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 (2,688) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,583 28,964 8
Proteins 6,553 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 process0.0001380.0001392Least InformativeDirect
Biological Process (BP)multicellular organismal process0.0002580.0001218Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0027625.484e-12Least InformativeInherited
Biological Process (BP)reproduction2.343e-060Moderately InformativeDirect
Biological Process (BP)organ development1.083e-050.648Moderately InformativeInherited
Biological Process (BP)reproductive system development2.58e-081.104e-06InformativeDirect
Biological Process (BP)cellular process involved in reproduction5.473e-080InformativeDirect
Biological Process (BP)single organism reproductive process1.182e-071.891e-05InformativeDirect
Biological Process (BP)cell cycle process2.099e-070InformativeDirect
Biological Process (BP)developmental process involved in reproduction2.234e-071.891e-06InformativeDirect
Biological Process (BP)sexual reproduction7.625e-080.9484InformativeInherited
Biological Process (BP)multicellular organismal reproductive process8.905e-080.2967InformativeInherited
Biological Process (BP)gonad development3.243e-107.45e-12Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.00025812.831e-07Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0033553.544e-11Least InformativeInherited
Cellular Component (CC)nuclear part5.022e-062.951e-11Moderately 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 0.0001392 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0001218 Least Informative Direct
Biological Process (BP) single-organism cellular process 5.484e-12 Least Informative Direct
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) cellular macromolecule metabolic process 1.34e-11 Least Informative Direct
Biological Process (BP) response to stimulus 7.392e-09 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 4.285e-08 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.2393 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01311 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organelle organization 2.466e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 1.018e-05 Moderately Informative Direct
Biological Process (BP) immune system process 5.658e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0001037 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.01473 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.02432 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.168 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.1927 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.01585 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.001476 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1385 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06827 Moderately Informative Inherited
Biological Process (BP) organ development 0.648 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1547 Moderately Informative Inherited
Biological Process (BP) reproductive system development 1.104e-06 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0 Informative Direct
Biological Process (BP) single organism reproductive process 1.891e-05 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) developmental process involved in reproduction 1.891e-06 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) chromosome organization 6.562e-14 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 1.757e-12 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 5.373e-11 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 2.018e-10 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 4.201e-10 Informative Direct
Biological Process (BP) organophosphate catabolic process 2.497e-08 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 7.448e-08 Informative Direct
Biological Process (BP) apoptotic process 1.956e-06 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 3.087e-06 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0001692 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001734 Informative Direct
Biological Process (BP) leukocyte activation 0.000319 Informative Direct
Biological Process (BP) immune effector process 0.0005594 Informative Direct
Biological Process (BP) response to light stimulus 0.5773 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.1105 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.2967 Informative Inherited
Biological Process (BP) sexual reproduction 0.9484 Informative Inherited
Biological Process (BP) immune response 0.01605 Informative Inherited
Biological Process (BP) gonad development 7.45e-12 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0 Highly Informative Direct
Biological Process (BP) meiosis 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 1.643e-13 Highly Informative Direct
Biological Process (BP) purine ribonucleoside monophosphate metabolic process 8.778e-13 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.141e-12 Highly Informative Direct
Biological Process (BP) B cell activation 3.13e-12 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 1.103e-11 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 1.123e-11 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 1.249e-11 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 1.938e-11 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 2.328e-11 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 2.517e-11 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 5.648e-11 Highly Informative Direct
Biological Process (BP) response to UV 1.261e-10 Highly Informative Direct
Biological Process (BP) DNA recombination 1.006e-09 Highly Informative Direct
Biological Process (BP) ovulation cycle process 8.431e-08 Highly Informative Direct
Biological Process (BP) spermatogenesis 1.422e-06 Highly Informative Direct
Biological Process (BP) aging 5.833e-06 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0006519 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 0.1216 Highly Informative Inherited
Molecular Function (MF) binding 8.269e-09 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.004408 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 3.396e-05 Moderately Informative Direct
Molecular Function (MF) anion binding 4.348e-05 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 1.46e-08 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 1.58e-08 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 2.605e-08 Informative Direct
Molecular Function (MF) nucleotide binding 7.015e-07 Informative Direct
Molecular Function (MF) structure-specific DNA binding 5.741e-12 Highly Informative Direct
Molecular Function (MF) ATP binding 4.22e-10 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 2.831e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 3.544e-11 Least Informative Direct
Cellular Component (CC) protein complex 9.181e-07 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02347 Least Informative Inherited
Cellular Component (CC) nuclear part 2.951e-11 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.1285 Moderately Informative Inherited
Cellular Component (CC) chromosome 3.438e-13 Informative Direct
Cellular Component (CC) nuclear chromosome part 8.353e-05 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 incidence3.786e-05Highly InformativeDirect
Mammalian Phenotype (MP)increased adenocarcinoma incidence4.213e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair5.013e-05Highly 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 variant4.012e-05Moderately 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 processMeiosis1.24e-06InformativeDirect
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 ]