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Conserved domains on  [gi|613390957|gb|EZZ94814|]
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RsmD family RNA methyltransferase [Staphylococcus aureus VET0057R]

Protein Classification

RsmD family RNA methyltransferase( domain architecture ID 10002368)

RsmD family RNA methyltransferase similar to 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD, which specifically methylates the guanine in position 966 of 16S rRNA in the assembled 30S particle

CATH:  3.40.50.150
EC:  2.1.1.-
Gene Ontology:  GO:0003676|GO:0031167|GO:0008168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 1-171 3.09e-77

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


:

Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 228.43  E-value: 3.09e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL-YDVSG-IGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:COG0742    1 MRIIGGKARGRKLKVPKGPGTRPTTDRVREALFNILgPDIEGaRVLDLFAGSGALGLEALSRGAASVVFVEKDRKAAAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  79 KSNLANLNLEAQSEVYKNNADRALKALSKRdiQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQ 158
Cdd:COG0742   81 RKNLEKLGLEDRARVIRGDALRFLKRLAGE--PFDLVFLDPPYAKGLLEKALELLAENGLLAPGGLIVVEHSKREELPEL 158

                        170
                 ....*....|....*
gi 613390957 159 P--FNMIKRYHYGLT 171
Cdd:COG0742  159 PagLELLKERKYGDT 173
 
Name Accession Description Interval E-value
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 1-171 3.09e-77

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 228.43  E-value: 3.09e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL-YDVSG-IGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:COG0742    1 MRIIGGKARGRKLKVPKGPGTRPTTDRVREALFNILgPDIEGaRVLDLFAGSGALGLEALSRGAASVVFVEKDRKAAAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  79 KSNLANLNLEAQSEVYKNNADRALKALSKRdiQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQ 158
Cdd:COG0742   81 RKNLEKLGLEDRARVIRGDALRFLKRLAGE--PFDLVFLDPPYAKGLLEKALELLAENGLLAPGGLIVVEHSKREELPEL 158

                        170
                 ....*....|....*
gi 613390957 159 P--FNMIKRYHYGLT 171
Cdd:COG0742  159 PagLELLKERKYGDT 173
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
1-171 2.08e-62

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 190.53  E-value: 2.08e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957    1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:pfam03602   1 MRIIGGKARGRKLKVPPGPGTRPTTDRVREALFNWLapYIEGARVLDLFAGSGALGLEALSRGAKRVTLVEKDKRAVQIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   79 KSNLANLNLEAQseVYKNNADRALKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQ 158
Cdd:pfam03602  81 KENLQLLGLPGA--VLVMDALLALLRLAGKGPVFDIVFLDPPYAKGLIEEVLDLLAEKGWLKPNALIYVETEKRGELPEQ 158

                         170
                  ....*....|....*
gi 613390957  159 P--FNMIKRYHYGLT 171
Cdd:pfam03602 159 PgnLELVREKKYGQT 173
TIGR00095 TIGR00095
16S rRNA (guanine(966)-N(2))-methyltransferase RsmD; This model represents a family of ...
 2-177 2.51e-54

16S rRNA (guanine(966)-N(2))-methyltransferase RsmD; This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188022 [Multi-domain]  Cd Length: 190  Bit Score: 170.67  E-value: 2.51e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957    2 RVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIK 79
Cdd:TIGR00095  11 RIIGGQYRGRKLKVPPGPSTRPTTDRVRESLFNILrpDIVGAHFLDLFAGSGALGLEALSRGAASAVFVEQDRKVAQTLK 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   80 SNLANLNLEAQSEVYKNNADRALKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQP 159
Cdd:TIGR00095  91 ENLSTLKKSGEQATVLNDAVRALLFLAKKQTPFDIIYLDPPFNRGLLEALLELLGENKWLNPKGLIVVEYDRENELPTVP 170

                         170       180
                  ....*....|....*....|
gi 613390957  160 --FNMIKRYHYGLTDTLLLE 177
Cdd:TIGR00095 171 etWSLLRQKVYGQSALRLYQ 190
rsmD PRK10909
16S rRNA m(2)G966-methyltransferase; Provisional
 1-148 2.48e-26

