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Conserved domains on  [gi|1011944946|ref|WP_062752871|]
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MULTISPECIES: TlyA family RNA methyltransferase [Bacillaceae]

Protein Classification

TlyA family RNA methyltransferase( domain architecture ID 11439687)

TlyA family RNA methyltransferase similar to Mycobacterium tuberculosis 16S/23S rRNA (cytidine-2'-O)-methyltransferase and Bacillus subtilis rRNA methyltransferase YqxC

CATH:  3.40.50.150
Gene Ontology:  GO:0008168|GO:0032259|GO:0003723
PubMed:  12826405|12504684

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
6-250 1.22e-159

Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 443.35  E-value: 1.22e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVLPYVSRGGLKLEKALRTFDVSVQDKI 85
Cdd:COG1189     1 ERLDVLLVERGLAESREKAQRLIMAGRVLVNGQVVDKPGTKVPEDAEIEVKGEELPYVSRGGLKLEGALDAFGIDVAGKV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  86 ILDIGASTGGFTDCALQHGAKLSYAVDVGYNQLAWKLRQDDRVVVMERTNFRYVTPDYFTkGLPQFATIDVSFISLKLIL 165
Cdd:COG1189    81 CLDIGASTGGFTDCLLQRGAAKVYAVDVGYGQLAWKLRQDPRVVVLERTNARYLTPEDLP-EPPDLVVIDVSFISLTLVL 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946 166 PVLKTVLVPESDVIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFALCEGFDVMNLSYSPITGGDGNIEFLLHLR 245
Cdd:COG1189   160 PALLALLKPGGELVALVKPQFEVGRERVGKGGVVRDPALHAEVIEKVLAAAAELGLRVLGLTPSPITGPDGNIEFLLWLR 239

                  ....*
gi 1011944946 246 FQGGK 250
Cdd:COG1189   240 KGGGP 244
 
Name Accession Description Interval E-value
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
6-250 1.22e-159

Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 443.35  E-value: 1.22e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVLPYVSRGGLKLEKALRTFDVSVQDKI 85
Cdd:COG1189     1 ERLDVLLVERGLAESREKAQRLIMAGRVLVNGQVVDKPGTKVPEDAEIEVKGEELPYVSRGGLKLEGALDAFGIDVAGKV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  86 ILDIGASTGGFTDCALQHGAKLSYAVDVGYNQLAWKLRQDDRVVVMERTNFRYVTPDYFTkGLPQFATIDVSFISLKLIL 165
Cdd:COG1189    81 CLDIGASTGGFTDCLLQRGAAKVYAVDVGYGQLAWKLRQDPRVVVLERTNARYLTPEDLP-EPPDLVVIDVSFISLTLVL 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946 166 PVLKTVLVPESDVIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFALCEGFDVMNLSYSPITGGDGNIEFLLHLR 245
Cdd:COG1189   160 PALLALLKPGGELVALVKPQFEVGRERVGKGGVVRDPALHAEVIEKVLAAAAELGLRVLGLTPSPITGPDGNIEFLLWLR 239

                  ....*
gi 1011944946 246 FQGGK 250
Cdd:COG1189   240 KGGGP 244
tly TIGR00478
TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA ...
7-239 7.06e-101

TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA from Mycobacterium tuberculosis, an rRNA methylase whose modifications are necessary to confer sensitivity to ribosome-targeting antibiotics capreomycin and viomycin. Homology supports identification as a methyltransferase. However, a parallel literature persists in calling some members hemolysins. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. A recent study (2013) on SCO1782 from Streptomyces coelicolor shows hemolysin activity as earlier described for a homolog from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. [Unknown function, General]


Pssm-ID: 129570 [Multi-domain]  Cd Length: 228  Bit Score: 294.02  E-value: 7.06e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946   7 RLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVlPYVSRGGLKLEKALRTFDVSVQDKII 86
Cdd:TIGR00478   1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQNP-LFVSRGGEKLKEALEEFNIDVKNKIV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  87 LDIGASTGGFTDCALQHGAKLSYAVDVGYNQLAWKLRQDDRVVVMERTNFRYVTPDYFTkglPQFATIDVSFISLKLILP 166
Cdd:TIGR00478  80 LDVGSSTGGFTDCALQKGAKEVYGVDVGYNQLAEKLRQDERVKVLERTNIRYVTPADIF---PDFATFDVSFISLISILP 156
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1011944946 167 VLKTVLVPeSDVIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFALCEGFDVMNLSYSPITGGDGNIE 239
Cdd:TIGR00478 157 ELDLLLNP-NDLTLLFKPQFEAGREKKNKKGVVRDKEAIALALHKVIDKGESPDFQEKKIIFSLTKGKRGNVE 228
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
62-246 1.70e-49

