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Conserved domains on  [gi|1113433013|gb|OJW95044|]
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MAG: RNA methyltransferase [Alicycliphilus sp. 69-12]

Protein Classification

THUMP domain-containing class I SAM-dependent RNA methyltransferase( domain architecture ID 11414754)

THUMP domain-containing class I SAM-dependent RNA methyltransferase catalyzes the methylation of a specific RNA substrate using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor, such as ribosomal RNA large subunit methyltransferase L that specifically methylates the guanine in position 2445 (m2G2445) of 23S rRNA

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0001510|GO:0008757|GO:1904047
PubMed:  11295541|12826405|12504684
SCOP:  3000118

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
RlmL COG0116
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ...
 4-403 0e+00

23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification


:

Pssm-ID: 439886 [Multi-domain]  Cd Length: 369  Bit Score: 518.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   4 LQLFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGD 83
Cdd:COG0116     1 FELFATCARGLEALLADE---LKELGAEDVKVENGGVSFEGDLEDIYRANLWLRTASRVLLPLAEFKARTFDDLYEGAKA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  84 VAWEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKSGSRPDVETRWPDVRIHLHLTREHAQLYIDTSGEP 163
Cdd:COG0116    78 IPWEEYLPPDGTFAVDATSVKSKLFHSQFAALRVKDAIVDRFREKYGARPSVDEDGPDVRIHVHLLKDRATLSLDTSGES 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 164 LFKRGWREDKGDAPLKETLAAAMIAATGWDPHGdqplPLYDPCCGSGTVVIEAAQIACRIAPGLRRRFGFEKLLPYQAHV 243
Cdd:COG0116   158 LHKRGYREAQGEAPLKETLAAALLLLSGWDGDR----PLVDPMCGSGTILIEAALIAANIAPGLNRDFAFEKWPDFDAEL 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 244 WSAIKEEAAGAVVT-SPVPIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPcEQPGVMLLNPPYGERIaaag 322
Cdd:COG0116   234 WQELREEAEARIKRdPPLPIFGSDIDPRAIEAARENAERAGVADLIEFEQADFRDLEPP-AEPGLIITNPPYGERL---- 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 323 sagrsarermavvaragresAQTEDGVDFFQQLAAHWKRHYAGWQAWLLTPDLKLPGKMRLKESRRVPLWNGPIECRMFR 402
Cdd:COG0116   309 --------------------GEEEELEALYRELGDVLKQRFKGWSAYILTSDPELEKAIGLKASKRRKLYNGGLECRLLQ 368


                  .
gi 1113433013 403 F 403
Cdd:COG0116   369 Y 369
 
Name Accession Description Interval E-value
RlmL COG0116
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ...
 4-403 0e+00

23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 439886 [Multi-domain]  Cd Length: 369  Bit Score: 518.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   4 LQLFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGD 83
Cdd:COG0116     1 FELFATCARGLEALLADE---LKELGAEDVKVENGGVSFEGDLEDIYRANLWLRTASRVLLPLAEFKARTFDDLYEGAKA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  84 VAWEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKSGSRPDVETRWPDVRIHLHLTREHAQLYIDTSGEP 163
Cdd:COG0116    78 IPWEEYLPPDGTFAVDATSVKSKLFHSQFAALRVKDAIVDRFREKYGARPSVDEDGPDVRIHVHLLKDRATLSLDTSGES 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 164 LFKRGWREDKGDAPLKETLAAAMIAATGWDPHGdqplPLYDPCCGSGTVVIEAAQIACRIAPGLRRRFGFEKLLPYQAHV 243
Cdd:COG0116   158 LHKRGYREAQGEAPLKETLAAALLLLSGWDGDR----PLVDPMCGSGTILIEAALIAANIAPGLNRDFAFEKWPDFDAEL 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 244 WSAIKEEAAGAVVT-SPVPIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPcEQPGVMLLNPPYGERIaaag 322
Cdd:COG0116   234 WQELREEAEARIKRdPPLPIFGSDIDPRAIEAARENAERAGVADLIEFEQADFRDLEPP-AEPGLIITNPPYGERL---- 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 323 sagrsarermavvaragresAQTEDGVDFFQQLAAHWKRHYAGWQAWLLTPDLKLPGKMRLKESRRVPLWNGPIECRMFR 402
Cdd:COG0116   309 --------------------GEEEELEALYRELGDVLKQRFKGWSAYILTSDPELEKAIGLKASKRRKLYNGGLECRLLQ 368


