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Conserved domains on  [gi|2771601570|ref|WP_367127882|]
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class I SAM-dependent methyltransferase, partial [Mongoliibacter sp.]

Protein Classification

class I SAM-dependent methyltransferase( domain architecture ID 15451136)

class I SAM-dependent methyltransferase catalyzes the methylation of one or more specific substrates using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor

CATH:  3.40.50.150
EC:  2.1.1.-
Gene Ontology:  GO:1904047|GO:0008168|GO:0032259|GO:0008757
PubMed:  12504684|12826405
SCOP:  3000118

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Thump_like pfam18096
THUMP domain-like; This is a domain of unknown function found in bacteria.
 301-362 4.82e-13

THUMP domain-like; This is a domain of unknown function found in bacteria.


:

Pssm-ID: 465646  Cd Length: 76  Bit Score: 63.83  E-value: 4.82e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2771601570 301 GRFFEIISEIQQPKKEIKSLFPE---GKVNVITRNYSLSADALKKKHKLKDGGDDFLLGAKTTNG 362
Cdd:pfam18096   1 GRAFRILEVLPFSKKALKKLLRErgiGKAEIKKRGFPLDPEELRKKLKIKDGGRTATLFLTRVGK 65
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 60-169 2.85e-08

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.).


The actual alignment was detected with superfamily member pfam03602:

Pssm-ID: 473071 [Multi-domain]  Cd Length: 179  Bit Score: 53.01  E-value: 2.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  60 AGHFKGSKMIDL---TGGLGVDAyfLGKNYEQATYCERDKNLFEISKHNLSHLSPGKFDFYNGDSLDFLRNTS--EKFDL 134
Cdd:pfam03602  37 APYIEGARVLDLfagSGALGLEA--LSRGAKRVTLVEKDKRAVQILKENLQLLGLPGAVLVMDALLALLRLAGkgPVFDI 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2771601570 135 IFVDPA-RRGGHNQKLYRLED-----------CE-------PDIIQNWELLRSK 169
Cdd:pfam03602 115 VFLDPPyAKGLIEEVLDLLAEkgwlkpnaliyVEtekrgelPEQPGNLELVREK 168
 
Name Accession Description Interval E-value
Thump_like pfam18096
THUMP domain-like; This is a domain of unknown function found in bacteria.
 301-362 4.82e-13

THUMP domain-like; This is a domain of unknown function found in bacteria.


Pssm-ID: 465646  Cd Length: 76  Bit Score: 63.83  E-value: 4.82e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2771601570 301 GRFFEIISEIQQPKKEIKSLFPE---GKVNVITRNYSLSADALKKKHKLKDGGDDFLLGAKTTNG 362
Cdd:pfam18096   1 GRAFRILEVLPFSKKALKKLLRErgiGKAEIKKRGFPLDPEELRKKLKIKDGGRTATLFLTRVGK 65
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
60-169 2.85e-08

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 53.01  E-value: 2.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  60 AGHFKGSKMIDL---TGGLGVDAyfLGKNYEQATYCERDKNLFEISKHNLSHLSPGKFDFYNGDSLDFLRNTS--EKFDL 134
Cdd:pfam03602  37 APYIEGARVLDLfagSGALGLEA--LSRGAKRVTLVEKDKRAVQILKENLQLLGLPGAVLVMDALLALLRLAGkgPVFDI 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2771601570 135 IFVDPA-RRGGHNQKLYRLED-----------CE-------PDIIQNWELLRSK 169
Cdd:pfam03602 115 VFLDPPyAKGLIEEVLDLLAEkgwlkpnaliyVEtekrgelPEQPGNLELVREK 168
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 60-139 1.66e-07

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: 50.85  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  60 AGHFKGSKMIDL---TGGLGVDAYFLGknYEQATYCERDKNLFEISKHNLSHL-SPGKFDFYNGDSLDFLRN-TSEKFDL 134
Cdd:COG0742    37 GPDIEGARVLDLfagSGALGLEALSRG--AASVVFVEKDRKAAAVIRKNLEKLgLEDRARVIRGDALRFLKRlAGEPFDL 114


                  ....*
gi 2771601570 135 IFVDP 139
Cdd:COG0742   115 VFLDP 119
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 67-171 1.55e-06

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: 46.27  E-value: 1.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  67 KMIDLTGGLGVDAYFLGKNY-EQATYCERDKNLFEISKHNLSHLSPGKFDFYNGDSLDFLRNTSEKFDLIFVDPARRggh 145
Cdd:cd02440     1 RVLDLGCGTGALALALASGPgARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDVIISDPPLH--- 77

