SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,431 16,169 12
Proteins 2,565 11,411 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 0.000000000001728 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000002502 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000001129 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000002165 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000002649 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000000109 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000000394 Least Informative Direct
Biological Process (BP) response to stimulus 0.0002469 Least Informative Direct
Biological Process (BP) biological regulation 0.5034 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5881 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4331 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) reproduction 0.00000000005845 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000618 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.7235 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01847 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.002498 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.02582 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1205 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.006465 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.09805 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.09726 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001285 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03118 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000001385 Informative Direct
Biological Process (BP) cell cycle process 0.00000000005447 Informative Direct
Biological Process (BP) response to radiation 0.000001125 Informative Direct
Biological Process (BP) chromosome organization 0.00009459 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0003484 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0003563 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0004765 Informative Direct
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0 Highly Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00000000001342 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.00000001117 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.00000008509 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000009087 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.0000298 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.00003467 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00005561 Highly Informative Direct
Biological Process (BP) DNA replication 0.004301 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.0000000002247 Least Informative Direct
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000000000001615 Moderately Informative Direct
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0 Informative Direct
Molecular Function (MF) ribonucleotide binding 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 0.000000000001744 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000001524 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00002432 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000468 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000000001309 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000008251 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000000000007623 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000006288 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 regulation0.01969Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.000000000000137InformativeDirect
Biological processTranscription termination0.00000000000000239Highly InformativeDirect
Cellular componentNucleus0.000000001078Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0004107Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0005538Moderately InformativeDirect

Document: KW 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) ]

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) · Internal database links ]