SUPERFAMILY 1.75 HMM library and genome assignments server


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 (88) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,343 62,409 190
Proteins 3,335 62,349 190


Functional annotation
General category Processes_EC
Detailed category Immune response

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)response to stimulus0.1380Least InformativeInherited
Biological Process (BP)developmental process0.00049891Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0014751Least InformativeInherited
Biological Process (BP)immune system process00Moderately InformativeDirect
Biological Process (BP)organ development4.727e-068.996e-05Moderately InformativeDirect
Biological Process (BP)positive regulation of response to stimulus9.125e-050Moderately InformativeDirect
Biological Process (BP)multi-organism process0.01091.422e-14Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.00049711Moderately InformativeInherited
Biological Process (BP)regulation of immune effector process01.909e-08InformativeDirect
Biological Process (BP)regulation of immune response9.175e-130InformativeDirect
Biological Process (BP)sensory organ development6.514e-120InformativeDirect
Biological Process (BP)positive regulation of immune system process6.372e-070InformativeDirect
Biological Process (BP)defense response0.00046860InformativeDirect
Biological Process (BP)response to other organism0.001583.814e-12InformativeInherited
Biological Process (BP)regulation of cell killing00Highly InformativeDirect
Biological Process (BP)positive regulation of adaptive immune response00Highly InformativeDirect
Biological Process (BP)inner ear development00Highly InformativeDirect
Biological Process (BP)regulation of adaptive immune response based on somatic recombination of immune receptors built from00Highly InformativeDirect
Biological Process (BP)regulation of lymphocyte mediated immunity00Highly InformativeDirect
Biological Process (BP)antigen processing and presentation3.606e-120Highly InformativeDirect
Biological Process (BP)positive regulation of leukocyte mediated immunity0.0018450Highly InformativeInherited
Molecular Function (MF)binding0.0066260Least InformativeInherited
Molecular Function (MF)amide binding3.215e-060InformativeDirect
Molecular Function (MF)peptide binding1.972e-070Highly InformativeDirect
Molecular Function (MF)antigen binding3.095e-050Highly InformativeDirect
Cellular Component (CC)membrane2.574e-050Least InformativeDirect
Cellular Component (CC)plasma membrane0.00044850Moderately InformativeDirect
Cellular Component (CC)cell surface1.459e-080InformativeDirect
Cellular Component (CC)external side of plasma membrane0.00080280Highly 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) response to stimulus 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0.08926 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9976 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3174 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) organ development 8.996e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 1.422e-14 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.067e-07 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0003219 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.01798 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of immune effector process 1.909e-08 Informative Direct
Biological Process (BP) regulation of immune response 0 Informative Direct
Biological Process (BP) sensory organ development 0 Informative Direct
Biological Process (BP) positive regulation of immune system process 0 Informative Direct
Biological Process (BP) defense response 0 Informative Direct
Biological Process (BP) response to other organism 3.814e-12 Informative Direct
Biological Process (BP) immune response 0 Informative Direct
Biological Process (BP) response to cytokine stimulus 0 Informative Direct
Biological Process (BP) regulation of cytokine production 3.722e-15 Informative Direct
Biological Process (BP) protein complex assembly 1.253e-14 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 6.48e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 9.458e-05 Informative Direct
Biological Process (BP) regulation of secretion 0.0001027 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.5085 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.06282 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.09612 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.7108 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.8636 Informative Inherited
Biological Process (BP) leukocyte activation 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.3063 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) regulation of response to stress 1 Informative Inherited
Biological Process (BP) immune effector process 1 Informative Inherited
Biological Process (BP) response to wounding 1 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 1 Informative Inherited
Biological Process (BP) regulation of cell killing 0 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0 Highly Informative Direct
Biological Process (BP) inner ear development 0 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 0 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte mediated immunity 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of nitric oxide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) protein tetramerization 3.722e-15 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 3.581e-11 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 1.566e-10 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 2.584e-10 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 1.018e-08 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 5.385e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 1.585e-06 Highly Informative Direct
Biological Process (BP) innate immune response 2.762e-06 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 6.539e-06 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 1.747e-05 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 3.176e-05 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.05917 Highly Informative Inherited
Biological Process (BP) activation of immune response 1 Highly Informative Inherited
Biological Process (BP) T cell differentiation 0.05892 Highly Informative Inherited
Biological Process (BP) positive regulation of defense response 0.7279 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.001822 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.00671 Highly Informative Inherited