                          90       100
                  ....*....|....*....|....*.
gi 2771601570 146 nqklYRLEDCEPDIIQNWELLRSKGV 171
Cdd:cd02440    78 ----HLVEDLARFLEEARRLLKPGGV 99
cbiT PRK00377
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
 37-210 3.36e-05

cobalt-precorrin-6Y C(15)-methyltransferase; Provisional


Pssm-ID: 234740  Cd Length: 198  Bit Score: 44.40  E-value: 3.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  37 PDLLF--PVNLSMEQASSGLTAKYKAGHFKGSKMIDL---TGGLGVDAYFLGKNYEQATYCERDKNLFEISKHNLShlsp 111
Cdd:PRK00377   11 PDEEFerDEEIPMTKEEIRALALSKLRLRKGDMILDIgcgTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAE---- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570 112 gKFDFYN------GDSLDFLRNTSEKFDLIFVdparrGGHNQKLyrledcePDIIQ-NWELLRSKGVdVLVKASPMLDIK 184
Cdd:PRK00377   87 -KFGVLNnivlikGEAPEILFTINEKFDRIFI-----GGGSEKL-------KEIISaSWEIIKKGGR-IVIDAILLETVN 152

                         170       180
                  ....*....|....*....|....*.
gi 2771601570 185 AALKSLNAIhkvivlSVKNEVKEVLL 210
Cdd:PRK00377  153 NALSALENI------GFNLEITEVII 172
 
Name Accession Description Interval E-value
Thump_like pfam18096
THUMP domain-like; This is a domain of unknown function found in bacteria.
 301-362 4.82e-13

THUMP domain-like; This is a domain of unknown function found in bacteria.


Pssm-ID: 465646  Cd Length: 76  Bit Score: 63.83  E-value: 4.82e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2771601570 301 GRFFEIISEIQQPKKEIKSLFPE---GKVNVITRNYSLSADALKKKHKLKDGGDDFLLGAKTTNG 362
Cdd:pfam18096   1 GRAFRILEVLPFSKKALKKLLRErgiGKAEIKKRGFPLDPEELRKKLKIKDGGRTATLFLTRVGK 65
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
60-169 2.85e-08

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 53.01  E-value: 2.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  60 AGHFKGSKMIDL---TGGLGVDAyfLGKNYEQATYCERDKNLFEISKHNLSHLSPGKFDFYNGDSLDFLRNTS--EKFDL 134
Cdd:pfam03602  37 APYIEGARVLDLfagSGALGLEA--LSRGAKRVTLVEKDKRAVQILKENLQLLGLPGAVLVMDALLALLRLAGkgPVFDI 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2771601570 135 IFVDPA-RRGGHNQKLYRLED-----------CE-------PDIIQNWELLRSK 169
Cdd:pfam03602 115 VFLDPPyAKGLIEEVLDLLAEkgwlkpnaliyVEtekrgelPEQPGNLELVREK 168
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 60-139 1.66e-07

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: 50.85  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  60 AGHFKGSKMIDL---TGGLGVDAYFLGknYEQATYCERDKNLFEISKHNLSHL-SPGKFDFYNGDSLDFLRN-TSEKFDL 134
Cdd:COG0742    37 GPDIEGARVLDLfagSGALGLEALSRG--AASVVFVEKDRKAAAVIRKNLEKLgLEDRARVIRGDALRFLKRlAGEPFDL 114


                  ....*
gi 2771601570 135 IFVDP 139
Cdd:COG0742   115 VFLDP 119
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 67-171 1.55e-06

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: 46.27  E-value: 1.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  67 KMIDLTGGLGVDAYFLGKNY-EQATYCERDKNLFEISKHNLSHLSPGKFDFYNGDSLDFLRNTSEKFDLIFVDPARRggh 145
Cdd:cd02440     1 RVLDLGCGTGALALALASGPgARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDVIISDPPLH--- 77

                          90       100
                  ....*....|....*....|....*.
gi 2771601570 146 nqklYRLEDCEPDIIQNWELLRSKGV 171
Cdd:cd02440    78 ----HLVEDLARFLEEARRLLKPGGV 99
SpeE COG0421
Spermidine synthase (polyamine aminopropyltransferase) [Amino acid transport and metabolism];
73-138 2.92e-05

Spermidine synthase (polyamine aminopropyltransferase) [Amino acid transport and metabolism];


