SUPERFAMILY 1.75 HMM library and genome assignments server


Ribbon-helix-helix superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Ribbon-helix-helix [ 47597]
Superfamily:   Ribbon-helix-helix [ 47598] (11)
Families:   Arc/Mnt-like phage repressors [ 47599] (2)
  CopG-like [ 100970] (4)
  Omega transcriptional repressor [ 100971]
  Met repressor, MetJ (MetR) [ 100972]
  NE0241-like [ 140544]
  SeqA N-terminal domain-like [ 140547]
  Trafficking protein A-like [ 140550]
  VCA0319-like [ 140553]
  VirC2-like [ 158482]
  PutA pre-N-terminal region-like [ 158485]
  MJ0366-like [ 158488]


Superfamily statistics
Genomes (1,926) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,081 24,485 28
Proteins 8,067 24,470 27


Functional annotation
General category Regulation
Detailed category DNA-binding

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) binding 0.8121 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.006083 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0.0006789 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors0InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)With a quinone or similar compound as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processAmino-acid biosynthesis4.015e-06Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding1.941e-08Least InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010985 SSF47598 Protein matches
Abstract

This entry represents domains with a ribbon-helix-helix core topology consisting of four helices in an open array of two hairpins. Such domains are found in several bacterial and phage repressors, including the Escherichia coli methionine repressor (MetJ), which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis [PubMed1943695]. Other bacterial and phage repressors containing domains with a similar fold include the bacterial plasmid-encoded repressors CopG , the bacterial omega transcription repressor [PubMed11733997], and the phage repressors Arc [PubMed9927650] and Mnt [PubMed7999761]. These repressors are usually obligate dimers, which pair through a single N-terminal strand, and possess a C-terminal helix-turn-helix unit [PubMed15808743].


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) ]

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 17 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 Ribbon-helix-helix 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 17 hidden Markov models representing the Ribbon-helix-helix 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) · Internal database links ]