SUPERFAMILY 1.75 HMM library and genome assignments server

TrpR-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   TrpR-like [ 48295] (3)
Families:   Trp repressor, TrpR [ 48296]
  Chromosomal replication initiation factor DnaA C-terminal domain IV [ 81695]
  SPO1678-like [ 158345]

Superfamily statistics
Genomes (2,607) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,427 42,195 10
Proteins 6,922 40,622 10

Functional annotation
General category Regulation
Detailed category DNA-binding

Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) 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) heterocycle metabolic process 0.00007722 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00008885 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0001612 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000355 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.1234 Least Informative Inherited
Biological Process (BP) DNA metabolic process 0.000001056 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.0004204Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010921 SSF48295 Protein matches

The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan [PubMed12475235]. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.

The bacterial chromosomal replication initiation factor DnaA is a monomeric protein that shows structural similarity to the TrpR, except that it contains additional N-terminal helices. DnaA is a member of the AAA+ family of ATPases, and forms a large, oligomeric assembly at the replication origin site (oriC); the oligomeric complex of DnaA recognises and processes specific origin sequences in order to initiate replication in bacteria [PubMed12234917].

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

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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 4 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 TrpR-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 4 hidden Markov models representing the TrpR-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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]