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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 disease0.01641Least InformativeInherited
Disease Ontology (DO)organ system cancer0.07738Least InformativeInherited
Disease Ontology (DO)cardiovascular system disease0.2705Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.00000002116Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.0000003937Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.000001342Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.00001499Moderately InformativeDirect
Disease Ontology (DO)skin disease0.00002323Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.00002563Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0001805Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003335Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006493Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.03826Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.0414Moderately InformativeInherited
Disease Ontology (DO)syndrome0.2881Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.713Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis0.0000000000006221InformativeDirect
Disease Ontology (DO)liver disease0.00000002113InformativeDirect
Disease Ontology (DO)alopecia0.00003447InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.000081InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003322InformativeDirect
Disease Ontology (DO)autosomal recessive disease0.0005318InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0007542InformativeDirect
Disease Ontology (DO)peripheral nervous system disease0.007506InformativeInherited
Disease Ontology (DO)arthropathy0.008614InformativeInherited
Disease Ontology (DO)bullous skin disease0.01666InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.03044InformativeInherited
Disease Ontology (DO)myeloid leukemia0.09162InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease0.00000000005062Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.00000004831Highly InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0000001408Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia0.00000192Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001994Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.00002809Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.0000599Highly InformativeDirect
Disease Ontology (DO)uveitis0.0001365Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001065Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.03281Highly InformativeInherited
Disease Ontology (DO)spondyloarthropathy0.4778Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.05847Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.06815Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.07308Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.07944Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1426Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.341Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.5625Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.5918Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.7235Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.00791Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.01441Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiovascular system physiology0.04236Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.04823Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.1285Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.1304Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1322Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.1564Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating metabolite concentration0.3198Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.3218Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.3295Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.3485Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.3938Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.4471Moderately InformativeInherited
Phenotypic Abnormality (PA)Unusual CNS infection0.00001289InformativeDirect
Phenotypic Abnormality (PA)Edema0.00004545InformativeDirect
Phenotypic Abnormality (PA)Venous thrombosis0.0004325InformativeDirect
Phenotypic Abnormality (PA)Arrhythmia0.0005292InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin physiology0.0006467InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pancreas0.01008InformativeInherited
Phenotypic Abnormality (PA)Constitutional symptom0.01426InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.01619InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral vasculature0.01966InformativeInherited
Phenotypic Abnormality (PA)Abnormal systemic arterial morphology0.03411InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.04032InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.05712InformativeInherited
Phenotypic Abnormality (PA)Abnormality of temperature regulation0.06368InformativeInherited
Phenotypic Abnormality (PA)Abnormality of body weight0.08315InformativeInherited
Phenotypic Abnormality (PA)Functional respiratory abnormality0.307InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.6931InformativeInherited
Phenotypic Abnormality (PA)Increased inflammatory response1InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pleura0.00000007222Highly InformativeDirect
Phenotypic Abnormality (PA)Pericarditis0.0000002384Highly InformativeDirect
Phenotypic Abnormality (PA)Cough0.000003467Highly InformativeDirect
Phenotypic Abnormality (PA)Meningitis0.000005944Highly InformativeDirect
Phenotypic Abnormality (PA)Arthralgia0.000006365Highly InformativeDirect
Phenotypic Abnormality (PA)Pulmonary infiltrates0.00002275Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal sputum0.00002591Highly InformativeDirect
Phenotypic Abnormality (PA)Abdominal pain0.00003277Highly InformativeDirect
Phenotypic Abnormality (PA)Weight loss0.00005874Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal erythrocyte sedimentation rate0.0001066Highly InformativeDirect
Phenotypic Abnormality (PA)Vasculitis0.000187Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigue0.0002965Highly InformativeDirect
Phenotypic Abnormality (PA)Restrictive ventilatory defect0.0003789Highly InformativeDirect
Phenotypic Abnormality (PA)Diabetes insipidus0.000413Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal C-reactive protein level0.0006823Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0008641Highly InformativeDirect
Phenotypic Abnormality (PA)Fever0.0009508Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of renal glomerulus morphology0.5063Highly 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 phenotype0.0000002946Least InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.000002711Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0006198Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3197Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.4362Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.6997Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B lymphocyte antigen presentation0.000134InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.0003105InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.001042InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.002687InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.1335InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.2022InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.3779InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.8213InformativeInherited
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007675Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.000998Highly InformativeDirect
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.109Highly InformativeInherited
Mammalian Phenotype (MP)decreased alpha-beta T cell number0.2535Highly 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)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.2695Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.0004139Highly 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 ]