254780904

254780904

tRNA/rRNA methyltransferase

GeneID in NCBI database:8209924Locus tag:CLIBASIA_04015
Protein GI in NCBI database:254780904Protein Accession:YP_003065317.1
Gene range:+(884347, 885153)Protein Length:268aa
Gene description:tRNA/rRNA methyltransferase
COG prediction:[J] rRNA methylase
KEGG prediction:lasT; tRNA/rRNA methyltransferase; K02533 tRNA/rRNA methyltransferase [EC:2.1.1.-]
SEED prediction:tRNA:Cm32/Um32 methyltransferase
Pathway involved in KEGG:not defined
Subsystem involved in SEED:tRNA modification Archaea
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
TOPPRED1 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-------27
MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVLLQKTEKSE
cccccccccccccccEEEEEccccccHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHcccHHHccEEEEEccHHHHHHcccEEEEEEccccccccEEEcHHHHHHHHHHHHcccccEEEEEccccccccHHHHHHcccEEEEcccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccc
ccccccHHHHHHcccEEEEEcccccccHHHHHHHHHHccccEEEEEccccccccHHHHHHHcccHHHHHHcHHHccHHHHHccccEEEEEcccccccccccccHHHHHHHHHHHHcccccEEEEEccccccccHHHHHHcccEEEccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccccEEEEEcccc
mtpyapqlqnsakgpviilvdpqlgenIGMVARAMWNFNLTQlrlvnprdgwpsekarsssanadcvIDSVRVFSNLKEAIADLHFIYATTarnrnnfksvlapKEAAIVLNERIFSGQNVGIIFgrerwgltnEEIALSNaiisfpvnplfpslniSQAVLLMVWECMENSIVSseknvkeqntpatkgeLLSFLDYLEISLeergyfrpvekKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDkfsrqssrrnNVLLQKTEKSE
mtpyapqlqnsakgpvIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSekarsssanadcVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNerifsgqnvGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSseknvkeqntpatkgellSFLDYLEISLEergyfrpvekkkkMLDDLYSIFIRPELMREEVFLLRGIVStldkfsrqssrrnnvllqktekse
MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVLLQKTEKSE
**************PVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECME*******************GELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVS************************
MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRD************NADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVS***********ATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNV*********
****APQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEK****QNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVL********
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MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVLLQKTEKSE
MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVLLQKTEKSE
MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQSSRRNNVLLQKTEKSE

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
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
315122619303 tRNA/rRNA methyltransferase [Candidatus Liberibacter so 1 1e-113
222148422286 tRNA/rRNA methyltransferase [Agrobacterium vitis S4] Le 1 2e-74
159184955277 tRNA/rRNA methyltransferase [Agrobacterium tumefaciens 1 3e-74
241204881276 RNA methyltransferase, TrmH family, group 1 [Rhizobium 1 1e-73
86357930276 tRNA/rRNA methyltransferase protein [Rhizobium etli CFN 1 2e-73
110633621262 RNA methyltransferase [Mesorhizobium sp. BNC1] Length = 1 3e-73
116252374276 rRNA methylase family protein [Rhizobium leguminosarum 1 3e-73
190892001276 tRNA/rRNA methyltransferase [Rhizobium etli CIAT 652] L 1 5e-73
13470359303 RNA methyltransferase [Mesorhizobium loti MAFF303099] L 1 6e-73
327190529276 putative tRNA/rRNA methyltransferase protein [Rhizobium 1 1e-72
>gi|315122619|ref|YP_004063108.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 303 Back     alignment and organism information
 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 202/268 (75%), Positives = 235/268 (87%)

Query: 1   MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSS 60
           M  +  +LQNS K P+I+LVDPQLGENIGMVARAM NFN+TQLRLVNPRDGWP++KARSS
Sbjct: 35  MAVHMQKLQNSTKSPIIVLVDPQLGENIGMVARAMLNFNITQLRLVNPRDGWPNDKARSS 94

Query: 61  SANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQN 120
           SANAD VIDSVRVFS+LKEAI+DL+F+YATTAR+R+NFKSV APKEAA+VLNERI SGQN
Sbjct: 95  SANADHVIDSVRVFSSLKEAISDLNFVYATTARSRDNFKSVFAPKEAAVVLNERIHSGQN 154

Query: 121 VGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNV 180
           VG+IFG ER GLTNEEIALSNAIISFPVNP F SLNI+QAVL+M WE MENS+V  +KNV
Sbjct: 155 VGLIFGCERSGLTNEEIALSNAIISFPVNPNFSSLNIAQAVLVMAWEWMENSVVVPKKNV 214

Query: 181 KEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLR 240
           KE + PAT+GELLSFLDY E SL ERGYFRP E+KKKMLDDL S+FIR ELMR+E+FLLR
Sbjct: 215 KESDIPATRGELLSFLDYTENSLAERGYFRPEERKKKMLDDLRSVFIRLELMRQEIFLLR 274

Query: 241 GIVSTLDKFSRQSSRRNNVLLQKTEKSE 268
           G++STLD+FSR+S R + V+ QK + + 
Sbjct: 275 GVISTLDRFSRESPRGSLVVPQKKQNNH 302


