+.+....   ..+.++++.+.+.+.++++|+.   ++.++|+++|
T Consensus        75 tggkvEilll~~~~~~~w~al~kp~kk~k~G~~l~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~---~~~~~l~~~G  151 (344)
T d1wdia_          75 TGGKVEILLVRERSPGLWEALLGPARKAPPGTRLLLLSPKDLAPVPGLQAEVVAVEEDGVRLLRFQG---DLVAHLEEVG  151 (344)
T ss_dssp             TSCEEEEEECBCC------CCBCCCSCCCSCEEEEECTTTTSCEEEEEEEECCCSSCC-------------CCEEESCCC
T ss_pred             CCCEEEEEEECCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCEEEEEEECCCCCEEEEECC---CHHHHHHHHC
T ss_conf             8974999983124897089995336778999889953764322236736999998068847997222---0677788755


Q ss_pred             CCCCCHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             35785222123456521143310134567574005556887899999999972155303787316566578874101356
Q gi|254780180|r  159 TIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDH  238 (360)
Q Consensus       159 ~iPLPPYI~r~r~~~~~D~~~YQTVyA~~~GSVAAPTAGLHFt~~ll~~L~~kGi~~~~iTLHVG~GTF~Pi~~~~i~~h  238 (360)
                      +|||||||+|+     .|.+|||||||+++|||||||||||||++||++|++|||++++||||||+|||+||++ ++.+|
T Consensus       152 ~~PLPPYI~r~-----~d~~rYQTVyA~~~GSVAAPTAGLHFt~~ll~~L~~kGi~~~~vTLHVG~GTF~Pv~~-~~~~H  225 (344)
T d1wdia_         152 EVPLPPYIKAK-----IPMERYQTVYARRPGSVAAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRPVKG-DPEKH  225 (344)
T ss_dssp             SCC------------------------------CCCCGGGGCCHHHHHHHHHTTCEEEEEEEEESGGGCCC---------
T ss_pred             CCCCCHHHHCC-----HHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEEECCCCCCCCCC-CCCCC
T ss_conf             79988023112-----2676566564168987516645577899999999974061567999623443355334-32357


Q ss_pred             CCCCHHEEECHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCEEEEEEEECCCCCHH
Q ss_conf             67700077859999999987537980999628789989999852898468887223665740961143125527755457
Q gi|254780180|r  239 IMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKS  318 (360)
Q Consensus       239 ~mH~E~~~i~~~~~~~I~~ak~~g~rIiAVGTT~~R~LEs~~~~~~~~~~~~g~T~lfI~Pg~~f~~vd~LiTNFH~P~S  318 (360)
                      +||+|||+||++|+++||+||++|+|||||||||||||||++..+|.+++++|||||||+|||+|++||+||||||+|||
T Consensus       226 ~mH~E~~~i~~~t~~~i~~ak~~g~rIiAVGTT~~RaLEs~~~~~~~~~~~~g~T~lfI~Pg~~f~~vd~LlTNFHlP~S  305 (344)
T d1wdia_         226 EMHAEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLFIRPPYTFKVVDALFTNFHLPRS  305 (344)
T ss_dssp             -CCCEEEEECHHHHHHHHHHHHTTCCEEEESHHHHHHHHHTEETTTEECCEEEEECCCCCSSCCCSSCSEEEEECCCTTC
T ss_pred             CCCCEEEEECHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCEECEEEECCCCCCC
T ss_conf             88874999839999999999973995899957899999999970898577887568697899977481862446847802


Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHCCCEEECCCCHHHCC
Q ss_conf             899999987198999999999998698261101022233
Q gi|254780180|r  319 TLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLF  357 (360)
Q Consensus       319 tll~Lv~Af~G~~~~~~~Y~~Ai~~~yrF~syGDamLi~  357 (360)
                      |||||||||+|+++|+++|++||+++||||||||||||+
T Consensus       306 tll~Lv~af~g~~~~~~~Y~~Ai~~~YrF~SyGDamlil  344 (344)
T d1wdia_         306 TLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLIL  344 (344)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHHHHTTCCBSTTSCEEEEC
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHCCCCEECCCHHHEEC
T ss_conf             999999995795999999999998799333303321109
>d1vkya_ e.53.1.1 (A:) Queuosine biosynthesis protein queA {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 360 S-adenosylmethionine:tRNA ribosyltransferase-isome
1wdi_A_345 (A:) Hypothetical protein TT0907; structural genom 1e-111
1yy3_A_1-67_171-346243 (A:1-67,A:171-346) S-adenosylmethionine:tRNA ribos 4e-68
1vky_A_1-76_174-347250 (A:1-76,A:174-347) S-adenosylmethionine:tRNA ribos 3e-67
1yy3_A_1-67_171-346243 (A:1-67,A:171-346) S-adenosylmethionine:tRNA ribos 1e-18
1vky_A_1-76_174-347250 (A:1-76,A:174-347) S-adenosylmethionine:tRNA ribos 2e-18
1yy3_A_68-170103 (A:68-170) S-adenosylmethionine:tRNA ribosyltransf 4e-15
1vky_A_77-17397 (A:77-173) S-adenosylmethionine:tRNA ribosyltransf 4e-14
>1wdi_A (A:) Hypothetical protein TT0907; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; HET: CIT; 2.10A {Thermus thermophilus}Length = 345 Back     alignment and structure
 Score =  396 bits (1019), Expect = e-111
 Identities = 151/361 (41%), Positives = 202/361 (55%), Gaps = 20/361 (5%)

Query: 1   MM-VKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAI 59
           M  ++ +D+ LPP +IA   V PRD ARLMVV+     P  ++   V DLP FL   D +
Sbjct: 1   MEGLEAYDYHLPPEQIAQEGVEPRDMARLMVVYRE--GPFRVAHKRVRDLPEFLRPGDVL 58

Query: 60  VFNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFS 119
           VFN +KVI A+L   +         ++   L    SP  W     P++    G  L   S
Sbjct: 59  VFNESKVIPARLLARK-----PTGGKVEILLVRERSPGLWEALLGPARKAPPGTRLLLLS 113

Query: 120 QDGQS---RLEATVIDKWNTGEILLVFSISGIELERQISLVGTIPLPPYIARKRPIDARD 176
               +    L+A V+     G  LL F    +    ++   G +PLPPYI  K P++   
Sbjct: 114 PKDLAPVPGLQAEVVAVEEDGVRLLRFQGDLVAHLEEV---GEVPLPPYIKAKIPME--- 167

Query: 177 YVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTD 236
              YQT YA+  GSVAAPTAGLHFT  LL RL  +G+++ F+TLHVG GTF PVK  D +
Sbjct: 168 --RYQTVYARRPGSVAAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRPVK-GDPE 224

Query: 237 DHIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIF 296
            H MH+E   I    A+A+N  K+ G R+V+VGTT +R LE+A  E   +    G T +F
Sbjct: 225 KHEMHAEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLF 284

Query: 297 ITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLL 356
           I P Y F+ VD L +NFHLP+STLLMLV+AF G E T + Y+ A++  YRFYS GD  L+
Sbjct: 285 IRPPYTFKVVDALFTNFHLPRSTLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLI 344

Query: 357 F 357
            
Sbjct: 345 L 345
>1yy3_A (A:1-67,A:171-346) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis}Length = 243 Back     alignment and structure
>1vky_A (A:1-76,A:174-347) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima}Length = 250 Back     alignment and structure
>1yy3_A (A:1-67,A:171-346) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis}Length = 243 Back     alignment and structure
>1vky_A (A:1-76,A:174-347) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima}Length = 250 Back     alignment and structure
>1yy3_A (A:68-170) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis}Length = 103 Back     alignment and structure
>1vky_A (A:77-173) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima}Length = 97 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target360 S-adenosylmethionine:tRNA ribosyltransferase-isomerase
1wdi_A_345 Hypothetical protein TT0907; structural genomics, 100.0
1yy3_A_1-67_171-346243 S-adenosylmethionine:tRNA ribosyltransferase- isom 100.0
1vky_A_1-76_174-347250 S-adenosylmethionine:tRNA ribosyltransferase- isom 100.0
1yy3_A_68-170103 S-adenosylmethionine:tRNA ribosyltransferase- isom 99.9
1vky_A_77-17397 S-adenosylmethionine:tRNA ribosyltransferase- isom 99.87
>1wdi_A (A:) Hypothetical protein TT0907; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; HET: CIT; 2.10A {Thermus thermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=1017.51  Aligned_cols=341  Identities=44%  Similarity=0.672  Sum_probs=319.9

