SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (1,925) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,055 48,728 28
Proteins 8,041 48,669 27


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
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)biological regulation0.041410.3319Least InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.00057660.0009176Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00060320.0009467Moderately InformativeDirect
Biological Process (BP)regulation of growth0.000053780.0003051InformativeDirect
Biological Process (BP)positive regulation of growth0.00000027710.0000004511Highly InformativeDirect
Molecular Function (MF)binding0.35310.4791Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.000013240.0000008944Moderately InformativeDirect
Molecular Function (MF)DNA binding0.000000088920.000000002733InformativeDirect
Cellular Component (CC)protein-DNA complex0.000023880.000000000009146InformativeDirect

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) biological regulation 0.3319 Least Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0009176 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0009467 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0009451 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.02063 Moderately Informative Inherited
Biological Process (BP) regulation of growth 0.0003051 Informative Direct
Biological Process (BP) positive regulation of growth 0.0000004511 Highly Informative Direct
Molecular Function (MF) binding 0.4791 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000008944 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.000000002733 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0002889 Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.0005703 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000004944 Highly Informative Direct
Cellular Component (CC) protein-DNA complex 0.000000000009146 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processAmino-acid biosynthesis0.000002625Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately 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-quality) · Gene Ontology (high-coverage) · 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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]