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148422|ref|YP_002549379.1| tRNA/rRNA methyltransferase [Agrobacterium vitis S4] Length = 286 Back     alignment and organism information
>gi|159184955|ref|NP_354849.2| tRNA/rRNA methyltransferase [Agrobacterium tumefaciens str. C58] Length = 277 Back     alignment and organism information
>gi|241204881|ref|YP_002975977.1| RNA methyltransferase, TrmH family, group 1 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 276 Back     alignment and organism information
>gi|86357930|ref|YP_469822.1| tRNA/rRNA methyltransferase protein [Rhizobium etli CFN 42] Length = 276 Back     alignment and organism information
>gi|110633621|ref|YP_673829.1| RNA methyltransferase [Mesorhizobium sp. BNC1] Length = 262 Back     alignment and organism information
>gi|116252374|ref|YP_768212.1| rRNA methylase family protein [Rhizobium leguminosarum bv. viciae 3841] Length = 276 Back     alignment and organism information
>gi|190892001|ref|YP_001978543.1| tRNA/rRNA methyltransferase [Rhizobium etli CIAT 652] Length = 276 Back     alignment and organism information
>gi|13470359|ref|NP_101925.1| RNA methyltransferase [Mesorhizobium loti MAFF303099] Length = 303 Back     alignment and organism information
>gi|327190529|gb|EGE57623.1| putative tRNA/rRNA methyltransferase protein [Rhizobium etli CNPAF512] Length = 276 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
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
TIGR00050233 TIGR00050, rRNA_methyl_1, RNA methyltransferase, TrmH f 5e-40
PRK15114245 PRK15114, PRK15114, tRNA (cytidine/uridine-2'-O-)-methy 3e-25
COG0565242 COG0565, LasT, rRNA methylase [Translation, ribosomal s 7e-63
PRK10433228 PRK10433, PRK10433, putative RNA methyltransferase; Pro 6e-31
pfam00588142 pfam00588, SpoU_methylase, SpoU rRNA Methylase family 3e-24
COG0566260 COG0566, SpoU, rRNA methylases [Translation, ribosomal 2e-04
>gnl|CDD|161682 TIGR00050, rRNA_methyl_1, RNA methyltransferase, TrmH family, group 1 Back     alignment and domain information
>gnl|CDD|185069 PRK15114, PRK15114, tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional Back     alignment and domain information
>gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|182456 PRK10433, PRK10433, putative RNA methyltransferase; Provisional Back     alignment and domain information
>gnl|CDD|144253 pfam00588, SpoU_methylase, SpoU rRNA Methylase family Back     alignment and domain information
>gnl|CDD|30912 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
COG0565242 LasT rRNA methylase [Translation, ribosomal structure a 100.0
TIGR00050253 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 100.0
PRK10433228 putative RNA methyltransferase; Provisional 100.0
PRK10358157 putative tRNA/rRNA methyltransferase YibK; Provisional 100.0
COG0566260 SpoU rRNA methylases [Translation, ribosomal structure 100.0
PRK11181244 23S rRNA (guanosine-2'-O-)-methyltransferase; Provision 99.98
PRK10864348 putative methyltransferase; Provisional 99.98
pfam00588142 SpoU_methylase SpoU rRNA Methylase family. This family 99.97
PRK11081229 tRNA guanosine-2'-O-methyltransferase; Provisional 99.97
COG0219155 CspR Predicted rRNA methylase (SpoU class) [Translation 99.94
TIGR00185161 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 99.93
KOG2506371 consensus 99.88
KOG0838271 consensus 99.72
TIGR00186271 rRNA_methyl_3 RNA methyltransferase, TrmH family, group 99.6
KOG08391477 consensus 99.26
pfam09936185 DUF2168 Uncharacterized protein conserved in bacteria ( 98.29
COG4080147 SpoU rRNA Methylase family enzyme [General function pre 98.11
pfam04407174 DUF531 Protein of unknown function (DUF531). Family of 96.57
COG4752190 Uncharacterized protein conserved in bacteria [Function 95.99
pfam09895105 DUF2122 RecB-family nuclease (DUF2122). This domain, fo 94.68
PRK00779308 ornithine carbamoyltransferase; Provisional 90.72
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1; InterPro: IPR004384 These proteins are part of the trmH (spoU) family of rRNA methylases Back     alignment and domain information
>PRK10433 putative RNA methyltransferase; Provisional Back     alignment and domain information
>PRK10358 putative tRNA/rRNA methyltransferase YibK; Provisional Back     alignment and domain information
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional Back     alignment and domain information
>PRK10864 putative methyltransferase; Provisional Back     alignment and domain information
>pfam00588 SpoU_methylase SpoU rRNA Methylase family Back     alignment and domain information
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional Back     alignment and domain information
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification Back     alignment and domain information
>KOG2506 consensus Back     alignment and domain information
>KOG0838 consensus Back     alignment and domain information
>TIGR00186 rRNA_methyl_3 RNA methyltransferase, TrmH family, group 3; InterPro: IPR004441 The RNA methyltransferase, TrmH family, group 3 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification Back     alignment and domain information
>KOG0839 consensus Back     alignment and domain information
>pfam09936 DUF2168 Uncharacterized protein conserved in bacteria (DUF2168) Back     alignment and domain information
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only] Back     alignment and domain information
>pfam04407 DUF531 Protein of unknown function (DUF531) Back     alignment and domain information
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>pfam09895 DUF2122 RecB-family nuclease (DUF2122) Back     alignment and domain information
>PRK00779 ornithine carbamoyltransferase; 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
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
3onp_A249 Crystal Structure Of TrnaRRNA METHYLTRANSFERASE SPO 8e-47
3ilk_A244 The Structure Of A Probable Methylase Family Protei 1e-32
3ic6_A223 Crystal Structure Of Putative Methylase Family Prot 3e-19
3n4j_A165 Putative Rna Methyltransferase From Yersinia Pestis 2e-18
1gz0_A253 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb 5e-17
1j85_A160 Structure Of Yibk From Haemophilus Influenzae (Hi07 6e-17
3e5y_A160 Crystal Structure Of Trmh Family Rna Methyltransfer 2e-16
3l8u_A182 Crystal Structure Of Smu.1707c, A Putative Rrna Met 3e-15
1x7p_A287 Crystal Structure Of The Spou Methyltransferase Avi 4e-13
1x7o_A287 Crystal Structure Of The Spou Methyltransferase Avi 2e-12
2i6d_A257 The Structure Of A Putative Rna Methyltransferase O 6e-11
1v2x_A194 Trmh Length = 194 3e-10
1zjr_A211 Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODI 2e-05
2ha8_A184 Methyltransferase Domain Of Human Tar (Hiv-1) Rna B 3e-04
3kty_A173 Crystal Structure Of Probable Methyltransferase Fro 7e-15
1ipa_A274 Crystal Structure Of Rna 2'-O Ribose Methyltransfer 3e-10
3gyq_A272 Structure Of The Thiostrepton-Resistance Methyltran 1e-07
3nk6_A277 Structure Of The Nosiheptide-Resistance Methyltrans 2e-06
>gi|306440754|pdb|3ONP|A Chain A, Crystal Structure Of TrnaRRNA METHYLTRANSFERASE SPOU FROM RHODOBACTER Sphaeroides Length = 249 Back     alignment and structure
 Score =  191 bits (485), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 94/241 (39%), Positives = 135/241 (56%), Gaps = 1/241 (0%)