16S rRNA m(2)G966-methyltransferase; Provisional


Pssm-ID: 236793  Cd Length: 199  Bit Score: 99.02  E-value: 2.48e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:PRK10909  13 IRIIGGQWRGRKLPVPDSPGLRPTTDRVRETLFNWLapVIVDARCLDCFAGSGALGLEALSRYAAGATLLEMDRAVAQQL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  79 KSNLANLNLEaQSEVYKNNAdraLKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCE 148
Cdd:PRK10909  93 IKNLATLKAG-NARVVNTNA---LSFLAQPGTPHNVVFVDPPFRKGLLEETINLLEDNGWLADEALIYVE 158
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 44-149 3.58e-11

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 57.05  E-value: 3.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNAdraLKALSKRDIQFDVIFLDPPY-- 121
Cdd:cd02440    3 LDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLAD-NVEVLKGDA---EELPPEADESFDVIISDPPLhh 78

                         90       100
                 ....*....|....*....|....*...
gi 613390957 122 NKGLIDKALKLISEfnLLKENGIIVCEF 149
Cdd:cd02440   79 LVEDLARFLEEARR--LLKPGGVLVLTL 104
 
Name Accession Description Interval E-value
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 1-171 3.09e-77

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 228.43  E-value: 3.09e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL-YDVSG-IGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:COG0742    1 MRIIGGKARGRKLKVPKGPGTRPTTDRVREALFNILgPDIEGaRVLDLFAGSGALGLEALSRGAASVVFVEKDRKAAAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  79 KSNLANLNLEAQSEVYKNNADRALKALSKRdiQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQ 158
Cdd:COG0742   81 RKNLEKLGLEDRARVIRGDALRFLKRLAGE--PFDLVFLDPPYAKGLLEKALELLAENGLLAPGGLIVVEHSKREELPEL 158

                        170
                 ....*....|....*
gi 613390957 159 P--FNMIKRYHYGLT 171
Cdd:COG0742  159 PagLELLKERKYGDT 173
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
1-171 2.08e-62

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 190.53  E-value: 2.08e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957    1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:pfam03602   1 MRIIGGKARGRKLKVPPGPGTRPTTDRVREALFNWLapYIEGARVLDLFAGSGALGLEALSRGAKRVTLVEKDKRAVQIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   79 KSNLANLNLEAQseVYKNNADRALKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQ 158
Cdd:pfam03602  81 KENLQLLGLPGA--VLVMDALLALLRLAGKGPVFDIVFLDPPYAKGLIEEVLDLLAEKGWLKPNALIYVETEKRGELPEQ 158

                         170
                  ....*....|....*
gi 613390957  159 P--FNMIKRYHYGLT 171
Cdd:pfam03602 159 PgnLELVREKKYGQT 173
TIGR00095 TIGR00095
16S rRNA (guanine(966)-N(2))-methyltransferase RsmD; This model represents a family of ...
 2-177 2.51e-54

16S rRNA (guanine(966)-N(2))-methyltransferase RsmD; This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188022 [Multi-domain]  Cd Length: 190  Bit Score: 170.67  E-value: 2.51e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957    2 RVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIK 79
Cdd:TIGR00095  11 RIIGGQYRGRKLKVPPGPSTRPTTDRVRESLFNILrpDIVGAHFLDLFAGSGALGLEALSRGAASAVFVEQDRKVAQTLK 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   80 SNLANLNLEAQSEVYKNNADRALKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCEFSNHEEIDYQP 159
Cdd:TIGR00095  91 ENLSTLKKSGEQATVLNDAVRALLFLAKKQTPFDIIYLDPPFNRGLLEALLELLGENKWLNPKGLIVVEYDRENELPTVP 170

                         170       180
                  ....*....|....*....|
gi 613390957  160 --FNMIKRYHYGLTDTLLLE 177
Cdd:TIGR00095 171 etWSLLRQKVYGQSALRLYQ 190
rsmD PRK10909
16S rRNA m(2)G966-methyltransferase; Provisional
 1-148 2.48e-26

