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S-adenosyl-L-methionine-dependent methyltransferases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   S-adenosyl-L-methionine-dependent methyltransferases [ 53334]
Superfamily:   S-adenosyl-L-methionine-dependent methyltransferases [ 53335] (57)
Families:   COMT-like [ 53336] (3)
  Plant O-methyltransferase, C-terminal domain [ 64111] (5)
  RNA methyltransferase FtsJ [ 53339]
  Fibrillarin homologue [ 53342]
  rRNA methyltransferase RlmA [ 102557]
  rRNA methyltransferase AviRa [ 89738]
  rRNA adenine dimethylase-like [ 88784] (4)
  mRNA cap methylase [ 88785] (2)
  mRNA cap (Guanine N-7) methyltransferase [ 102560]
  Hypothetical protein MJ0882 [ 53345]
  Hypothetical protein HI0319 (YecO) [ 69544]
  Glycine N-methyltransferase [ 53348]
  Arylamine N-methyltransferase [ 69547] (2)
  Histamine methyltransferase [ 75261]
  Hypothetical Protein YjhP [ 82469]
  Salicylic acid carboxyl methyltransferase (SAMT) [ 102563]
  Thiopurine S-methyltransferase [ 102566]
  Leucine carboxy methyltransferase Ppm1 [ 102569]
  Precorrin-6Y methyltransferase (CbiT) [ 82472]
  MraW-like putative methyltransferases [ 82475]
  N5-glutamine methyltransferase, HemK [ 89743]
  Catalytic, N-terminal domain of histone methyltransferase Dot1l [ 89746]
  Guanidinoacetate methyltransferase [ 69550]
  Arginine methyltransferase [ 53351] (3)
  Protein-L-isoaspartyl O-methyltransferase [ 53354]
  Glucose-inhibited division protein B (GidB) [ 75264]
  tRNA(1-methyladenosine) methyltransferase-like [ 64117] (4)
  NOL1/NOP2/sun [ 102575] (3)
  Ribosomal protein L11 methyltransferase PrmA [ 102578]
  (Uracil-5-)-methyltransferase [ 102581]
  Chemotaxis receptor methyltransferase CheR, C-terminal domain [ 53357]
  C5 cytosine-specific DNA methylase, DCM [ 88786] (3)
  DNA methylase TaqI, N-terminal domain [ 88787]
  N6 adenine-specific DNA methylase, DAM [ 88788] (2)
  Type II DNA methylase [ 53377] (3)
  Spermidine synthase [ 69557] (2)
  Mycolic acid cyclopropane synthase [ 69560] (6)
  Ta1320-like [ 89751] (2)
  UbiE/COQ5-like [ 110671] (5)
  AD-003 protein-like [ 117685] (2)
  CAC2371-like [ 117688] (3)
  TehB-like [ 142603]
  N-6 DNA Methylase-like [ 142606] (3)
  YhhF-like [ 142611] (5)
  Met-10+ protein-like [ 142622]
  Nsp15 N-terminal domain-like [ 142625]
  BC2162-like [ 142629]
  CmcI-like [ 142632]
  hypothetical RNA methyltransferase [ 142635] (4)
  RPA4359-like [ 142644]
  TrmB-like [ 142647]
  Methyltransferase 10 domain [ 142651]
  YhiQ-like [ 159686]
  FkbM-like [ 159691]
  ML2640-like [ 159694]
  TRM1-like [ 159697]
  LPG1296-like [ 159700]


Superfamily statistics
Genomes (3,261) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 195,048 1,311,842 166
Proteins 189,633 1,291,380 166


Functional annotation
General category Metabolism
Detailed category Transferases

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an1Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)Cysteine endopeptidases0.03493Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-CH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Flavivirin0InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphatase0InformativeDirect
Enzyme Commission (EC)SARS coronavirus main proteinase0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Fatty-acid synthase0.000000809InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-acetyltransferase0.000002852InformativeDirect
Enzyme Commission (EC)3-hydroxypalmitoyl-[acyl-carrier-protein] dehydrat0.000002852InformativeDirect
Enzyme Commission (EC)Enoyl-[acyl-carrier-protein] reductase (NADPH, B-s0.000004862InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0.00002048InformativeDirect
Enzyme Commission (EC)mRNA (nucleoside-2'-O-)-methyltransferase0.0002104InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases1InformativeInherited
Enzyme Commission (EC)mRNA guanylyltransferase0.000000000000004166Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0.0000000000001039Highly InformativeDirect
Enzyme Commission (EC)DNA (cytosine-5-)-methyltransferase0.00001852Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.475Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.5243Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cell physiology0.003487InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the voice0.111Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.9606Least InformativeInherited
Worm Phenotype (WP)apoptosis variant0.5769Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6888Moderately InformativeInherited
Worm Phenotype (WP)cell stress response variant0.1595InformativeInherited
Worm Phenotype (WP)cell gamma ray response variant0.000008683Highly InformativeDirect
Worm Phenotype (WP)apoptosis increased0.00369Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.2026Least InformativeInherited
Yeast Phenotype (YP)RNA modification0.0000009665Highly InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0.02678Least InformativeInherited
Xenopus ANatomical entity (XAN)germ line cell0.0009387Moderately InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptidases)1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.00000004616InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0.01236InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Thiolester hydrolases1InformativeInherited
Enzyme Commission (EC)Serine endopeptidases1InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases1InformativeInherited
Enzyme Commission (EC)In phosphorus-containing anhydrides1InformativeInherited
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Flavivirin0Highly InformativeDirect
Enzyme Commission (EC)SARS coronavirus main proteinase0Highly InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)0.0000003743Highly InformativeDirect
Enzyme Commission (EC)Fatty-acid synthase0.0000007974Highly InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0.000003598Highly InformativeDirect
Enzyme Commission (EC)Lovastatin nonaketide synthase0.00000706Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-acetyltransferase0.00001208Highly InformativeDirect
Enzyme Commission (EC)Methyltransferase cap10.00005251Highly InformativeDirect
Enzyme Commission (EC)Oleoyl-[acyl-carrier-protein] hydrolase0.0001607Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 127 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a S-adenosyl-L-methionine-dependent methyltransferases domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 127 hidden Markov models representing the S-adenosyl-L-methionine-dependent methyltransferases superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]