                  .
gi 1113433013 403 F 403
Cdd:COG0116   369 Y 369
rlmL PRK11783
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ...
 4-413 5.46e-120

bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL;


Pssm-ID: 236981 [Multi-domain]  Cd Length: 702  Bit Score: 364.51  E-value: 5.46e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   4 LQLFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGD 83
Cdd:PRK11783    2 NSLFASCAKGLEELLKDE---LEALGASECKVVQGGVHFEGDLELAYRSCLWSRLASRILLPLAEFKVYSDLDLYLGVQA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  84 VAWEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKSGSRPDVETRWPDVRIHLHLTREHAQLYIDTSGEP 163
Cdd:PRK11783   79 IDWTEHFSPDKTFAVDFSGTNDEIRNTQFGALKVKDAIVDRFRRKGGPRPSVDKEQPDIRINARLNKGEATISLDLSGES 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 164 LFKRGWREDKGDAPLKETLAAAMIAATGWDPHGDqplPLYDPCCGSGTVVIEAAQIACRIAPGLRR-RFGFEKLLPYQAH 242
Cdd:PRK11783  159 LHQRGYRQATGEAPLKENLAAAILLRSGWPQEGT---PLLDPMCGSGTLLIEAAMMAADIAPGLHReRWGFSGWLGHDEA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 243 VWSAIKEEA----AGAVVTSPVPIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDA--LQRMPPCEQPGVMLLNPPYGE 316
Cdd:PRK11783  236 LWQELLEEAqeraRAGLAELPSKFYGSDIDPRVIQAARKNARRAGVAELITFEVKDVadLKNPLPKGPTGLVISNPPYGE 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 317 RIAaagsagrsarERMAVVAragresaqtedgvdFFQQLAAHWKRHYAGWQAWLLTPDLKLPGKMRLKESRRVPLWNGPI 396
Cdd:PRK11783  316 RLG----------EEPALIA--------------LYSQLGRRLKQQFGGWNAALFSSSPELLSCLGLRADKQYKLKNGAL 371

                         410
                  ....*....|....*..
gi 1113433013 397 ECRMFRFDLVAGPARPR 413
Cdd:PRK11783  372 ECVLKNYTIAEESTSSD 388
THUMP_AdoMetMT cd11715
THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of ...
 6-161 1.12e-50

THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of this family contain an N-terminal THUMP domain and a C-terminal S-adenosylmethionine-dependent methyltransferase domain. Members have been implicated in the modification of 23S RNA m2G2445, a highly conserved modification in bacteria and in the m2G6 modification of tRNA. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212584  Cd Length: 152  Bit Score: 167.76  E-value: 1.12e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   6 LFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGDVA 85
Cdd:cd11715     1 FFATCPPGLEELLAAE---LKALGAEDVEVGPGGVSFEGDLEDAYRANLWLRTAHRVLLLLAEFEAEDFDDLYELAKAID 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113433013  86 WEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKsGSRPDVETRWPDVRIHLHLTREHAQLYIDTSG 161
Cdd:cd11715    78 WEDYLDPDGTFAVRATRVGSKLFHSQFAALRVKDAIVDRFREK-GKRPSVDLDNPDVRIRVHLSKDRATLSLDLSG 152
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 167-400 1.76e-33