Pssm-ID: 440190 [Multi-domain]  Cd Length: 195  Bit Score: 44.43  E-value: 2.92e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2771601570  73 GGLGVDAYFLGKNY--EQATYCERDKNLFEISKHNLSHLSPG----KFDFYNGDSLDFLRNTSEKFDLIFVD 138
Cdd:COG0421    46 GGDGGLARELLKHPpvERVDVVEIDPEVVELAREYFPLLAPAfddpRLRVVIGDGRAFLREAEESYDVIIVD 117
cbiT PRK00377
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
 37-210 3.36e-05

cobalt-precorrin-6Y C(15)-methyltransferase; Provisional


Pssm-ID: 234740  Cd Length: 198  Bit Score: 44.40  E-value: 3.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  37 PDLLF--PVNLSMEQASSGLTAKYKAGHFKGSKMIDL---TGGLGVDAYFLGKNYEQATYCERDKNLFEISKHNLShlsp 111
Cdd:PRK00377   11 PDEEFerDEEIPMTKEEIRALALSKLRLRKGDMILDIgcgTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAE---- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570 112 gKFDFYN------GDSLDFLRNTSEKFDLIFVdparrGGHNQKLyrledcePDIIQ-NWELLRSKGVdVLVKASPMLDIK 184
Cdd:PRK00377   87 -KFGVLNnivlikGEAPEILFTINEKFDRIFI-----GGGSEKL-------KEIISaSWEIIKKGGR-IVIDAILLETVN 152

                         170       180
                  ....*....|....*....|....*.
gi 2771601570 185 AALKSLNAIhkvivlSVKNEVKEVLL 210
Cdd:PRK00377  153 NALSALENI------GFNLEITEVII 172
PRK00811 PRK00811
polyamine aminopropyltransferase;
87-138 1.57e-04

polyamine aminopropyltransferase;


Pssm-ID: 234843 [Multi-domain]  Cd Length: 283  Bit Score: 42.84  E-value: 1.57e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2771601570  87 EQATYCERDKNLFEISKHNLSHLSPGKFD-----FYNGDSLDFLRNTSEKFDLIFVD 138
Cdd:PRK00811  101 EKITLVEIDERVVEVCRKYLPEIAGGAYDdprveLVIGDGIKFVAETENSFDVIIVD 157
TrmR COG4122
tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; ...
 92-174 3.94e-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: 40.55  E-value: 3.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  92 CERDKNLFEISKHNLSHLS-PGKFDFYNGDSLDFL-RNTSEKFDLIFVDparrGGHNQKLYRLEDCEPdiiqnweLLRSK 169
Cdd:COG4122    47 IEIDPERAAIARENFARAGlADRIRLILGDALEVLpRLADGPFDLVFID----ADKSNYPDYLELALP-------LLRPG 115


                  ....*....
gi 2771601570 170 GV----DVL 174
Cdd:COG4122   116 GLivadNVL 124
rlmL PRK11783
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ...
 102-139 1.55e-03

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: 40.56  E-value: 1.55e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2771601570 102 SKHNLS--HLSPGKFDFYNGDSLDFLRNTSEKFDLIFVDP 139
Cdd:PRK11783  577 AERNFAlnGLSGRQHRLIQADCLAWLKEAREQFDLIFIDP 616
Spermine_synth pfam01564
Spermine/spermidine synthase domain; Spermine and spermidine are polyamines. This family ...
 84-138 1.74e-03

Spermine/spermidine synthase domain; Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyzes the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase.


Pssm-ID: 396237 [Multi-domain]  Cd Length: 183  Bit Score: 38.84  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2771601570  84 KNYEQATYCERDKNLFEISKHNLSHLSPGKFDF----YNGDSLDFLRNTSEKFDLIFVD 138
Cdd:pfam01564  40 PSVEKITLVDIDEKVIDFSKKFLPSLAIGFQDPrvkvVIGDGFKFLKDYLNTFDVIIVD 98
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 41-169 2.96e-03

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: 39.39  E-value: 2.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  41 FPVNLSMEQASSGLTAKYkAGHFKGSKMIDLTGGLGVDAYFLGKNYEQATYCERDKNLFEISKHNLSHLSPGKFDFYNGD 120
Cdd:COG2265   211 FQVNPEQAEALYAAALEW-LDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGD 289

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2771601570 121 SLDFLRN--TSEKFDLIFVDPARRGghnqklyrledCEPDIIQnwELLRSK 169
Cdd:COG2265   290 LEEVLPEllWGGRPDVVVLDPPRAG-----------AGPEVLE--ALAALG 327
COG4262 COG4262
Predicted spermidine synthase with an N-terminal membrane domain [General function prediction ...
 87-139 3.82e-03

Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only];


Pssm-ID: 443404 [Multi-domain]  Cd Length: 426  Bit Score: 39.08  E-value: 3.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771601570  87 EQATYCERDKNLFEISKHN--LSHLSPGKFD-----FYNGDSLDFLRNTSEKFDLIFVDP 139
Cdd:COG4262   311 ESVTLVDLDPEVTDLAKTNpfLRELNGGALNdprvtVVNADAFQFLRETDEKYDVIIVDL 370
 
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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