Query: 15  PVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVF 74
           PV ILV PQ GENIG  ARA  NF L +LR+V+PRDGWP+ KA + ++ A  ++D   +F
Sbjct: 5   PVFILVRPQXGENIGAAARAXLNFGLGRLRIVDPRDGWPNPKAVAXASGAGRLLDHAGLF 64

Query: 75  SNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTN 134
             + EAI D  +++ATTAR R   K V  P+ A          G+ VGI+FG ER GL N
Sbjct: 65  PTVAEAIRDCDYVFATTARGRELTKPVXTPERAXAHGRALTGEGRRVGILFGPERTGLEN 124

Query: 135 EEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPA-TKGELL 193
           E++AL+NAI++ PVNP F SLN++Q VLL+ +E       +  + +        +  E+ 
Sbjct: 125 EDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQHDETPPEVIDXARVDFASGLEVE 184

Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQS 253
              D+ E  LE  G+F P EK      +L + + R  L R +V  L G +  +    +Q 
Sbjct: 185 KLGDHFEEKLEAAGFFFPPEKAPGXKLNLRNXWARLPLTRADVQTLHGXLRQIAWKLKQE 244

Query: 254 S 254
           +
Sbjct: 245 N 245


>gi|257097728|pdb|3ILK|A Chain A, The Structure Of A Probable Methylase Family Protein From Haemophilus Influenzae Rd Kw20 Length = 244 Back     alignment and structure
>gi|255311931|pdb|3IC6|A Chain A, Crystal Structure Of Putative Methylase Family Protein From Neisseria Gonorrhoeae Length = 223 Back     alignment and structure
>gi|299689343|pdb|3N4J|A Chain A, Putative Rna Methyltransferase From Yersinia Pestis Length = 165 Back     alignment and structure
>gi|24987276|pdb|1GZ0|A Chain A, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb Length = 253 Back     alignment and structure
gi|28948421|pdb|1J85|A Chain A, Structure Of Yibk From Haemophilus Influenzae (Hi0766), A Truncated Sequence Homolog Of Trna (Guanosine-2'-O-) Methyltransferase (Spou) Length = 160 Back     alignment and structure
>gi|197305217|pdb|3E5Y|A Chain A, Crystal Structure Of Trmh Family Rna Methyltransferase From Burkholderia Pseudomallei Length = 160 Back     alignment and structure
>gi|316983221|pdb|3L8U|A Chain A, Crystal Structure Of Smu.1707c, A Putative Rrna Methyltransferase From Streptococcus Mutans Ua159 Length = 182 Back     alignment and structure
>gi|60593968|pdb|1X7P|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From Streptomyces Viridochromogenes In Complex With The Cofactor Adomet Length = 287 Back     alignment and structure
>gi|60593966|pdb|1X7O|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From Streptomyces Viridochromogenes Length = 287 Back     alignment and structure
>gi|118138229|pdb|2I6D|A Chain A, The Structure Of A Putative Rna Methyltransferase Of The Trmh Family From Porphyromonas Gingivalis Length = 257 Back     alignment and structure
gi|48425869|pdb|1V2X|A Chain A, Trmh Length = 194 Back     alignment and structure
gi|75765771|pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING Enzyme Length = 211 Back     alignment and structure
>gi|112491246|pdb|2HA8|A Chain A, Methyltransferase Domain Of Human Tar (Hiv-1) Rna Binding Protein 1 Length = 184 Back     alignment and structure
>gi|270346815|pdb|3KTY|A Chain A, Crystal Structure Of Probable Methyltransferase From Bordetella Pertussis Tohama I Length = 173 Back     alignment and structure
>gi|22218790|pdb|1IPA|A Chain A, Crystal Structure Of Rna 2'-O Ribose Methyltransferase Length = 274 Back     alignment and structure
>gi|226887998|pdb|3GYQ|A Chain A, Structure Of The Thiostrepton-Resistance Methyltransferase S-Adenosyl-L-Methionine Complex Length = 272 Back     alignment and structure
>gi|301016090|pdb|3NK6|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase Length = 277 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
3onp_A249 TRNA/RRNA methyltransferase (SPOU); structural genomics 7e-47
3ilk_A244 Uncharacterized tRNA/RRNA methyltransferase HI0380; APC 3e-27
3ic6_A223 Putative methylase family protein; structural genomics, 5e-30
3dcm_X192 AdoMet, uncharacterized protein TM_1570; trefoil knot, 3e-24
3kty_A173 Probable methyltransferase; alpha-beta-alpha sandwich, 1e-21
1gz0_A253 Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-meth 4e-14
3n4j_A165 RNA methyltransferase; center for structural genomics o 4e-14
1mxi_A160 YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; 5e-13
3e5y_A160 TRMH family RNA methyltransferase; ssgcid, protein knot 5e-12
3nk6_A277 23S rRNA methyltransferase; nosiheptide, nosiheptide-re 1e-11
1ipa_A274 RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil k 2e-11
1zjr_A211 TRNA (guanosine-2'-O-)-methyltransferase; methylase, RN 1e-10
1x7o_A287 Avirb, rRNA methyltransferase; SPOU, C-terminal knot, s 2e-09
2ha8_A184 TAR (HIV-1) RNA loop binding protein; methyltransferase 7e-09