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 123.62  E-value: 1.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 167 RGWREDKGDAPLKETLAAAMIAATGWDPhGDqplPLYDPCCGSGTVVIEAAQIACRIAPGLrrrFGFEKLLPyqahvwsa 246
Cdd:pfam01170   1 RGYRPFNGPAPLKETLAAAMVNLAGWKP-GD---PLLDPMCGSGTILIEAALMGANIAPGK---FDARVRAP-------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 247 ikeeaagavvtspvpIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPCEQPGVMLLNPPYGERIAaagsagr 326
Cdd:pfam01170  66 ---------------LYGSDIDRRMVQGARLNAENAGVGDLIEFVQADAADLPLLEGSVDVIVTNPPYGIRLG------- 123

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113433013 327 sarermavvaragresaQTEDGVDFFQQLAAHWKRHYA--GWQAWLLTPDLKLPGKMRLKESRRVPLWNGPIECRM 400
Cdd:pfam01170 124 -----------------SKGALEALYPEFLREAKRVLRggGWLVLLTAENKDFEKAARERAWRKKKEFNVHIGGTR 182
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 73-158 3.61e-17

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 75.77  E-value: 3.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   73 SENDIYALAGDVA-WEAWFTPRQSFKVEVTAQHsplKSLNFAALRVKDAVADRFRAKSGSRPdVETRWPDVRIHLHLTRE 151
Cdd:smart00981   1 DLEDLYETALELIrWEKIFKEGKTFAVRAKRRG---KNHEFTSLEVKRAIGDKLLEKTGGRK-VDLKNPDVVIRVELRKD 76


                   ....*..
gi 1113433013  152 HAQLYID 158
Cdd:smart00981  77 KAYLSID 83
 
Name Accession Description Interval E-value
RlmL COG0116
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ...
 4-403 0e+00

23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 439886 [Multi-domain]  Cd Length: 369  Bit Score: 518.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   4 LQLFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGD 83
Cdd:COG0116     1 FELFATCARGLEALLADE---LKELGAEDVKVENGGVSFEGDLEDIYRANLWLRTASRVLLPLAEFKARTFDDLYEGAKA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  84 VAWEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKSGSRPDVETRWPDVRIHLHLTREHAQLYIDTSGEP 163
Cdd:COG0116    78 IPWEEYLPPDGTFAVDATSVKSKLFHSQFAALRVKDAIVDRFREKYGARPSVDEDGPDVRIHVHLLKDRATLSLDTSGES 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 164 LFKRGWREDKGDAPLKETLAAAMIAATGWDPHGdqplPLYDPCCGSGTVVIEAAQIACRIAPGLRRRFGFEKLLPYQAHV 243
Cdd:COG0116   158 LHKRGYREAQGEAPLKETLAAALLLLSGWDGDR----PLVDPMCGSGTILIEAALIAANIAPGLNRDFAFEKWPDFDAEL 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 244 WSAIKEEAAGAVVT-SPVPIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPcEQPGVMLLNPPYGERIaaag 322
Cdd:COG0116   234 WQELREEAEARIKRdPPLPIFGSDIDPRAIEAARENAERAGVADLIEFEQADFRDLEPP-AEPGLIITNPPYGERL---- 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 323 sagrsarermavvaragresAQTEDGVDFFQQLAAHWKRHYAGWQAWLLTPDLKLPGKMRLKESRRVPLWNGPIECRMFR 402
Cdd:COG0116   309 --------------------GEEEELEALYRELGDVLKQRFKGWSAYILTSDPELEKAIGLKASKRRKLYNGGLECRLLQ 368


                  .
gi 1113433013 403 F 403
Cdd:COG0116   369 Y 369
rlmL PRK11783
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ...
 4-413 5.46e-120

bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL;