Q ss_pred             CCCCCCCCCCCHHHHCCCCCCCCCCCEEEEECCCCCCCCEEEEEEHHHHHHHCCCCCEEEEECCCEEEEEEEEEEECCCC
Q ss_conf             98633588889778616998781203135663788875315310143478726988799994795688899876404677
Q gi|254780180|r    1 MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIVFNNTKVITAQLNGVRFCHIN   80 (360)
Q Consensus         1 M~lsdfDy~LP~elIAq~P~~~Rd~SRLLV~~r~~~~~~~i~h~~F~dl~~~L~~gDLLV~NnTKVipARL~g~k~~~~~   80 (360)
                      |++|||||+||+|+|||+|+++||+|||||++|+++.  .|+|+.|+||++||+||||||||||||+||||+|+|     
T Consensus         2 m~ls~fdf~LP~elIAq~P~~~Rd~sRLLVl~r~~g~--~i~h~~F~dl~~~L~~GDlLV~NdTkVipARL~g~k-----   74 (345)
T 1wdi_A            2 EGLEAYDYHLPPEQIAQEGVEPRDMARLMVVYREGPF--RVAHKRVRDLPEFLRPGDVLVFNESKVIPARLLARK-----   74 (345)
T ss_dssp             CGGGGGCCCCCGGGBCSSCCSSGGGSEEEEECSSSSC--CEEEEEGGGHHHHCCTTCEEEEEEEEECCEEEEEEC-----
T ss_pred             CCHHHCCCCCCHHHHCCCCCCCCCCCEEEEEECCCCC--EEEECCHHHHHHHCCCCCEEEEECCEEEEEEEEEEE-----
T ss_conf             9756769998959976899998611138999889998--576331623676479998999989989788999770-----


Q ss_pred             CCCCEEEEEEECCCCCCCHHHHHHCCCCCCCCCEEEECCCCCCC---CEEEEEEECCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             77650589981124866101122115643698579970578874---069999603557724999726786300025442
Q gi|254780180|r   81 RREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQDGQS---RLEATVIDKWNTGEILLVFSISGIELERQISLV  157 (360)
Q Consensus        81 ~~g~~ieill~~~~~~~~w~~l~kp~kklk~G~~l~~~~~~~~~---~l~~~vi~~~~~g~~~i~f~~~~~~~~~~L~~~  157 (360)
                      .+|++||++++++++++.|.|++||+||+|+|+++.|.+.....   .+.++++++.+.+.++..+.   .++.++|+++
T Consensus        75 ~tg~~iEilll~~l~~~~w~~lv~p~kk~k~G~~l~~~~~~~~~~~~~l~a~v~~~~~~~~~~~~~~---~~~~~~l~~~  151 (345)
T 1wdi_A           75 PTGGKVEILLVRERSPGLWEALLGPARKAPPGTRLLLLSPKDLAPVPGLQAEVVAVEEDGVRLLRFQ---GDLVAHLEEV  151 (345)
T ss_dssp             TTSCEEEEEECBCC------CCBCCCSCCCSCEEEEECTTTTSCEEEEEEEECCCSSCC-------------CCEEESCC
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCEEEEEEEECCCCEEEEEC---CCHHHHHHHH
T ss_conf             6897089998414576135421210567898988996377532212673799999706872798612---3168898875


