SUPERFAMILY 1.75 HMM library and genome assignments server

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Rad51 N-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   Rad51 N-terminal domain-like [ 47794] (3)
Families:   DNA repair protein Rad51, N-terminal domain [ 47795]
  NusA extra C-terminal domains [ 109873]
  Hypothetical protein AF1548, C-terminal domain [ 116936]

Superfamily statistics
Genomes (1,921) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,431 0 12
Proteins 2,565 0 12

Functional annotation
General category Information
Detailed category DNA replication/repair

Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation0.0199Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.0000000000001458InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentNucleus0.000000001218Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0004319Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0005597Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010995 SSF47794 Protein matches

This entry represents an alpha-helical bundle domain, which has a SAM domain-like fold. This compact domain consists of a 4-5 helical bundle of two orthogonally packed alpha-hairpins, and contains one classic and one pseudo HhH (helix-hairpin-helix) motif. This domain is found at N-terminal of the DNA repair protein Rad1, at the C-terminal of the transcription elongation protein NusA, and at the C-terminal of the hypothetical protein AF1548.

Human Rad51 protein is a homologue of Escherichia coli RecA protein, and functions in DNA repair and recombination [PubMed10390347]. In higher eukaryotes, Rad51 protein is essential for cell viability. The N-terminal region of Rad51 is highly conserved among eukaryotic Rad51 proteins but is absent from RecA, suggesting a Rad51-specific function for this region. The-terminal domain is involved in interactions with DNA and proteins; DNA binding may be regulated via phosphorylation within the N-terminal domain.

NusA (N utilisation substance A) from Escherichia coli is an essential transcription factor that associates with the RNA polymerase (RNAP) core enzyme, where it modulates transcriptional pausing, termination and anti-termination [PubMed15987884]. The C-terminal of NusA consists of two repeat units, and is responsible for the interaction of NisA with the C-terminal of RNAP, and with its interaction with protein N from phage lambda during anti-termination [PubMed15365170].

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 · 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 6 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 Rad51 N-terminal domain-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 6 hidden Markov models representing the Rad51 N-terminal domain-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 · UniProtKB KeyWords (KW) · Internal database links ]