Pssm-ID: 236981 [Multi-domain]  Cd Length: 702  Bit Score: 364.51  E-value: 5.46e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   4 LQLFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGD 83
Cdd:PRK11783    2 NSLFASCAKGLEELLKDE---LEALGASECKVVQGGVHFEGDLELAYRSCLWSRLASRILLPLAEFKVYSDLDLYLGVQA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  84 VAWEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKSGSRPDVETRWPDVRIHLHLTREHAQLYIDTSGEP 163
Cdd:PRK11783   79 IDWTEHFSPDKTFAVDFSGTNDEIRNTQFGALKVKDAIVDRFRRKGGPRPSVDKEQPDIRINARLNKGEATISLDLSGES 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 164 LFKRGWREDKGDAPLKETLAAAMIAATGWDPHGDqplPLYDPCCGSGTVVIEAAQIACRIAPGLRR-RFGFEKLLPYQAH 242
Cdd:PRK11783  159 LHQRGYRQATGEAPLKENLAAAILLRSGWPQEGT---PLLDPMCGSGTLLIEAAMMAADIAPGLHReRWGFSGWLGHDEA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 243 VWSAIKEEA----AGAVVTSPVPIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDA--LQRMPPCEQPGVMLLNPPYGE 316
Cdd:PRK11783  236 LWQELLEEAqeraRAGLAELPSKFYGSDIDPRVIQAARKNARRAGVAELITFEVKDVadLKNPLPKGPTGLVISNPPYGE 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 317 RIAaagsagrsarERMAVVAragresaqtedgvdFFQQLAAHWKRHYAGWQAWLLTPDLKLPGKMRLKESRRVPLWNGPI 396
Cdd:PRK11783  316 RLG----------EEPALIA--------------LYSQLGRRLKQQFGGWNAALFSSSPELLSCLGLRADKQYKLKNGAL 371

                         410
                  ....*....|....*..
gi 1113433013 397 ECRMFRFDLVAGPARPR 413
Cdd:PRK11783  372 ECVLKNYTIAEESTSSD 388
THUMP_AdoMetMT cd11715
THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of ...
 6-161 1.12e-50

THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of this family contain an N-terminal THUMP domain and a C-terminal S-adenosylmethionine-dependent methyltransferase domain. Members have been implicated in the modification of 23S RNA m2G2445, a highly conserved modification in bacteria and in the m2G6 modification of tRNA. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212584  Cd Length: 152  Bit Score: 167.76  E-value: 1.12e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   6 LFLPCAAGVEGFLADEvhgLTGLAGQDLLVGRAGVLVRAAWRDALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGDVA 85
Cdd:cd11715     1 FFATCPPGLEELLAAE---LKALGAEDVEVGPGGVSFEGDLEDAYRANLWLRTAHRVLLLLAEFEAEDFDDLYELAKAID 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113433013  86 WEAWFTPRQSFKVEVTAQHSPLKSLNFAALRVKDAVADRFRAKsGSRPDVETRWPDVRIHLHLTREHAQLYIDTSG 161
Cdd:cd11715    78 WEDYLDPDGTFAVRATRVGSKLFHSQFAALRVKDAIVDRFREK-GKRPSVDLDNPDVRIRVHLSKDRATLSLDLSG 152
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 167-400 1.76e-33

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 123.62  E-value: 1.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 167 RGWREDKGDAPLKETLAAAMIAATGWDPhGDqplPLYDPCCGSGTVVIEAAQIACRIAPGLrrrFGFEKLLPyqahvwsa 246
Cdd:pfam01170   1 RGYRPFNGPAPLKETLAAAMVNLAGWKP-GD---PLLDPMCGSGTILIEAALMGANIAPGK---FDARVRAP-------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 247 ikeeaagavvtspvpIFGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPCEQPGVMLLNPPYGERIAaagsagr 326
Cdd:pfam01170  66 ---------------LYGSDIDRRMVQGARLNAENAGVGDLIEFVQADAADLPLLEGSVDVIVTNPPYGIRLG------- 123

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113433013 327 sarermavvaragresaQTEDGVDFFQQLAAHWKRHYA--GWQAWLLTPDLKLPGKMRLKESRRVPLWNGPIECRM 400
Cdd:pfam01170 124 -----------------SKGALEALYPEFLREAKRVLRggGWLVLLTAENKDFEKAARERAWRKKKEFNVHIGGTR 182
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 73-158 3.61e-17

