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  Home > SCOP hierarchy > MHC antigen-recognition domain superfamily


MHC antigen-recognition domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   MHC antigen-recognition domain [ 54451]
Superfamily:   MHC antigen-recognition domain [ 54452]
Families:   MHC antigen-recognition domain [ 54453] (12)

Superfamily statistics
Genomes (93) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,661 96,097 190
Proteins 3,650 95,956 190

 Functional annotation
General category Processes_EC
Detailed category Immune response

Document: Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.01629Least InformativeInherited
Disease Ontology (DO)organ system cancer0.0776Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.00000002116Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.0000003932Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.000001342Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.00001503Moderately InformativeDirect
Disease Ontology (DO)skin disease0.00002326Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.00002566Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0001805Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003338Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006504Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.03828Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.04129Moderately InformativeInherited
Disease Ontology (DO)syndrome0.2878Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.7136Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis0.0000000000006221InformativeDirect
Disease Ontology (DO)liver disease0.00000002116InformativeDirect
Disease Ontology (DO)alopecia0.00003451InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.00008117InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003324InformativeDirect
Disease Ontology (DO)autosomal recessive disease0.0005322InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0007548InformativeDirect
Disease Ontology (DO)peripheral nervous system disease0.007535InformativeInherited
Disease Ontology (DO)arthropathy0.008618InformativeInherited
Disease Ontology (DO)bullous skin disease0.01667InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.03044InformativeInherited
Disease Ontology (DO)myeloid leukemia0.0916InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease0.00000000005062Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.00000004832Highly InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0000001408Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia0.000001921Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001996Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.00002806Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.00005997Highly InformativeDirect
Disease Ontology (DO)uveitis0.0001366Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001067Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.03283Highly InformativeInherited
Disease Ontology (DO)spondyloarthropathy0.4777Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Heterogeneous0.0002273InformativeDirect
Mode of Inheritance (MI)Multifactorial inheritance0.00000000001268Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the integument0.03577Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.09479Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.2251Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.233Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2607Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.3293Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3977Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.4211Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.49Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.01093Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.05373Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.05404Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.0984Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating metabolite concentration0.102Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.1584Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.2314Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.2347Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.3589Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.3918Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.4164Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.5476Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Nausea and vomiting0.00001997InformativeDirect
Phenotypic Abnormality (PA)Unusual CNS infection0.00006082InformativeDirect
Phenotypic Abnormality (PA)Inflammatory abnormality of the eye0.0001771InformativeDirect
Phenotypic Abnormality (PA)Peripheral neuropathy0.000246InformativeDirect
Phenotypic Abnormality (PA)Edema0.0004445InformativeDirect
Phenotypic Abnormality (PA)Constitutional symptom0.004499InformativeInherited
Phenotypic Abnormality (PA)Abnormal hair quantity0.01078InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral mucosa morphology0.03692InformativeInherited
Phenotypic Abnormality (PA)Decreased body weight0.05062InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.05188InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.05413InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.1045InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.1249InformativeInherited
Phenotypic Abnormality (PA)Functional respiratory abnormality0.2671InformativeInherited
Phenotypic Abnormality (PA)Arthralgia0.00000002295Highly InformativeDirect
Phenotypic Abnormality (PA)Abdominal pain0.0000009914Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pleura0.000001114Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal sputum0.00001566Highly InformativeDirect
Phenotypic Abnormality (PA)Meningitis0.00002128Highly InformativeDirect
Phenotypic Abnormality (PA)Pulmonary infiltrates0.00002728Highly InformativeDirect
Phenotypic Abnormality (PA)Weight loss0.00002803Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal pericardium morphology0.00003305Highly InformativeDirect
Phenotypic Abnormality (PA)Recurrent aphthous stomatitis0.00009758Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal erythrocyte sedimentation rate0.0002635Highly InformativeDirect
Phenotypic Abnormality (PA)Vasculitis0.0005221Highly InformativeDirect
Phenotypic Abnormality (PA)Serositis0.0005873Highly InformativeDirect
Phenotypic Abnormality (PA)Diabetes insipidus0.0008123Highly InformativeDirect
Phenotypic Abnormality (PA)Inflammatory abnormality of the skin0.0274Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating protein level0.1766Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.0000002957Least InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.000002706Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0006216Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3188Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.4349Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.698Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B lymphocyte antigen presentation0.0001346InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.0003109InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.001021InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.002675InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.1338InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.2026InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.3787InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.8213InformativeInherited
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007649Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.0009941Highly InformativeDirect
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.1096Highly InformativeInherited
Mammalian Phenotype (MP)decreased alpha-beta T cell number0.2547Highly InformativeInherited

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.2717Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.000418Highly InformativeDirect

Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR011162 SSF54452 Protein matches
Abstract

This entry represents MHC class I and II-like antigen-recognition domains from:

  • MHC class II, N-terminal domains of alpha and beta chains [PubMed9768757]
  • MHC class I, alpha-1 and alpha-2 domains [PubMed15454423]
  • MHC class I related proteins, such as gammadelta T-cell ligand [PubMed17291278], Ulbp3 [PubMed12857997], Fc (IgG) receptor (alpha-1 and -2 domains) [PubMed7969498], CD1 (alpha-1 and -2 domains) [PubMed11677624], zinc-alpha-2-glycoprotein ZAG (fat depleting factor) [PubMed16475792]
  • Immunomodulatory protein m144, alpha-1 and alpha-2 domains [PubMed16500675]
  • Haemochromatosis protein Hfe, alpha-1 and alpha-2 domains [PubMed12667138]
  • NK cell ligand RAE-1 beta [PubMed12594837]
  • Endothelial protein C receptor (phospholipid-binding protein) [PubMed17327234]

More information about these proteins can be found at Protein of the Month: MHC.


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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) ]

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 92 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 MHC antigen-recognition domain 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 92 hidden Markov models representing the MHC antigen-recognition domain 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.