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 (1,905) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,405 15,274 12
Proteins 2,537 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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
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) response to stimulus 0.003495 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5462 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07415 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.0175 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9984 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.07585 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.2839 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.7831 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 5.754e-13 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 8.553e-13 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 3.413e-12 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 3.975e-10 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 4.235e-09 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 5.363e-09 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.8412 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01331 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.09281 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.04187 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.0623 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.03993 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.09373 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.02867 Moderately Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 0 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 1.402e-09 Informative Direct
Biological Process (BP) chromosome organization 3.877e-08 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 8.988e-06 Informative Direct
Biological Process (BP) regulation of response to stress 0.0002108 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0002852 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0004354 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.0004388 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.000667 Informative Direct
Biological Process (BP) single organism reproductive process 0.01075 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.02097 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0 Highly Informative Direct
Biological Process (BP) meiosis 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 2.089e-12 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 7.494e-11 Highly Informative Direct
Biological Process (BP) response to alkaloid 9.406e-10 Highly Informative Direct
Biological Process (BP) double-strand break repair 6.997e-08 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 7.778e-07 Highly Informative Direct
Biological Process (BP) cellular response to radiation 3.59e-05 Highly Informative Direct
Biological Process (BP) spermatogenesis 6.389e-05 Highly Informative Direct
Biological Process (BP) DNA replication 0.02433 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 2.646e-09 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) structure-specific DNA binding 0 Highly Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 8.223e-10 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 6.335e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 7.152e-05 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 3.344e-14 Moderately Informative Direct
Cellular Component (CC) nuclear part 3.729e-08 Moderately Informative Direct
Cellular Component (CC) chromosome 1.192e-11 Informative Direct
Cellular Component (CC) condensed chromosome 1.069e-08 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 2.421e-06 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 regulation0.01613Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis4.865e-14InformativeDirect
Biological processTranscription termination3.23e-15Highly InformativeDirect
Cellular componentNucleus4.025e-10Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0002606Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionDNA-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 ]