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 75.77  E-value: 3.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   73 SENDIYALAGDVA-WEAWFTPRQSFKVEVTAQHsplKSLNFAALRVKDAVADRFRAKSGSRPdVETRWPDVRIHLHLTRE 151
Cdd:smart00981   1 DLEDLYETALELIrWEKIFKEGKTFAVRAKRRG---KNHEFTSLEVKRAIGDKLLEKTGGRK-VDLKNPDVVIRVELRKD 76


                   ....*..
gi 1113433013  152 HAQLYID 158
Cdd:smart00981  77 KAYLSID 83
THUMP pfam02926
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and ...
 48-159 5.70e-13

THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 460749  Cd Length: 143  Bit Score: 65.92  E-value: 5.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013  48 DALLLNLHSRLAQRVLVQLAERPYRSENDIYALAGDVAWEAWFTPRQSFKVEVTAqhsPLKSLNFAALRVKDAVADRFRA 127
Cdd:pfam02926  37 RELLKEALEKAPGIERFPVAETCEADLEDILELAKEIIKDKFKKEGETFAVRVKR---RGKNHEFTSLEINREVGKAIVE 113

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1113433013 128 KSGSRPDVETrwPDVRIHLHLTREHAQLYIDT 159
Cdd:pfam02926 114 KTGLKVDLEN--PDIVVHVEIIKDKAYISIDR 143
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 178-315 1.98e-09

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 56.50  E-value: 1.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013 178 LKETLAAAMIAATGWDPhGDQplpLYDPCCGSGTVVIEAAQIACRiapglrrrfgfekllpyqahvwsaikeeaagavvt 257
Cdd:COG1041    10 LDPRLARALVNLAGAKE-GDT---VLDPFCGTGTILIEAGLLGRR----------------------------------- 50

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1113433013 258 spvpIFGSDVSHRMVDFAQRNAERAGVTGAVQLRgGDAlQRMP-PCEQPGVMLLNPPYG 315
Cdd:COG1041    51 ----VIGSDIDPKMVEGARENLEHYGYEDADVIR-GDA-RDLPlADESVDAIVTDPPYG 103
THUMP cd11688
THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, ...
 6-156 8.19e-04

THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212583  Cd Length: 148  Bit Score: 39.78  E-value: 8.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113433013   6 LFLPCAAGVEGFLADEVHGLTGLAGQDLLV-----GRAGVLVRAAwRDALLLNLHSRLAQRVLVQLAERPYrSENDIYAL 80
Cdd:cd11688     1 VFATTGKGLEEILAAELYELLEVRGFDAEIqvvphGRVHFKTDTD-EAVYQLVMWSRLISRIMPPLGECKA-DLEDLYET 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1113433013  81 AGDVAWEAWFTPRQSFKVEVT-AQHSPLKSLNfAALRVKDAVADRFRAKsgsrpdVETRWPDVRIHLHLTREHAQLY 156
Cdd:cd11688    79 ALEINEPEMGNEGAKFAVRARrRNKTILNSQE-IAMKVGDAIVDAFNPE------VDLDNPDIVVNVEVHKEIASIA 148
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 246-314 2.46e-03

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 39.36  E-value: 2.46e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1113433013 246 AIKEEAAGAVVTspvpifGSDVSHRMVDFAQRNAERAGVTGAVQLRGGDALQRMPPCEQPGVMLLNPPY 314
Cdd:COG2890   129 ALAKERPDARVT------AVDISPDALAVARRNAERLGLEDRVRFLQGDLFEPLPGDGRFDLIVSNPPY 191
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 246-314 9.16e-03

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 37.09  E-value: 9.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1113433013 246 AIKEEAAGAVVTspvpifGSDVSHRMVDFAQRNAERAGVTGaVQLRGGDALQRMPPcEQPGVMLLNPPY 314
Cdd:COG2813    66 ALAKRNPEARVT------LVDVNARAVELARANAAANGLEN-VEVLWSDGLSGVPD-GSFDLILSNPPF 126
 
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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