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Conserved domains on  [gi|79362513|ref|NP_175422|]
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methyltransferase [Arabidopsis thaliana]

Protein Classification

RsmE family RNA methyltransferase( domain architecture ID 10003624)

RsmE family RNA methyltransferase similar to 16S rRNA (uracil(1498)-N(3))-methyltransferase RsmE that specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA

EC:  2.1.1.-
Gene Ontology:  GO:0008168|GO:0006364
PubMed:  16431987
SCOP:  4000398|4000479

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RsmE COG1385
16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
53-286 7.64e-66

16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA U1498 N3-methylase RsmE is part of the Pathway/BioSystem: 16S rRNA modification


:

Pssm-ID: 440995 [Multi-domain]  Cd Length: 245  Bit Score: 206.16  E-value: 7.64e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  53 LPRFFSDDlPSRKGGVVRVQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDF--IAQEDQKVILPQgmq 130
Cdd:COG1385   3 MPRFFVPP-ELAAGDTVTLDGEEAHHLVRVLRLKPGDEVILFDGRGGEYLAEITEIGKKSVTLriLEQLEREPEPPL--- 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 131 wQVFAAFGTLKGGRADWLIEKCTELGASSVTPLLTERS-----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFG 205
Cdd:COG1385  79 -RLTLAQALPKGDRMDLIVQKATELGVDRIVPVITERSvvkldGERAEKKLERWQKIAIEAAEQSGRARLPEVAPPVSLA 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 206 TLLDHILKSKLCLVA-TAEAKPLLNAVNSSAKESsgLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLA 284
Cdd:COG1385 158 ELLAELPAGDLRLVLhEEEAKASLKELLPPGGSV--ALLIGPEGGFSEEEIELLRAAGFQPVSLGPRILRTETAALAALA 235

                ..
gi 79362513 285 TL 286
Cdd:COG1385 236 AL 237
 
Name Accession Description Interval E-value
RsmE COG1385
16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
53-286 7.64e-66

16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA U1498 N3-methylase RsmE is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440995 [Multi-domain]  Cd Length: 245  Bit Score: 206.16  E-value: 7.64e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  53 LPRFFSDDlPSRKGGVVRVQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDF--IAQEDQKVILPQgmq 130
Cdd:COG1385   3 MPRFFVPP-ELAAGDTVTLDGEEAHHLVRVLRLKPGDEVILFDGRGGEYLAEITEIGKKSVTLriLEQLEREPEPPL--- 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 131 wQVFAAFGTLKGGRADWLIEKCTELGASSVTPLLTERS-----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFG 205
Cdd:COG1385  79 -RLTLAQALPKGDRMDLIVQKATELGVDRIVPVITERSvvkldGERAEKKLERWQKIAIEAAEQSGRARLPEVAPPVSLA 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 206 TLLDHILKSKLCLVA-TAEAKPLLNAVNSSAKESsgLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLA 284
Cdd:COG1385 158 ELLAELPAGDLRLVLhEEEAKASLKELLPPGGSV--ALLIGPEGGFSEEEIELLRAAGFQPVSLGPRILRTETAALAALA 235

                ..
gi 79362513 285 TL 286
Cdd:COG1385 236 AL 237
PRK11713 PRK11713
16S ribosomal RNA methyltransferase RsmE; Provisional
53-289 4.39e-55

16S ribosomal RNA methyltransferase RsmE; Provisional


Pssm-ID: 236959 [Multi-domain]  Cd Length: 234  Bit Score: 178.15  E-value: 4.39e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   53 LPRFFsddLPSRKGGVVRVQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDFIAQEDQKVILPQGMQWQ 132
Cdd:PRK11713   1 MPRLF---VLLAAGETLILDGEEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEILEKLELEPEPPLRLT 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  133 VFAAFgtLKGGRADWLIEKCTELGASSVTPLLTERS-----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTL 207
Cdd:PRK11713  78 LAQAL--PKGDRLELILQKATELGVSAIIPLISERSvvkldGERADKKLERWQKIAIEAAEQSGRTRIPEVRPPISLKEF 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  208 LDHILKsklclvatAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATLV 287
Cdd:PRK11713 156 LEELLP--------ADLKAGLKLVLHPEAGGKVLLLIGPEGGFSPEEIELLREAGFTPVSLGPRILRTETAALAALAALQ 227

                 ..
gi 79362513  288 MW 289
Cdd:PRK11713 228 AL 229
Methyltrans_RNA pfam04452
RNA methyltransferase domain; RNA methyltransferases modify nucleotides during ribosomal RNA ...
132-286 2.62e-49

RNA methyltransferase domain; RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.


