SUPERFAMILY 1.75 HMM library and genome assignments server


DNA repair protein MutS, domain II superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribonuclease H-like motif [ 53066] (7)
Superfamily:   DNA repair protein MutS, domain II [ 53150]
Families:   DNA repair protein MutS, domain II [ 53151]


Superfamily statistics
Genomes (2,543) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,428 0 8
Proteins 3,426 0 8


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 1.224e-12 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.13e-11 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.666e-09 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.2e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 8.329e-13 Least Informative Direct
Biological Process (BP) response to stimulus 0.0009019 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 6.069e-12 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.1796 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4148 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.8732 Least Informative Inherited
Biological Process (BP) developmental process 0.2694 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.586 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9502 Least Informative Inherited
Biological Process (BP) reproduction 1.229e-08 Moderately Informative Direct
Biological Process (BP) cellular response to stress 3.722e-15 Moderately Informative Direct
Biological Process (BP) organelle organization 0.1283 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.09408 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.01724 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.09058 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.01265 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.007619 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.07022 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.03971 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01885 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0004167 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 2.644e-08 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 1.755e-07 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 6.296e-07 Informative Direct
Biological Process (BP) cell cycle process 8.29e-08 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 3.823e-07 Informative Direct
Biological Process (BP) organophosphate catabolic process 6.714e-06 Informative Direct
Biological Process (BP) cellular process involved in reproduction 1.453e-11 Informative Direct
Biological Process (BP) chromosome organization 0.0003741 Informative Direct
Biological Process (BP) reproductive system development 0.0004648 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 1.342e-05 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 1.439e-05 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.06145 Informative Inherited
Biological Process (BP) DNA recombination 0.0006831 Highly Informative Direct
Biological Process (BP) meiosis 2.302e-07 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 6.357e-09 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 1.078e-07 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 6.863e-08 Highly Informative Direct
Biological Process (BP) ATP metabolic process 9.142e-09 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 9.674e-08 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 4.51e-08 Highly Informative Direct
Molecular Function (MF) binding 0.0004527 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.01479 Least Informative Inherited
Molecular Function (MF) anion binding 0.0001571 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.005133 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 8.402e-06 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 5.402e-06 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 8.718e-07 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 6.145e-07 Informative Direct
Molecular Function (MF) ATP binding 4.641e-08 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 7.481e-06 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02791 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01914 Least Informative Inherited
Cellular Component (CC) protein complex 0.01841 Least Informative Inherited
Cellular Component (CC) nuclear part 3.37e-05 Moderately Informative Direct

Document: GO annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007860 SSF53150 Protein matches
Abstract This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with several other domains, , , and . The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [PubMed8036718]. This domain corresponds to domain II in Thermus aquaticus MutS as characterised in [PubMed11048710], and has similarity to RNAse-H-like domains (see ).

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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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 2 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 DNA repair protein MutS, domain II 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 2 hidden Markov models representing the DNA repair protein MutS, domain II 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]