16S rRNA m(2)G966-methyltransferase; Provisional


Pssm-ID: 236793  Cd Length: 199  Bit Score: 99.02  E-value: 2.48e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   1 MRVIAGKHKSKALESMEGRNTRPTMDKVKEGIFNSL--YDVSGIGLDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVI 78
Cdd:PRK10909  13 IRIIGGQWRGRKLPVPDSPGLRPTTDRVRETLFNWLapVIVDARCLDCFAGSGALGLEALSRYAAGATLLEMDRAVAQQL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  79 KSNLANLNLEaQSEVYKNNAdraLKALSKRDIQFDVIFLDPPYNKGLIDKALKLISEFNLLKENGIIVCE 148
Cdd:PRK10909  93 IKNLATLKAG-NARVVNTNA---LSFLAQPGTPHNVVFVDPPFRKGLLEETINLLEDNGWLADEALIYVE 158
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 44-152 1.28e-12

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 64.82  E-value: 1.28e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLAnLN-LEAQSEVYKNNADRALKALSKRDIQFDVIFLDPP-- 120
Cdd:COG1092  221 LNLFSYTGGFSVHAAAGGAKSVTSVDLSATALEWAKENAA-LNgLDDRHEFVQADAFDWLRELAREGERFDLIILDPPaf 299

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 613390957 121 -------------YnKGLIDKALKlisefnLLKENGIIVCeFSNH 152
Cdd:COG1092  300 akskkdlfdaqrdY-KDLNRLALK------LLAPGGILVT-SSCS 336
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 44-149 3.58e-11

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 57.05  E-value: 3.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNAdraLKALSKRDIQFDVIFLDPPY-- 121
Cdd:cd02440    3 LDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLAD-NVEVLKGDA---EELPPEADESFDVIISDPPLhh 78

                         90       100
                 ....*....|....*....|....*...
gi 613390957 122 NKGLIDKALKLISEfnLLKENGIIVCEF 149
Cdd:cd02440   79 LVEDLARFLEEARR--LLKPGGVLVLTL 104
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 44-146 1.17e-10

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: 57.27  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDkVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNAdralKALSKRDIQFDVIFLDPPYN- 122
Cdd:COG1041   31 LDPFCGTGTILIEAGLLGRR-VIGSDIDPKMVEGARENLEHYGYE-DADVIRGDA----RDLPLADESVDAIVTDPPYGr 104

                         90       100       110
                 ....*....|....*....|....*....|.
gi 613390957 123 --KGLIDKALKLISEF-----NLLKENGIIV 146
Cdd:COG1041  105 ssKISGEELLELYEKAleeaaRVLKPGGRVV 135
TRM1 COG1867
tRNA G26 N,N-dimethylase Trm1 [Translation, ribosomal structure and biogenesis]; tRNA G26 N, ...
 33-139 4.59e-09

tRNA G26 N,N-dimethylase Trm1 [Translation, ribosomal structure and biogenesis]; tRNA G26 N,N-dimethylase Trm1 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441472  Cd Length: 383  Bit Score: 54.49  E-value: 4.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  33 FNSLYDVSGIGLDLFAGSGALGIE-ALSRGMdKVIFVDQNFKAVKVIKSNLANLNLEAqSEVYKNNAdRALkaLSKRDIQ 111
Cdd:COG1867   51 YRERLKREISYLDALAASGIRGLRyALEVGI-KVTLNDIDPEAVELIRENLELNGLED-VEVYNRDA-NAL--LHELGRR 125

                         90       100       110
                 ....*....|....*....|....*....|...
gi 613390957 112 FDVIFLDP-----PYnkglIDKALKLISEFNLL 139
Cdd:COG1867  126 FDVVDLDPfgspaPF----IDSALRAARKGGLL 154
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 38-155 6.62e-09

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: 52.88  E-value: 6.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  38 DVSGIGLDLFAGSGALGIEALSRGMD-KVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNADRALKalskrDIQFDVIF 116
Cdd:COG2813   48 PLGGRVLDLGCGYGVIGLALAKRNPEaRVTLVDVNARAVELARANAAANGLE-NVEVLWSDGLSGVP-----DGSFDLIL 121