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 161.60  E-value: 1.70e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  62 YVSRGGLKLEKALRTFDVSVQDKIILDIGASTGGFTDCALQHGAKLSYAVDVGYNQLaWKLRQDDRVVVMeRTNFRYVTP 141
Cdd:pfam01728   1 YRSRAAYKLLEIDEKFGLLKPGKTVLDLGAAPGGWSQVALQRGAGKVVGVDLGPMQL-WKPRNDPGVTFI-QGDIRDPET 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946 142 DY----FTKGLPQFATIDVS-FISLKLILPVLKTvlvpesdvIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFA 216
Cdd:pfam01728  79 LDlleeLLGRKVDLVLSDGSpFISGNKVLDHLRS--------LDLVKAALEVALELLRKGGNFVCKVFQGEDFSELLYLL 150
                         170       180       190
                  ....*....|....*....|....*....|
gi 1011944946 217 LCeGFDVMNLSYSPITGGDGNIEFLLHLRF 246
Cdd:pfam01728 151 KL-GFEKVGVFKPPASRPESSEEYLVCLGF 179
S4 smart00363
S4 RNA-binding domain;
7-61 1.42e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 47.59  E-value: 1.42e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1011944946    7 RLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVLP 61
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
6-57 2.30e-06

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 44.16  E-value: 2.30e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKV-PADIpLTIKG 57
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVkPGDV-IEVDG 52
 
Name Accession Description Interval E-value
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
6-250 1.22e-159

Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 443.35  E-value: 1.22e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVLPYVSRGGLKLEKALRTFDVSVQDKI 85
Cdd:COG1189     1 ERLDVLLVERGLAESREKAQRLIMAGRVLVNGQVVDKPGTKVPEDAEIEVKGEELPYVSRGGLKLEGALDAFGIDVAGKV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  86 ILDIGASTGGFTDCALQHGAKLSYAVDVGYNQLAWKLRQDDRVVVMERTNFRYVTPDYFTkGLPQFATIDVSFISLKLIL 165
Cdd:COG1189    81 CLDIGASTGGFTDCLLQRGAAKVYAVDVGYGQLAWKLRQDPRVVVLERTNARYLTPEDLP-EPPDLVVIDVSFISLTLVL 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946 166 PVLKTVLVPESDVIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFALCEGFDVMNLSYSPITGGDGNIEFLLHLR 245
Cdd:COG1189   160 PALLALLKPGGELVALVKPQFEVGRERVGKGGVVRDPALHAEVIEKVLAAAAELGLRVLGLTPSPITGPDGNIEFLLWLR 239

                  ....*
gi 1011944946 246 FQGGK 250
Cdd:COG1189   240 KGGGP 244
tly TIGR00478
TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA ...
7-239 7.06e-101

TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA from Mycobacterium tuberculosis, an rRNA methylase whose modifications are necessary to confer sensitivity to ribosome-targeting antibiotics capreomycin and viomycin. Homology supports identification as a methyltransferase. However, a parallel literature persists in calling some members hemolysins. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. A recent study (2013) on SCO1782 from Streptomyces coelicolor shows hemolysin activity as earlier described for a homolog from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. [Unknown function, General]


Pssm-ID: 129570 [Multi-domain]  Cd Length: 228  Bit Score: 294.02  E-value: 7.06e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946   7 RLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVlPYVSRGGLKLEKALRTFDVSVQDKII 86
Cdd:TIGR00478   1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQNP-LFVSRGGEKLKEALEEFNIDVKNKIV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  87 LDIGASTGGFTDCALQHGAKLSYAVDVGYNQLAWKLRQDDRVVVMERTNFRYVTPDYFTkglPQFATIDVSFISLKLILP 166
Cdd:TIGR00478  80 LDVGSSTGGFTDCALQKGAKEVYGVDVGYNQLAEKLRQDERVKVLERTNIRYVTPADIF---PDFATFDVSFISLISILP 156
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1011944946 167 VLKTVLVPeSDVIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFALCEGFDVMNLSYSPITGGDGNIE 239
Cdd:TIGR00478 157 ELDLLLNP-NDLTLLFKPQFEAGREKKNKKGVVRDKEAIALALHKVIDKGESPDFQEKKIIFSLTKGKRGNVE 228
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
62-246 1.70e-49

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 161.60  E-value: 1.70e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946  62 YVSRGGLKLEKALRTFDVSVQDKIILDIGASTGGFTDCALQHGAKLSYAVDVGYNQLaWKLRQDDRVVVMeRTNFRYVTP 141
Cdd:pfam01728   1 YRSRAAYKLLEIDEKFGLLKPGKTVLDLGAAPGGWSQVALQRGAGKVVGVDLGPMQL-WKPRNDPGVTFI-QGDIRDPET 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011944946 142 DY----FTKGLPQFATIDVS-FISLKLILPVLKTvlvpesdvIALVKPQFEAGKEKVGKKGIVRDPNVHEEVLTSIIDFA 216
Cdd:pfam01728  79 LDlleeLLGRKVDLVLSDGSpFISGNKVLDHLRS--------LDLVKAALEVALELLRKGGNFVCKVFQGEDFSELLYLL 150
                         170       180       190
                  ....*....|....*....|....*....|
gi 1011944946 217 LCeGFDVMNLSYSPITGGDGNIEFLLHLRF 246
Cdd:pfam01728 151 KL-GFEKVGVFKPPASRPESSEEYLVCLGF 179
S4 smart00363
S4 RNA-binding domain;
7-61 1.42e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 47.59  E-value: 1.42e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1011944946    7 RLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKVPADIPLTIKGDVLP 61
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
6-47 4.28e-07

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 45.56  E-value: 4.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKV 47
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRV 42
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
6-57 2.30e-06

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 44.16  E-value: 2.30e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1011944946   6 ERLDVLLVQRGLIETREKAKRAIMAGLVYSNEIRLDKPGEKV-PADIpLTIKG 57
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVkPGDV-IEVDG 52
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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