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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 (1,918) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,421 15,274 12
Proteins 2,555 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) heterocycle metabolic process 0.000000000004986 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000007222 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000002874 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000005609 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000001657 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000004879 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000001239 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001752 Least Informative Direct
Biological Process (BP) biological regulation 0.4673 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6654 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.3738 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000004655 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.09806 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.7162 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01967 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0894 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.004114 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.002078 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001174 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001137 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.02312 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.0159 Moderately Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000000001449 Informative Direct
Biological Process (BP) cell cycle process 0.000000000535 Informative Direct
Biological Process (BP) response to radiation 0.0000007991 Informative Direct
Biological Process (BP) chromosome organization 0.00003172 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0003349 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0003708 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0004777 Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0 Highly Informative Direct
Biological Process (BP) nuclear division 0.000000000000007367 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00000000001914 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.00000001494 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.000000078 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.000001173 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.00003321 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.00004183 Highly Informative Direct
Biological Process (BP) response to alcohol 0.0000666 Highly Informative Direct
Biological Process (BP) DNA replication 0.003745 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.0000000002255 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000000000001646 Moderately Informative Direct
Molecular Function (MF) purine nucleotide binding 0 Informative Direct
Molecular Function (MF) ribonucleotide binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.000000000001585 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000004339 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00006368 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00009368 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000000004666 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000001826 Moderately Informative Direct
Cellular Component (CC) chromosome 0.00000000004046 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000005808 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 regulation0.01958Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.0000000000001291InformativeDirect
Biological processTranscription termination0.000000000000002626Highly InformativeDirect
Cellular componentNucleus0.00000000101Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0004048Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0000801Moderately 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 ]