Pssm-ID: 461315  Cd Length: 165  Bit Score: 161.18  E-value: 2.62e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   132 QVFAAFGTLKGGRADWLIEKCTELGASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTL 207
Cdd:pfam04452   6 PITLAQALPKGDRMELILQKATELGVDRIVPLISERSvvklDKRVDKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKEL 85
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79362513   208 LDHILKSKLCLVATAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATL 286
Cdd:pfam04452  86 LEELDDYDLKLILHEEGEKPLEDLEALSAGGKILLIIGPEGGFSPKEIELLKEAGFTPVSLGPRILRTETAALAALSAL 164
RsmE-like cd18084
SPOUT superfamily RNA methyltransferase RsmE-like; 16S rRNA m3U1498 methyltransferase RsmE ...
136-284 5.39e-47

SPOUT superfamily RNA methyltransferase RsmE-like; 16S rRNA m3U1498 methyltransferase RsmE modifies nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. RsmE is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349957  Cd Length: 159  Bit Score: 155.01  E-value: 5.39e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 136 AFGTLKGGRADWLIEKCTELGASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTLLDHI 211
Cdd:cd18084   4 AQALPKGDRMEWILEKATELGVTRIIPVISERSvvkyDKKAEKKLERWQKIAIEAAEQSGRTRLPEIEPPISLKELLLLL 83
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 79362513 212 LKSKLCLVA-TAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLA 284
Cdd:cd18084  84 PDDDLRLVAhEGEEQSLLLLLLLLKSSKRILLLIGPEGGFSEEEIELLKEAGFKPVSLGPRILRTETAAIAALS 157
TIGR00046 TIGR00046
RNA methyltransferase, RsmE family; Members of this protein family, previously called ...
78-286 7.11e-35

RNA methyltransferase, RsmE family; Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272873 [Multi-domain]  Cd Length: 240  Bit Score: 126.35  E-value: 7.11e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513    78 HMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDFIAQEDQ--KVILPQgmqwQVFAAFGTLKGGRADWLIEKCTEL 155
Cdd:TIGR00046  25 HLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCKVLEGEseKRELPL----KIHLAIVLIKGKKMEFIIRKLTEL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   156 GASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTLLDHILKSKLCLVATAEAKPLLNav 231
Cdd:TIGR00046 101 GVSKIIPFNAERSvvklDIEAIKKLERWQKIAIEAAEQSGRNIVPEIKPPMNLKEKCAEAYEEALKLNFHPEASPLSN-- 178
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79362513   232 NSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATL 286
Cdd:TIGR00046 179 NLPIPAGNIVIIIGPEGGFSEKEIQLLAEKGFTPVLLGPRILRTETAPLYALSIL 233
 
Name Accession Description Interval E-value
RsmE COG1385
16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
53-286 7.64e-66

16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]; 16S rRNA U1498 N3-methylase RsmE is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440995 [Multi-domain]  Cd Length: 245  Bit Score: 206.16  E-value: 7.64e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  53 LPRFFSDDlPSRKGGVVRVQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDF--IAQEDQKVILPQgmq 130
Cdd:COG1385   3 MPRFFVPP-ELAAGDTVTLDGEEAHHLVRVLRLKPGDEVILFDGRGGEYLAEITEIGKKSVTLriLEQLEREPEPPL--- 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 131 wQVFAAFGTLKGGRADWLIEKCTELGASSVTPLLTERS-----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFG 205
Cdd:COG1385  79 -RLTLAQALPKGDRMDLIVQKATELGVDRIVPVITERSvvkldGERAEKKLERWQKIAIEAAEQSGRARLPEVAPPVSLA 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 206 TLLDHILKSKLCLVA-TAEAKPLLNAVNSSAKESsgLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLA 284
Cdd:COG1385 158 ELLAELPAGDLRLVLhEEEAKASLKELLPPGGSV--ALLIGPEGGFSEEEIELLRAAGFQPVSLGPRILRTETAALAALA 235

                ..
gi 79362513 285 TL 286
Cdd:COG1385 236 AL 237
PRK11713 PRK11713
16S ribosomal RNA methyltransferase RsmE; Provisional
53-289 4.39e-55