1v2x_A194 TRNA (GM18) methyltransferase; DEEP trefoil knot, riken 6e-08
3gyq_A272 RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltr 3e-07
2i6d_A257 RNA methyltransferase, TRMH family; stuctural genomics, 4e-05
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides} Length = 249 Back     alignment and structure
 Score =  182 bits (463), Expect = 7e-47
 Identities = 97/239 (40%), Positives = 142/239 (59%), Gaps = 1/239 (0%)

Query: 15  PVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVF 74
           PV ILV PQ+GENIG  ARAM NF L +LR+V+PRDGWP+ KA + ++ A  ++D   +F
Sbjct: 5   PVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLF 64

Query: 75  SNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTN 134
             + EAI D  +++ATTAR R   K V+ P+ A          G+ VGI+FG ER GL N
Sbjct: 65  PTVAEAIRDCDYVFATTARGRELTKPVMTPERAMAHGRALTGEGRRVGILFGPERTGLEN 124

Query: 135 EEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKE-QNTPATKGELL 193
           E++AL+NAI++ PVNP F SLN++Q VLL+ +E       +  + +   +   A+  E+ 
Sbjct: 125 EDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQHDETPPEVIDMARVDFASGLEVE 184

Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQ 252
              D+ E  LE  G+F P EK   M  +L +++ R  L R +V  L G++  +    +Q
Sbjct: 185 KLGDHFEEKLEAAGFFFPPEKAPGMKLNLRNMWARLPLTRADVQTLHGMLRQIAWKLKQ 243


>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} Length = 244 Back     alignment and structure
>3ic6_A Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090} Length = 223 Back     alignment and structure
>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} Length = 192 Back     alignment and structure
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis} Length = 173 Back     alignment and structure
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} SCOP: c.116.1.1 d.79.3.3 Length = 253 Back     alignment and structure
>3n4j_A RNA methyltransferase; center for structural genomics of INF diseases, csgid; 1.47A {Yersinia pestis} PDB: 3n4k_A* 1mxi_A* 1j85_A* Length = 165 Back     alignment and structure
>1mxi_A YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; S-adenosylhomocysteine, SPOU family, structure 2 function project; HET: SAH; 1.70A {Haemophilus influenzae} SCOP: c.116.1.1 PDB: 1j85_A* Length = 160 Back     alignment and structure
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} Length = 160 Back     alignment and structure
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A* Length = 277 Back     alignment and structure
>1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} SCOP: c.116.1.1 d.79.3.3 Length = 274 Back     alignment and structure
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Length = 211 Back     alignment and structure
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Length = 287 Back     alignment and structure
>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens} Length = 184 Back     alignment and structure
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1 Length = 194 Back     alignment and structure
>3gyq_A RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase, spout mtases, SAM, trefoil knot, antibiotic resistance; HET: SAM; 2.45A {Streptomyces cyaneus} Length = 272 Back     alignment and structure
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83} Length = 257 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
3onp_A249 TRNA/RRNA methyltransferase (SPOU); structural genomics 100.0
3ilk_A244 Uncharacterized tRNA/RRNA methyltransferase HI0380; APC 100.0
3ic6_A223 Putative methylase family protein; structural genomics, 100.0
1x7o_A287 Avirb, rRNA methyltransferase; SPOU, C-terminal knot, s 100.0
1v2x_A194 TRNA (GM18) methyltransferase; DEEP trefoil knot, riken 100.0
1zjr_A211 TRNA (guanosine-2'-O-)-methyltransferase; methylase, RN 100.0
1ipa_A274 RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil k 100.0
3n4j_A165 RNA methyltransferase; center for structural genomics o 99.98
3kty_A173 Probable methyltransferase; alpha-beta-alpha sandwich, 100.0
1gz0_A253 Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-meth 100.0
2i6d_A257 RNA methyltransferase, TRMH family; stuctural genomics, 100.0
3nk6_A277 23S rRNA methyltransferase; nosiheptide, nosiheptide-re 100.0
3dcm_X192 AdoMet, uncharacterized protein TM_1570; trefoil knot, 100.0
2ha8_A184 TAR (HIV-1) RNA loop binding protein; methyltransferase 100.0
3e5y_A160 TRMH family RNA methyltransferase; ssgcid, protein knot 99.97
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides} Back     alignment and structure
Probab=100.00  E-value=0  Score=421.46  Aligned_cols=243  Identities=40%  Similarity=0.597  Sum_probs=225.4