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 613390957 117 LDPPYNKGL-IDK--ALKLISE-FNLLKENGIIVC--------------EFSNHEEI 155
Cdd:COG2813  122 SNPPFHAGRaVDKevAHALIADaARHLRPGGELWLvanrhlpyerkleeLFGNVEVL 178
PRK04338 PRK04338
N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
 44-145 9.01e-09

N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional


Pssm-ID: 235286  Cd Length: 382  Bit Score: 53.38  E-value: 9.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIE-ALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAqSEVYKNNADralkALSKRDIQFDVIFLDP--- 119
Cdd:PRK04338  62 LDALSASGIRGIRyALETGVEKVTLNDINPDAVELIKKNLELNGLEN-EKVFNKDAN----ALLHEERKFDVVDIDPfgs 136

                         90       100
                 ....*....|....*....|....*...
gi 613390957 120 --PYnkglIDKAlkliseFNLLKENGII 145
Cdd:PRK04338 137 paPF----LDSA------IRSVKRGGLL 154
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 44-137 1.34e-08

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 52.87  E-value: 1.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIeALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNADRALKALSKRDiQFDVIFLDPPYnK 123
Cdd:COG2265  238 LDLYCGVGTFAL-PLARRAKKVIGVEIVPEAVEDARENARLNGLK-NVEFVAGDLEEVLPELLWGG-RPDVVVLDPPR-A 313

                         90
                 ....*....|....
gi 613390957 124 GLIDKALKLISEFN 137
Cdd:COG2265  314 GAGPEVLEALAALG 327
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 40-125 1.32e-06

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 46.04  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   40 SGIGLDLFAGSGALGIEALSRGMD-KVIFVDQNFKAVKVIKSNLANLNLEAqSEVYKNNADRALKalskrDIQFDVIFLD 118
Cdd:pfam05175  32 SGKVLDLGCGAGVLGAALAKESPDaELTMVDINARALESARENLAANGLEN-GEVVASDVYSGVE-----DGKFDLIISN 105


                  ....*..
gi 613390957  119 PPYNKGL 125
Cdd:pfam05175 106 PPFHAGL 112
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 44-148 1.53e-06

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


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 46.68  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIE-ALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAQSEVYKNNADRALKAlskrDIQFDVIFLDPPY- 121
Cdd:COG2890  117 LDLGTGSGAIALAlAKERPDARVTAVDISPDALAVARRNAERLGLEDRVRFLQGDLFEPLPG----DGRFDLIVSNPPYi 192

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 613390957 122 ------------------------NKGLIDkaLKLISEF--NLLKENGIIVCE 148
Cdd:COG2890  193 pedeiallppevrdheprlaldggEDGLDF--YRRIIAQapRLLKPGGWLLLE 243
PRK14968 PRK14968
putative methyltransferase; Provisional
 41-145 4.09e-05

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 42.19  E-value: 4.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  41 GIGLDLFAGSGALGIEALSRGmDKVIFVDQNFKAVKVIKSNLANLNLEAQS-EVYKNNADRALkalskRDIQFDVIFLDP 119
Cdd:PRK14968  25 DRVLEVGTGSGIVAIVAAKNG-KKVVGVDINPYAVECAKCNAKLNNIRNNGvEVIRSDLFEPF-----RGDKFDVILFNP 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 613390957 120 PY--------NKGLIDKAL-------KLISEF-----NLLKENGII 145
Cdd:PRK14968  99 PYlpteeeeeWDDWLNYALsggkdgrEVIDRFldevgRYLKPGGRI 144
PRK15128 PRK15128
23S rRNA (cytosine(1962)-C(5))-methyltransferase RlmI;
44-146 5.15e-05

23S rRNA (cytosine(1962)-C(5))-methyltransferase RlmI;


Pssm-ID: 185082 [Multi-domain]  Cd Length: 396  Bit Score: 42.52  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSN--LANLNLeAQSEVYKNNADRALKALSKRDIQFDVIFLDPPY 121
Cdd:PRK15128 225 LNCFSYTGGFAVSALMGGCSQVVSVDTSQEALDIARQNveLNKLDL-SKAEFVRDDVFKLLRTYRDRGEKFDVIVMDPPK 303

