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 (1,923) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,053 47,065 28
Proteins 8,039 47,036 27

Functional annotation
General category Regulation
Detailed category DNA-binding

Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)regulation of growth0.000016190.00004055InformativeDirect
Biological Process (BP)positive regulation of growth0.00000028170.000000045Highly InformativeDirect
Molecular Function (MF)binding0.61530.6839Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.002980.003444Moderately InformativeInherited
Molecular Function (MF)DNA binding0.00022850.0003041InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of growth 0.00004055 Informative Direct
Biological Process (BP) positive regulation of growth 0.000000045 Highly Informative Direct
Molecular Function (MF) binding 0.6839 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.003444 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0.0003041 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 aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH 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 biosynthesis0.000003612Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0.00000005309Least InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid degradation0Moderately InformativeDirect
UniPathway (UP)L-proline degradation0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR010985 SSF47598 Protein matches

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-quality) · 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 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]