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHCCCCCEEEEC
Q ss_conf             89689994288854799999999971998049808888999999999853101344420013778998412553101201
Q gi|254780904|r   13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTA   92 (268)
Q Consensus        13 ~~~~vVLv~p~~p~NiGaiaRa~~~fG~~~L~lv~P~~~~~~~~a~~~a~~a~~~~~~~~~~~~~~~a~~~~~~~~~~~~   92 (268)
                      ..|+||||+||+|+|||||+|+|+|||+++|+||+|+|+++++++.+.|+|+.+.+..+.++.+++++..++....+++.
T Consensus         3 ~~p~iVLv~p~~p~NiGai~R~~~~fG~~~l~lv~p~~~~~~~~~~~~a~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (249)
T 3onp_A            3 IEPVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLFPTVAEAIRDCDYVFATTA   82 (249)
T ss_dssp             CCCEEEEESCCCHHHHHHHHHHHHHTTCCCEEEESCTTCSSCHHHHHHHGGGHHHHHTCEEESSHHHHHTTCSEEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHCCCHHEECEEEEECCHHHHHHHHCCHHHHHH
T ss_conf             99889993899987499999999982899899918988999889998847873220211364459999763000132222


Q ss_pred             CCCCCCEEEECCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             12234303412420356665531158816999945888424310001232220476787341016889999999999962
Q gi|254780904|r   93 RNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENS  172 (268)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~valVFG~E~~GLs~eel~~cd~~v~IPt~~~~~SLNLS~AvaIvlYEl~r~~  172 (268)
                      +.+........+.............++++|||||+|++||+++++++||++++|||++.|+||||||||+|+||||+++.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kvalVFG~E~~GLs~e~l~~cd~~v~IP~~~~~~SLNls~AvaIvlyEl~r~~  162 (249)
T 3onp_A           83 RGRELTKPVMTPERAMAHGRALTGEGRRVGILFGPERTGLENEDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQH  162 (249)
T ss_dssp             SCCCSSSCEECHHHHHHHHHHHHHTTCCEEEEECCTTTCCCHHHHTTSSEEEECCCCTTCCCCCHHHHHHHHHHHHHHC-
T ss_pred             HHCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHCCCEEEEECCCCCCCCEEHHHHHHHHHHHHHHHH
T ss_conf             31357864100113467778765047765999947877888788740251898348999886159999999999999984


Q ss_pred             CCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             13665444-33333468888999999999999872899875438999999999863169998999999999999998410
Q gi|254780904|r  173 IVSSEKNV-KEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSR  251 (268)
Q Consensus       173 ~~~~~~~~-~~~~~~a~~~~l~~~~~~l~~~l~~~~f~~~~~~~~~~~~~lrrl~~R~~l~~~E~~~L~Gil~~l~~~~~  251 (268)
                      ........ .....+|++++++.|++++.+.|+++|||.|++++++++.+|||||+|+.||++|+++|||++++++|+++
T Consensus       163 ~~~~~~~~~~~~~~~a~~~~~~~l~~~l~~~l~~~~f~~~~~~~~~~~~~lr~l~~r~~l~~~E~~~L~Gi~~~i~~~l~  242 (249)
T 3onp_A          163 DETPPEVIDMARVDFASGLEVEKLGDHFEEKLEAAGFFFPPEKAPGMKLNLRNMWARLPLTRADVQTLHGMLRQIAWKLK  242 (249)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             15787654310012110889999999999999976999984112799999999997379999999999999999999974


Q ss_pred             CCCC
Q ss_conf             3421
Q gi|254780904|r  252 QSSR  255 (268)
Q Consensus       252 ~~~~  255 (268)
                      +...
T Consensus       243 ~~~~  246 (249)
T 3onp_A          243 QENL  246 (249)
T ss_dssp             ----
T ss_pred             CCCC
T ss_conf             6576



>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} Back     alignment and structure
>3ic6_A Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090} Back     alignment and structure
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Back     alignment and structure
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1 Back     alignment and structure
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Back     alignment and structure
>1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} SCOP: c.116.1.1 d.79.3.3 Back     alignment and structure
>3n4j_A RNA methyltransferase; center for structural genomics of INF diseases, csgid; 1.47A {Yersinia pestis} PDB: 3n4k_A* 1mxi_A* 1j85_A* Back     alignment and structure
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis} Back     alignment and structure
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} SCOP: c.116.1.1 d.79.3.3 Back     alignment and structure
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83} Back     alignment and structure
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A* Back     alignment and structure
>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} Back     alignment and structure
>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens} Back     alignment and structure
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} 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 268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
d1gz0a1166 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherich 6e-13
d1mxia_156 c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease 3e-11
d1v2xa_191 c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Ther 2e-09
d1ipaa1158 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {T 6e-08
>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 166 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: RlmB, C-terminal domain
species: Escherichia coli [TaxId: 562]
 Score = 68.3 bits (166), Expect = 6e-13
 Identities = 29/165 (17%), Positives = 56/165 (33%), Gaps = 12/165 (7%)