Biological Process (BP) immune response-regulating signaling pathway 0.004588 Highly Informative Inherited
Biological Process (BP) regulation of innate immune response 1 Highly Informative Inherited
Biological Process (BP) inflammatory response 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) receptor binding 0.0001199 Informative Direct
Molecular Function (MF) lipid binding 0.9519 Informative Inherited
Molecular Function (MF) receptor activity 0.006969 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.03784 Informative Inherited
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Molecular Function (MF) antigen binding 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.4531 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 2.781e-08 Least Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 2.177e-08 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) vacuolar part 0 Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0 Informative Direct
Cellular Component (CC) lytic vacuole 0 Informative Direct
Cellular Component (CC) integral to membrane 0.7061 Informative Inherited
Cellular Component (CC) intrinsic to plasma membrane 1 Informative Inherited
Cellular Component (CC) external side of plasma membrane 0 Highly Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 0 Highly Informative Direct
Cellular Component (CC) endosomal part 0 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 0 Highly Informative Direct
Cellular Component (CC) lysosome 0 Highly Informative Direct
Cellular Component (CC) Golgi membrane 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 6.161e-15 Highly Informative Direct
Cellular Component (CC) early endosome 1.637e-14 Highly Informative Direct
Cellular Component (CC) late endosome 3.275e-11 Highly Informative Direct
Cellular Component (CC) anchored to membrane 0.1696 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease9.704e-06Least InformativeDirect
Disease Ontology (DO)nervous system disease0.02581Least InformativeInherited
Disease Ontology (DO)organ system cancer0.06265Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease5.781e-08Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism2.011e-06Moderately InformativeDirect
Disease Ontology (DO)skin disease8.132e-06Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0002172Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0003455Moderately InformativeDirect
Disease Ontology (DO)musculoskeletal system disease0.004011Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.006521Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.04091Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.04594Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.1356Moderately InformativeInherited
Disease Ontology (DO)syndrome0.2267Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.5755Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis3.148e-12InformativeDirect
Disease Ontology (DO)liver disease6.287e-08InformativeDirect
Disease Ontology (DO)Kawasaki disease1.025e-07InformativeDirect
Disease Ontology (DO)vasculitis2.349e-06InformativeDirect
Disease Ontology (DO)alopecia3.065e-05InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.0003742InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003795InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0005206InformativeDirect
Disease Ontology (DO)liver carcinoma0.0006808InformativeDirect
Disease Ontology (DO)autosomal recessive disease0.000727InformativeDirect
Disease Ontology (DO)thyroid gland disease0.003319InformativeInherited
Disease Ontology (DO)arthropathy0.005371InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.02354InformativeInherited
Disease Ontology (DO)connective tissue disease0.1054InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease1.212e-09Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia7.378e-07Highly InformativeDirect
Disease Ontology (DO)spondylitis6.895e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus1.321e-05Highly InformativeDirect
Disease Ontology (DO)sarcoidosis1.897e-05Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis5.748e-05Highly InformativeDirect
Disease Ontology (DO)leprosy0.0004665Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.00149Highly 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 nervous system physiology0.4534Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07841Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.02484InformativeInherited
Phenotypic Abnormality (PA)Arrhythmia0.002706Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology9.405e-06Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte morphology1.484e-05Moderately InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to infection0.0002944Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune cell physiology0.07489Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.07895Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.0876Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.1224Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.1803Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology7.78e-07InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte cell number2.505e-06InformativeDirect
Mammalian Phenotype (MP)abnormal antigen presentation8.485e-06InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.0002305InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.06421InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.3428InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.5377InformativeInherited
Mammalian Phenotype (MP)decreased leukocyte cell number0.6152InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder6.758e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007412Highly InformativeDirect
Mammalian Phenotype (MP)decreased T cell number0.2942Highly InformativeInherited
Mammalian Phenotype (MP)abnormal single-positive T cell number0.6977Highly InformativeInherited

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum6.421e-16Moderately InformativeDirect
Cellular componentGolgi apparatus2.658e-14Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Cellular componentGPI-anchor0.0007612InformativeDirect
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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 72 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 72 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]