SUPERFAMILY 1.75 HMM library and genome assignments server

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 (1,912) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,407 15,274 12
Proteins 2,541 9,585 12


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000005255 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00004844 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8187 Least Informative Inherited
Biological Process (BP) response to stimulus 0.007878 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.3306 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.05741 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000000000001451 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000000000007433 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000002125 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000002688 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000003124 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.01471 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.01745 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8517 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.04403 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.001049 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.04045 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.02674 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2352 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03204 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.08932 Moderately Informative Inherited
Biological Process (BP) organelle fission 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) cell division 0 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000000004741 Informative Direct
Biological Process (BP) cell cycle process 0.000002082 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.00001731 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00007398 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0002093 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0004956 Informative Direct
Biological Process (BP) chromosome organization 0.03568 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.0145 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1355 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.000000000002587 Highly Informative Direct
Biological Process (BP) response to alkaloid 0.00000000002199 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000000148 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.00000008519 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.000001186 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.00004847 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00006891 Highly Informative Direct
Biological Process (BP) DNA replication 0.005653 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.00000000327 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0000000009423 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00002899 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00005098 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000000000000003071 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000005131 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000000000007101 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000002848 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation0.01639Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.00000000000004963InformativeDirect
Biological processTranscription termination0.000000000000003003Highly InformativeDirect
Cellular componentNucleus0.0000000004035Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0002609Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)poly-(R)-3-hydroxybutanoate biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR010995 SSF47794 Protein matches
Abstract

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