Query: 6   PQLQNSAKGP-VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANA 64
           P L  S   P ++IL       N+G   R+     +  + +   R    +  A+  +  A
Sbjct: 9   PDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGA 68

Query: 65  DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGII 124
              +  +R  +NL   +  L                 L           +      + ++
Sbjct: 69  AESVPLIR-VTNLARTMRMLQEENIWIVGTAGEADHTL----------YQSKMTGRLALV 117

Query: 125 FGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
            G E  G+        + +IS P+     SLN+S A  + ++E +
Sbjct: 118 MGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAV 162


>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]} Length = 156 Back     information, alignment and structure
>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]} Length = 191 Back     information, alignment and structure
>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 158 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
d1gz0a1166 RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} 100.0
d1ipaa1158 RrmA (RrmH), C-terminal domain {Thermus thermophilus [T 100.0
d1mxia_156 Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK ho 99.97
d1v2xa_191 tRNA (Gm18) methyltransferase TrmH {Thermus thermophilu 100.0
d1pvva2163 Ornithine transcarbamoylase {Archaeon Pyrococcus furios 91.74
>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: RlmB, C-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=3.4e-35  Score=238.40  Aligned_cols=153  Identities=16%  Similarity=0.124  Sum_probs=123.2

Q ss_pred             HCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHCCCCCE
Q ss_conf             21348968999428885479999999997199804980888899999999985310134442001377899841255310
Q gi|254780904|r    9 QNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIY   88 (268)
Q Consensus         9 ~~~~~~~~vVLv~p~~p~NiGaiaRa~~~fG~~~L~lv~P~~~~~~~~a~~~a~~a~~~~~~~~~~~~~~~a~~~~~~~~   88 (268)
                      ....+..+|||+++++|+|+|+|+|+|++||++.++++.++++++++++.+.|+|+.+.+... .+.++.++++.+....
T Consensus        13 ~~~~~~~~vvLd~i~~p~N~GaiiRta~afG~~~v~~~~~~~~~~~~~~~r~s~g~~~~v~~~-~~~~~~~~l~~~~~~~   91 (166)
T d1gz0a1          13 ASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLI-RVTNLARTMRMLQEEN   91 (166)
T ss_dssp             HTCSSCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEESSSSCCCCHHHHHHHTTHHHHSCEE-EESCHHHHHHHHHHTT
T ss_pred             HCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHEECCCCCEEECEE-ECCCHHHHHHHHCCCC
T ss_conf             466898799995788865599999999852886465402543110012312313750376506-6399999998701243


Q ss_pred             EEECCCCCCCEEEECCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             12011223430341242035666553115881699994588842431000123222047678734101688999999999
Q gi|254780904|r   89 ATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWEC  168 (268)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~valVFG~E~~GLs~eel~~cd~~v~IPt~~~~~SLNLS~AvaIvlYEl  168 (268)
                      ..         .... ..............++++||||+|++|||+++++.||..++|||.+.++|||||+|++|+|||+
T Consensus        92 ~~---------~~~~-~~~~~~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~~v~IPm~~~~~SLNvs~A~~I~lye~  161 (166)
T d1gz0a1          92 IW---------IVGT-AGEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEA  161 (166)
T ss_dssp             CE---------EEEE-CTTCSEEGGGSCCCSSEEEEEEBTTTBSCHHHHHTCSEEEECCCSSSSCCCCHHHHHHHHHHHH
T ss_pred             CC---------CCCC-CCCCCCCHHHHHCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCCCCCCCEEHHHHHHHHHHHH
T ss_conf             21---------1123-4544454788514687389966676787799998689899970968997546999999999999


Q ss_pred             HHHH
Q ss_conf             9962
Q gi|254780904|r  169 MENS  172 (268)
Q Consensus       169 ~r~~  172 (268)
                      +||.
T Consensus       162 ~rqr  165 (166)
T d1gz0a1         162 VRQR  165 (166)
T ss_dssp             HHHT
T ss_pred             HHCC
T ss_conf             9755