Q ss_pred             HCCCCCHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             03578522212345652114331013456757400555688789999999997215530378731656657887410135
Q gi|254780180|r  158 GTIPLPPYIARKRPIDARDYVDYQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDD  237 (360)
Q Consensus       158 G~iPLPPYI~r~r~~~~~D~~~YQTVyA~~~GSVAAPTAGLHFt~~ll~~L~~kGi~~~~iTLHVG~GTF~Pi~~~~i~~  237 (360)
                      |+|||||||+|     +.|.+|||||||+++|||||||||||||++||++|++|||++++||||||+|||+||+ +++++
T Consensus       152 G~~PLPpYI~r-----~~d~e~YQTVyA~~~GsVAAPTAGLHFt~~ll~~l~~kGv~~a~iTLHVG~GTF~pv~-~di~~  225 (345)
T 1wdi_A          152 GEVPLPPYIKA-----KIPMERYQTVYARRPGSVAAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRPVK-GDPEK  225 (345)
T ss_dssp             CSCC------------------------------CCCCGGGGCCHHHHHHHHHTTCEEEEEEEEESGGGCCC--------
T ss_pred             CCCCCCCHHCC-----CCHHHHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCC-CCCCC
T ss_conf             47998810202-----4225667778616898552566877778999999997415056799962244446533-52235


Q ss_pred             CCCCCHHEEECHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCEEEEEEEECCCCCH
Q ss_conf             66770007785999999998753798099962878998999985289846888722366574096114312552775545
Q gi|254780180|r  238 HIMHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPK  317 (360)
Q Consensus       238 h~mH~E~~~i~~~~~~~I~~ak~~g~rIiAVGTT~~R~LEs~~~~~~~~~~~~g~T~lfI~Pg~~f~~vd~LiTNFH~P~  317 (360)
                      |+||+|||+||++|+++||+||++|||||||||||||||||+++.+|.+++++|||||||+|||+|++||+||||||+||
T Consensus       226 H~mh~E~~~i~~~ta~~i~~ak~~G~RviAVGTT~vRaLEsaa~~~g~l~~~~G~T~lfI~Pgy~fkvvD~LiTNFHlP~  305 (345)
T 1wdi_A          226 HEMHAEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLFIRPPYTFKVVDALFTNFHLPR  305 (345)
T ss_dssp             --CCCEEEEECHHHHHHHHHHHHTTCCEEEESHHHHHHHHHTEETTTEECCEEEEECCCCCSSCCCSSCSEEEEECCCTT
T ss_pred             CCCCCEEEEECHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHCCCCCCCCCCEECEEECCCCCCCCCCEEEECCCCCC
T ss_conf             78776599982999999999997399489984689999999997289866778302459649997748187455684780


Q ss_pred             HHHHHHHHHHHCHHHHHHHHHHHHHCCCEEECCCCHHHCC
Q ss_conf             7899999987198999999999998698261101022233
Q gi|254780180|r  318 STLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLF  357 (360)
Q Consensus       318 Stll~Lv~Af~G~~~~~~~Y~~Ai~~~yrF~syGDamLi~  357 (360)
                      ||||||||||+|+++|+++|++||+++||||||||||||+
T Consensus       306 STllmLvsAFaG~e~~~~aY~~Ai~~~YrF~SyGDamLIl  345 (345)
T 1wdi_A          306 STLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLIL  345 (345)
T ss_dssp             CHHHHHHHHHHCHHHHHHHHHHHHHTTCCBSTTSCEEEEC
T ss_pred             CHHHHHHHHHCCHHHHHHHHHHHHHCCCCEECCCHHHEEC
T ss_conf             2999999995896999999999998798433313320219
>1yy3_A (A:1-67,A:171-346) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis} Back     alignment and structure
>1vky_A (A:1-76,A:174-347) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima} Back     alignment and structure
>1yy3_A (A:68-170) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; beta-barrel, QUEA, quein queuosine, tRNA- modification; 2.88A {Bacillus subtilis} Back     alignment and structure
>1vky_A (A:77-173) S-adenosylmethionine:tRNA ribosyltransferase- isomerase; TM0574, structural genomics, JCSG, protein structure initiative, PSI; 2.00A {Thermotoga maritima} Back     alignment and structure