                         90       100       110
                 ....*....|....*....|....*....|...
gi 613390957 122 ---NKGLIDKALKLISEFN-----LLKENGIIV 146
Cdd:PRK15128 304 fveNKSQLMGACRGYKDINmlaiqLLNPGGILL 336
COG4076 COG4076
Predicted RNA methylase [General function prediction only];
44-146 6.80e-05

Predicted RNA methylase [General function prediction only];


Pssm-ID: 443253 [Multi-domain]  Cd Length: 230  Bit Score: 41.95  E-value: 6.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAQSEVYKNNAdralkalskRDIQF----DVI---F 116
Cdd:COG4076   40 LDIGTGSGLLSMLAARAGAKKVYAVEVNPDIAAVARRIIAANGLSDRITVINADA---------TDLDLpekaDVIiseM 110

                         90       100       110
                 ....*....|....*....|....*....|..
gi 613390957 117 LDppyNKGLIDKALKLISEF--NLLKENGIIV 146
Cdd:COG4076  111 LD---TALLDEGQVPILNHArkRLLKPGGRII 139
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 44-143 9.59e-05

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 39.47  E-value: 9.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAQSEVyknnADraLKALSKRDIQFDVIF------- 116
Cdd:pfam13649   2 LDLGCGTGRLTLALARRGGARVTGVDLSPEMLERARERAAEAGLNVEFVQ----GD--AEDLPFPDGSFDLVVssgvlhh 75

                          90       100
                  ....*....|....*....|....*..
gi 613390957  117 LDPPYnkglIDKALKLIseFNLLKENG 143
Cdd:pfam13649  76 LPDPD----LEAALREI--ARVLKPGG 96
TRM pfam02005
N2,N2-dimethylguanosine tRNA methyltransferase; This enzyme EC:2.1.1.32 used S-AdoMet to ...
 44-139 1.74e-04

N2,N2-dimethylguanosine tRNA methyltransferase; This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria


Pssm-ID: 396545  Cd Length: 375  Bit Score: 40.83  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   44 LDLFAGSGALGIEAL--SRGMDKVIFVDQNFKAVKVIKSNLanlNLEAQSEVYKNNADRALKALSKRDIQFDVIFLDP-- 119
Cdd:pfam02005  54 LDALSASGIRAIRFAleVPGVEEVFANDISPKAVESIKENV---KLNEVENIVVINGDDANAFMRENHRRFDVIDLDPfg 130

                          90       100
                  ....*....|....*....|...
gi 613390957  120 ---PYnkglIDKALKLISEFNLL 139
Cdd:pfam02005 131 spaPF----LDSAVQSVKRGGLL 149
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 44-148 2.09e-04

HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. [Protein fate, Protein modification and repair]


Pssm-ID: 273125 [Multi-domain]  Cd Length: 284  Bit Score: 40.41  E-value: 2.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   44 LDLFAGSGALGIE-ALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAQSEVYKNNADRALKALskrdiQFDVIFLDPPY- 121
Cdd:TIGR00536 119 LDLGTGSGCIALAlAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEPLAGQ-----KIDIIVSNPPYi 193

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 613390957  122 ----------------NKGLI--DKALKLISEF-----NLLKENGIIVCE 148
Cdd:TIGR00536 194 deedladlpnvvrfepLLALVggDDGLNILRQIielapDYLKPNGFLVCE 243
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 44-151 2.97e-04

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 38.85  E-value: 2.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDkVIFVDQNFKAVKVIKSNLANLNLEAQsevyknNADraLKALSKRDIQFDVIFL------ 117
Cdd:COG2227   29 LDVGCGTGRLALALARRGAD-VTGVDISPEALEIARERAAELNVDFV------QGD--LEDLPLEDGSFDLVICsevleh 99

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 613390957 118 --DPpynkgliDKALKLIseFNLLKENGIIVCEFSN 151
Cdd:COG2227  100 lpDP-------AALLREL--ARLLKPGGLLLLSTPN 126
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
44-132 3.46e-04