>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1pvva2 c.78.1.1 (A:151-313) Ornithine transcarbamoylase {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 268 tRNA/rRNA methyltransferase [Candidatus Liberibact
3kty_A_173 (A:) Probable methyltransferase; alpha-beta-alpha 8e-22
3dcm_X_192 (X:) AdoMet, uncharacterized protein TM_1570; tref 3e-20
3ilk_A_1-174174 (A:1-174) Uncharacterized tRNA/RRNA methyltransfer 2e-19
3ic6_A_1-201201 (A:1-201) Putative methylase family protein; struc 5e-19
1x7o_A_119-287169 (A:119-287) Avirb, rRNA methyltransferase; SPOU, C 3e-18
2i6d_A_99-257159 (A:99-257) RNA methyltransferase, TRMH family; stu 3e-18
1v2x_A_21-176156 (A:21-176) TRNA (GM18) methyltransferase; DEEP tre 2e-17
1gz0_A_90-253164 (A:90-253) Hypothetical tRNA/RRNA methyltransferas 3e-17
3gyq_A_113-272160 (A:113-272) RRNA (adenosine-2'-O-)-methyltransfera 4e-17
1zjr_A_24-180157 (A:24-180) TRNA (guanosine-2'-O-)-methyltransferas 4e-17
1ipa_A_109-274166 (A:109-274) RRMH, RNA 2'-O-ribose methyltransferas 7e-16
2ha8_A_184 (A:) TAR (HIV-1) RNA loop binding protein; methylt 9e-16
1mxi_A_160 (A:) YIBK, hypothetical tRNA/RRNA methyltransferas 3e-15
3e5y_A_160 (A:) TRMH family RNA methyltransferase; ssgcid, pr 2e-14
3ilk_A_175-24470 (A:175-244) Uncharacterized tRNA/RRNA methyltransf 9e-11
>3kty_A (A:) Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis}Length = 173 Back     alignment and structure
 Score = 98.4 bits (244), Expect = 8e-22
 Identities = 50/168 (29%), Positives = 75/168 (44%), Gaps = 6/168 (3%)

Query: 7   QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGW--PSEKARSSSANA 64
               +      I   P    N+G  ARA+      +L LV PR        +A + ++ A
Sbjct: 3   AXTQAFSRVRFIXTQPSHPGNVGSAARAIKTXGFGELVLVAPRFPDXTAQPEAVALASGA 62

Query: 65  DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKE---AAIVLNERIFSGQNV 121
             V++   V   L+EA+A +   +A T R R+        +E    A    +   +G  V
Sbjct: 63  LDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAG-VV 121

Query: 122 GIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
            I+ G ER GLTN +I L + I   P NP + SLN++QA+ L  WE  
Sbjct: 122 AIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELR 169


>3dcm_X (X:) AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima}Length = 192 Back     alignment and structure
>3ilk_A (A:1-174) Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae}Length = 174 Back     alignment and structure
>3ic6_A (A:1-201) Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090}Length = 201 Back     alignment and structure
>1x7o_A (A:119-287) Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A*Length = 169 Back     alignment and structure
>2i6d_A (A:99-257) RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83}Length = 159 Back     alignment and structure
>1v2x_A (A:21-176) TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus}Length = 156 Back     alignment and structure
>1gz0_A (A:90-253) Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli}Length = 164 Back     alignment and structure
>3gyq_A (A:113-272) RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase, spout mtases, SAM, trefoil knot, antibiotic resistance; HET: SAM; 2.45A {Streptomyces cyaneus}Length = 160 Back     alignment and structure
>1zjr_A (A:24-180) TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus}Length = 157 Back     alignment and structure
>1ipa_A (A:109-274) RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus}Length = 166 Back     alignment and structure
>2ha8_A (A:) TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens}Length = 184 Back     alignment and structure
>1mxi_A (A:) YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; S-adenosylhomocysteine, SPOU family, structure 2 function project; HET: SAH; 1.70A {Haemophilus influenzae}Length = 160 Back     alignment and structure
>3e5y_A (A:) TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305}Length = 160 Back     alignment and structure
>3ilk_A (A:175-244) Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae}Length = 70 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target268 tRNA/rRNA methyltransferase [Candidatus Liberibacter as
3ic6_A_1-201201 Putative methylase family protein; structural geno 100.0
3gyq_A_113-272160 RRNA (adenosine-2'-O-)-methyltransferase; rRNA met 100.0
1x7o_A_119-287169 Avirb, rRNA methyltransferase; SPOU, C-terminal kn 100.0
3kty_A_173 Probable methyltransferase; alpha-beta-alpha sandw 100.0
1gz0_A_90-253164 Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O 100.0
1ipa_A_109-274166 RRMH, RNA 2'-O-ribose methyltransferase; DEEP tref 100.0
2i6d_A_99-257159 RNA methyltransferase, TRMH family; stuctural geno 100.0
1mxi_A_160 YIBK, hypothetical tRNA/RRNA methyltransferase HI0 100.0
3ilk_A_1-174174 Uncharacterized tRNA/RRNA methyltransferase HI0380 100.0
2ha8_A_184 TAR (HIV-1) RNA loop binding protein; methyltransf 99.98
3e5y_A_160 TRMH family RNA methyltransferase; ssgcid, protein 99.97
1v2x_A_21-176156 TRNA (GM18) methyltransferase; DEEP trefoil knot, 99.97
1zjr_A_24-180157 TRNA (guanosine-2'-O-)-methyltransferase; methylas 99.97
3dcm_X_192 AdoMet, uncharacterized protein TM_1570; trefoil k 99.97
1k3r_A_1-84_161-268192 Conserved protein MT0001; beta barrel, structural 94.38
1z85_A_83-234152 Hypothetical protein TM1380; structural genomics, 93.26
3ilk_A_175-24470 Uncharacterized tRNA/RRNA methyltransferase HI0380 99.45
1duv_G_153-278126 Octase-1, ornithine transcarbamoylase; enzyme-inhi 92.31
1dxh_A_153-274122 Ornithine carbamoyltransferase; transcarbamylase; 91.72
1vlv_A_165-294130 Otcase, ornithine carbamoyltransferase; TM1097, st 90.9
>3ic6_A (A:1-201) Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090} Back     alignment and structure
Probab=100.00  E-value=1.8e-35  Score=242.51  Aligned_cols=172  Identities=28%  Similarity=0.381  Sum_probs=154.9

