SUPERFAMILY 1.75 HMM library and genome assignments server

DNA repair protein MutS, domain III superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA repair protein MutS, domain III [ 48333]
Superfamily:   DNA repair protein MutS, domain III [ 48334]
Families:   DNA repair protein MutS, domain III [ 48335]


Superfamily statistics
Genomes (2,689) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,586 28,964 8
Proteins 6,556 28,941 8


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)developmental process0.00013940.000138Least InformativeDirect
Biological Process (BP)multicellular organismal process0.00023250.00005715Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0077680.000000000000001913Least InformativeInherited
Biological Process (BP)reproductive process0.0000012220.00000000000205Moderately InformativeDirect
Biological Process (BP)multi-organism process0.000013420.0002671Moderately InformativeDirect
Biological Process (BP)organ development0.000010530.6197Moderately InformativeInherited
Biological Process (BP)reproductive structure development0.000000048710.00001933InformativeDirect
Biological Process (BP)cell cycle process0.0000002230InformativeDirect
Biological Process (BP)single organism reproductive process0.00000052120.000000002649InformativeDirect
Biological Process (BP)gonad development0.00000000032150.000000004307Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.00025530.0000002032Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0030260.00000000001232Least InformativeInherited
Cellular Component (CC)nuclear part0.0000044060.000000000002607Moderately InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0.000138 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00005715 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000000000001913 Least Informative Direct
Biological Process (BP) cellular aromatic compound 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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000000000001071 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000000000001587 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000000000007633 Least Informative Direct
Biological Process (BP) response to stimulus 0.000000007343 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.2534 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01697 Least Informative Inherited
Biological Process (BP) reproductive process 0.00000000000205 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0002671 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00004531 Moderately Informative Direct
Biological Process (BP) immune system process 0.00005579 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0001192 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0009935 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.1344 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01878 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1698 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06495 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.02969 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.01829 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.002305 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.2907 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1623 Moderately Informative Inherited
Biological Process (BP) organ development 0.6197 Moderately Informative Inherited
Biological Process (BP) reproductive structure development 0.00001933 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000002649 Informative Direct
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) organelle fission 0 Informative Direct
Biological Process (BP) cell division 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.000000000007183 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0000000001523 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0000000005082 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.0000000009971 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.00000001943 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.00000005993 Informative Direct
Biological Process (BP) chromosome organization 0.0000000627 Informative Direct
Biological Process (BP) apoptotic process 0.000001945 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0.000002487 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001718 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0002688 Informative Direct
Biological Process (BP) leukocyte activation 0.0003128 Informative Direct
Biological Process (BP) immune effector process 0.0005699 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.2019 Informative Inherited
Biological Process (BP) immune response 0.01588 Informative Inherited
Biological Process (BP) response to light stimulus 0.5718 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.1 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) gonad development 0.000000004307 Highly Informative Direct
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.0000000000001592 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.000000000001111 Highly Informative Direct
Biological Process (BP) B cell activation 0.000000000003052 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.00000000001068 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 0.00000000001095 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.00000000001211 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0000000000188 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.00000000002259 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.00000000006044 Highly Informative Direct
Biological Process (BP) response to UV 0.000000000153 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000000001115 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.00000003994 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000001435 Highly Informative Direct
Biological Process (BP) aging 0.00005626 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0006167 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 0.09196 Highly Informative Inherited
Molecular Function (MF) binding 0.00000001064 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.004476 Least Informative Inherited
Molecular Function (MF) anion binding 0.00004365 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00004498 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0008172 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.002144 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.00000001456 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00000001597 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.00000002614 Informative Direct
Molecular Function (MF) nucleotide binding 0.0000007013 Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.000000000005657 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000000004243 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.0000002032 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000001232 Least Informative Direct
Cellular Component (CC) protein complex 0.0000008262 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.02511 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000000002607 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.05965 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0000000000001676 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0001682 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.2395Least InformativeInherited
Disease Ontology (DO)urinary system cancer0.0008475InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.0506Least InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.00312Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.008011Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04015Moderately InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0002162InformativeDirect
Mammalian Phenotype (MP)increased malignant tumor incidence0.0005797InformativeDirect
Mammalian Phenotype (MP)increased integument system tumor incidence0.00003786Highly InformativeDirect
Mammalian Phenotype (MP)increased adenocarcinoma incidence0.00004213Highly InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.00005013Highly InformativeDirect
Mammalian Phenotype (MP)abnormal skin condition0.00032Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.004687Least InformativeInherited
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)cell death variant0.00004012Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processMeiosis0.00000124InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0.001536Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007696 SSF48334 Protein matches
Abstract

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with MutS_V, MutS_II, MutS_I and MutS_IV. 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. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS.


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-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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 III 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 III 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-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]