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 39.50  E-value: 3.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSNLANLNLEAqsEVYKNNADRALKALSkrdiqFDVIFLDPP--- 120
Cdd:COG2263   50 LDLGCGTGMLAIGAALLGAKKVVGVDIDPEALEIARENAERLGVRV--DFIRADVTRIPLGGS-----VDTVVMNPPfga 122

                         90
                 ....*....|....*.
gi 613390957 121 YNKGL----IDKALKL 132
Cdd:COG2263  123 QRRHAdrpfLEKALEI 138
TrmR COG4122
tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; ...
 47-147 3.47e-04

tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; tRNA 5-hydroxyU34 O-methylase TrmR/YrrM is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443298  Cd Length: 173  Bit Score: 39.40  E-value: 3.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  47 FAGSGALgieALSRGMD---KVIFVDQNFKAVKVIKSNLANLNLEAQSEVYKNNADRALKALskRDIQFDVIFLD--PPY 121
Cdd:COG4122   26 GTGYSTL---WLARALPddgRLTTIEIDPERAAIARENFARAGLADRIRLILGDALEVLPRL--ADGPFDLVFIDadKSN 100

                         90       100
                 ....*....|....*....|....*.
gi 613390957 122 NKGLIDKALKlisefnLLKENGIIVC 147
Cdd:COG4122  101 YPDYLELALP------LLRPGGLIVA 120
CobL COG2242
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ...
 36-146 9.59e-04

Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 441843 [Multi-domain]  Cd Length: 403  Bit Score: 38.99  E-value: 9.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  36 LYDvsgIGldlfAGSGALGIEA--LSRGMdKVIFVDQNFKAVKVIKSNLANLNLEaQSEVYKNNADRALKALSKrdiqFD 113
Cdd:COG2242  251 LWD---IG----AGSGSVSIEAarLAPGG-RVYAIERDPERAALIRANARRFGVP-NVEVVEGEAPEALADLPD----PD 317

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 613390957 114 VIFL--DPPYNKGLIDKALKlisefnLLKENGIIV 146
Cdd:COG2242  318 AVFIggSGGNLPEILEACWA------RLRPGGRLV 346
PRK14967 PRK14967
putative methyltransferase; Provisional
 44-121 1.98e-03

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 37.34  E-value: 1.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIEALSRGMDKVIFVDQNFKAVKVIKSN--LANLNLeaqsEVYKNNADRALkalskRDIQFDVIFLDPPY 121
Cdd:PRK14967  41 LDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNalLAGVDV----DVRRGDWARAV-----EFRPFDVVVSNPPY 111
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 44-149 2.21e-03

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 37.45  E-value: 2.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957  44 LDLFAGSGALGIeALSRGMD--KVIFVDQNFKAVKVIKSNlANLNLEAQSEVYKNNadrALKALSkrDIQFDVIFLDPPY 121
Cdd:PRK09328 113 LDLGTGSGAIAL-ALAKERPdaEVTAVDISPEALAVARRN-AKHGLGARVEFLQGD---WFEPLP--GGRFDLIVSNPPY 185

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 613390957 122 ----NKGLIDK---------AL-----------KLISE-FNLLKENGIIVCEF 149
Cdd:PRK09328 186 ipeaDIHLLQPevrdhephlALfggedgldfyrRIIEQaPRYLKPGGWLLLEI 238
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 44-158 3.96e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 36.24  E-value: 3.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390957   44 LDLFAGSGALGIEA--LSRGMDKVIFVDQNFKAVKVIKSNLANLNLE----AQSEVYKnnadralKALSKRDIQFDVIFL 117
Cdd:pfam13847   8 LDLGCGTGHLSFELaeELGPNAEVVGIDISEEAIEKARENAQKLGFDnvefEQGDIEE-------LPELLEDDKFDVVIS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 613390957  118 DPPYNkGLIDKALKLISEFNLLKENGI-IVCEFSNHEEIDYQ 158
Cdd:pfam13847  81 NCVLN-HIPDPDKVLQEILRVLKPGGRlIISDPDSLAELPAH 121
 
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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