Q ss_pred             HHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCCC-------------------CCCCCHHHHHHHHHCCC
Q ss_conf             55321348968999428885479999999997199804980888-------------------89999999998531013
Q gi|254780904|r    6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPR-------------------DGWPSEKARSSSANADC   66 (268)
Q Consensus         6 ~~l~~~~~~~~vVLv~p~~p~NiGaiaRa~~~fG~~~L~lv~P~-------------------~~~~~~~a~~~a~~a~~   66 (268)
                      +.+......++|||+++++|+|+|+|+|+|++||++.++|++|+                   .+++++++++.|+|+.+
T Consensus         9 ~~~~~~~~~~~ivld~v~~p~NiG~i~Rsa~afGv~~i~lv~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~a~ga~~   88 (201)
T 3ic6_A            9 PALPDYLGNIRIILTRTSHPANIGSAARAXKTXGLHRLTIVTPNLXATPXTENPPVFNPDDVQSFALPEESFILASGAAD   88 (201)
T ss_dssp             CCCCGGGGGEEEEEESCCCHHHHHHHHHHHHHTTCCCEEEESCCCCCBTTBSSCCCCCTTCGGGCCCCHHHHHHHGGGHH
T ss_pred             CCCHHHHCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHCCCHH
T ss_conf             23200205828999379888719999999998599869997887787534655431045321245566899999467698


Q ss_pred             CCCCHHCCCCHHHHHHCCCCCEEEECCCCCCCEEEECCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCEEEC
Q ss_conf             44420013778998412553101201122343034124203566655311588169999458884243100012322204
Q gi|254780904|r   67 VIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISF  146 (268)
Q Consensus        67 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~valVFG~E~~GLs~eel~~cd~~v~I  146 (268)
                      .+.........+.+.........+..........................+.++++||||+|++|||+++++.||..+.|
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvlG~E~~Gls~~~l~~~d~~v~I  168 (201)
T 3ic6_A           89 VLHNAEIVATLDEALADTTIACALTSRRREITAPLQTPRDLVPELLQAANRGEKVALVFGNETFGLSIEEVRACNRLXTI  168 (201)
T ss_dssp             HHHTCEEESCHHHHHTTEEEEEEECCSCC--CCCCBCHHHHHHHHHHHHHTTCEEEEEECBTTTBCCHHHHHTCSEEECC
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHEEC
T ss_conf             87665401239999975122102222100243332252100101222104787347876765577216899864222404


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             7678734101688999999999996213665
Q gi|254780904|r  147 PVNPLFPSLNISQAVLLMVWECMENSIVSSE  177 (268)
Q Consensus       147 Pt~~~~~SLNLS~AvaIvlYEl~r~~~~~~~  177 (268)
                      ||.+.++|||||+|++|+|||++||...+..
T Consensus       169 P~~g~~~SLNvs~A~aI~l~e~~rq~~~~~~  199 (201)
T 3ic6_A          169 NGNPDYFSLNLAQAVQVVCYEIFSQTDSPXT  199 (201)
T ss_dssp             CCCTTCCCCCHHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCEEHHHHHHHHHHHHHHHHCCCCC
T ss_conf             6789988670999999999999996167665



>3gyq_A (A:113-272) RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase, spout mtases, SAM, trefoil knot, antibiotic resistance; HET: SAM; 2.45A {Streptomyces cyaneus} Back     alignment and structure
>1x7o_A (A:119-287) Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Back     alignment and structure
>3kty_A (A:) Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis} Back     alignment and structure
>1gz0_A (A:90-253) Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} Back     alignment and structure
>1ipa_A (A:109-274) RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} Back     alignment and structure
>2i6d_A (A:99-257) RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83} Back     alignment and structure
>1mxi_A (A:) YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; S-adenosylhomocysteine, SPOU family, structure 2 function project; HET: SAH; 1.70A {Haemophilus influenzae} Back     alignment and structure
>3ilk_A (A:1-174) Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} Back     alignment and structure
>2ha8_A (A:) TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens} Back     alignment and structure
>3e5y_A (A:) TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} Back     alignment and structure
>1v2x_A (A:21-176) TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} Back     alignment and structure
>1zjr_A (A:24-180) TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Back     alignment and structure
>3dcm_X (X:) AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} Back     alignment and structure
>1k3r_A (A:1-84,A:161-268) Conserved protein MT0001; beta barrel, structural genomics, PSI, protein structure initiative; 2.30A {Methanothermobacterthermautotrophicus} Back     alignment and structure
>1z85_A (A:83-234) Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8} Back     alignment and structure
>3ilk_A (A:175-244) Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} Back     alignment and structure
>1duv_G (G:153-278) Octase-1, ornithine transcarbamoylase; enzyme-inhibitor complex; HET: PSQ; 1.70A {Escherichia coli} Back     alignment and structure
>1dxh_A (A:153-274) Ornithine carbamoyltransferase; transcarbamylase; 2.50A {Pseudomonas aeruginosa} Back     alignment and structure
>1vlv_A (A:165-294) Otcase, ornithine carbamoyltransferase; TM1097, structural genomics, JCSG, protein structure initiative, PSI; 2.25A {Thermotoga maritima} Back     alignment and structure