SUPERFAMILY 1.75 HMM library and genome assignments server


Cobalamin (vitamin B12)-dependent enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Cobalamin (vitamin B12)-dependent enzymes [ 51703] (4)
Families:   Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [ 51704] (2)
  Glutamate mutase, large subunit [ 51707]
  Diol dehydratase, alpha subunit [ 51710]
  D-lysine 5,6-aminomutase alpha subunit, KamD [ 117392]


Superfamily statistics
Genomes (1,075) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,214 0 8
Proteins 2,194 0 8


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) isomerase activity 2.598e-11 Moderately Informative Direct
Molecular Function (MF) intramolecular transferase activity 8.97e-15 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring other groups7.849e-08InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMitochondrion1.496e-05Moderately InformativeDirect
DomainTransit peptide6.133e-07Moderately InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationAcetylation0.0004176Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.01711Least InformativeInherited
UniPathway (UP)organic acid metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation3.592e-12Moderately InformativeDirect
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)metabolic intermediate degradation0InformativeDirect
UniPathway (UP)fermentation0InformativeDirect
UniPathway (UP)L-glutamate degradation0Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 6 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 Cobalamin (vitamin B12)-dependent enzymes 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 6 hidden Markov models representing the Cobalamin (vitamin B12)-dependent enzymes 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]