SUPERFAMILY 1.75 HMM library and genome assignments server


CbiD-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   CbiD-like [ 111341]
Superfamily:   CbiD-like [ 111342]
Families:   CbiD-like [ 111343]


Superfamily statistics
Genomes (714) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 723 3,704 1
Proteins 720 3,698 1


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details) Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCobalamin biosynthesis0Highly InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)macrocycle metabolism0Moderately InformativeDirect
UniPathway (UP)porphyrin-containing compound metabolism0Moderately InformativeDirect
UniPathway (UP)adenosylcobalamin biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR002748 SSF111342 Protein matches
Abstract

This entry represents CbiD, an essential protein for cobalamin biosynthesis in both S. typhimurium and B. megaterium. A deletion mutant of CbiD suggests that this enzyme is involved in C-1 methylation and deacylation reactions required during the ring contraction process in the anaerobic pathway to cobalamin (similar role as CobF) [PubMed15741157]. The CbiD protein has a putative S-AdoMet binding site [PubMed9742225]. CbiD has no counterpart in the aerobic pathway.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · 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 1 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 CbiD-like 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 1 hidden Markov models representing the CbiD-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]