16S ribosomal RNA methyltransferase RsmE; Provisional


Pssm-ID: 236959 [Multi-domain]  Cd Length: 234  Bit Score: 178.15  E-value: 4.39e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   53 LPRFFsddLPSRKGGVVRVQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDFIAQEDQKVILPQGMQWQ 132
Cdd:PRK11713   1 MPRLF---VLLAAGETLILDGEEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEILEKLELEPEPPLRLT 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  133 VFAAFgtLKGGRADWLIEKCTELGASSVTPLLTERS-----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTL 207
Cdd:PRK11713  78 LAQAL--PKGDRLELILQKATELGVSAIIPLISERSvvkldGERADKKLERWQKIAIEAAEQSGRTRIPEVRPPISLKEF 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513  208 LDHILKsklclvatAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATLV 287
Cdd:PRK11713 156 LEELLP--------ADLKAGLKLVLHPEAGGKVLLLIGPEGGFSPEEIELLREAGFTPVSLGPRILRTETAALAALAALQ 227

                 ..
gi 79362513  288 MW 289
Cdd:PRK11713 228 AL 229
Methyltrans_RNA pfam04452
RNA methyltransferase domain; RNA methyltransferases modify nucleotides during ribosomal RNA ...
132-286 2.62e-49

RNA methyltransferase domain; RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.


Pssm-ID: 461315  Cd Length: 165  Bit Score: 161.18  E-value: 2.62e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   132 QVFAAFGTLKGGRADWLIEKCTELGASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTL 207
Cdd:pfam04452   6 PITLAQALPKGDRMELILQKATELGVDRIVPLISERSvvklDKRVDKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKEL 85
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79362513   208 LDHILKSKLCLVATAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATL 286
Cdd:pfam04452  86 LEELDDYDLKLILHEEGEKPLEDLEALSAGGKILLIIGPEGGFSPKEIELLKEAGFTPVSLGPRILRTETAALAALSAL 164
RsmE-like cd18084
SPOUT superfamily RNA methyltransferase RsmE-like; 16S rRNA m3U1498 methyltransferase RsmE ...
136-284 5.39e-47

SPOUT superfamily RNA methyltransferase RsmE-like; 16S rRNA m3U1498 methyltransferase RsmE modifies nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. RsmE is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349957  Cd Length: 159  Bit Score: 155.01  E-value: 5.39e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513 136 AFGTLKGGRADWLIEKCTELGASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTLLDHI 211
Cdd:cd18084   4 AQALPKGDRMEWILEKATELGVTRIIPVISERSvvkyDKKAEKKLERWQKIAIEAAEQSGRTRLPEIEPPISLKELLLLL 83
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 79362513 212 LKSKLCLVA-TAEAKPLLNAVNSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLA 284
Cdd:cd18084  84 PDDDLRLVAhEGEEQSLLLLLLLLKSSKRILLLIGPEGGFSEEEIELLKEAGFKPVSLGPRILRTETAAIAALS 157
TIGR00046 TIGR00046
RNA methyltransferase, RsmE family; Members of this protein family, previously called ...
78-286 7.11e-35

RNA methyltransferase, RsmE family; Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272873 [Multi-domain]  Cd Length: 240  Bit Score: 126.35  E-value: 7.11e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513    78 HMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDFIAQEDQ--KVILPQgmqwQVFAAFGTLKGGRADWLIEKCTEL 155
Cdd:TIGR00046  25 HLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCKVLEGEseKRELPL----KIHLAIVLIKGKKMEFIIRKLTEL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79362513   156 GASSVTPLLTERS----PIISENRVDRLERVSFAAAKQCQRLHQMVLNPPIKFGTLLDHILKSKLCLVATAEAKPLLNav 231
Cdd:TIGR00046 101 GVSKIIPFNAERSvvklDIEAIKKLERWQKIAIEAAEQSGRNIVPEIKPPMNLKEKCAEAYEEALKLNFHPEASPLSN-- 178
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79362513   232 NSSAKESSGLLIVGPEGDFTKKEVEMMLEAGGTAVGLGPHRLRVETATIALLATL 286
Cdd:TIGR00046 179 NLPIPAGNIVIIIGPEGGFSEKEIQLLAEKGFTPVLLGPRILRTETAPLYALSIL 233
PUA_4 pfam20260
RNA methyltransferase PUA domain; RNA methyltransferases modify nucleotides during ribosomal ...
71-116 3.26e-10

RNA methyltransferase PUA domain; RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.


Pssm-ID: 466411 [Multi-domain]  Cd Length: 48  Bit Score: 54.44  E-value: 3.26e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 79362513    71 VQGSEFWHMAKVLRLKQEDRVELFNGKGGLVEGCIQSIDKTGVDFI 116
Cdd:pfam20260   1 LTGEEAHHLVRVLRLKEGDKLILFDGDGGEYLAEIEKIGKKSLTVK 46
 
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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