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 (93) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,661 62,409 190
Proteins 3,650 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 stimulus0.15540Least InformativeInherited
Biological Process (BP)developmental process0.00058481Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0016911Least InformativeInherited
Biological Process (BP)immune system process00Moderately InformativeDirect
Biological Process (BP)organ development5.899e-064.408e-05Moderately InformativeDirect
Biological Process (BP)positive regulation of response to stimulus8.882e-050Moderately InformativeDirect
Biological Process (BP)multi-organism process0.013733.296e-14Moderately InformativeInherited
Biological Process (BP)regulation of immune effector process02.448e-09InformativeDirect
Biological Process (BP)regulation of immune response1.406e-120InformativeDirect
Biological Process (BP)sensory organ development9.03e-120InformativeDirect
Biological Process (BP)positive regulation of immune system process4.935e-070InformativeDirect
Biological Process (BP)response to bacterium0.00026842.538e-13InformativeDirect
Biological Process (BP)defense response0.00054670InformativeDirect
Biological Process (BP)ear development00Highly InformativeDirect
Biological Process (BP)positive regulation of adaptive immune response00Highly InformativeDirect
Biological Process (BP)regulation of adaptive immune response based on somatic recombination of immune receptors built from00Highly InformativeDirect
Biological Process (BP)antigen processing and presentation3.477e-120Highly InformativeDirect
Biological Process (BP)positive regulation of lymphocyte mediated immunity0.0081345.378e-11Highly InformativeInherited
Biological Process (BP)positive regulation of leukocyte mediated cytotoxicity0.059691.474e-08Highly InformativeInherited
Molecular Function (MF)binding0.0086460Least InformativeInherited
Molecular Function (MF)amide binding2.952e-060InformativeDirect
Molecular Function (MF)peptide binding2.09e-070Highly InformativeDirect
Molecular Function (MF)antigen binding2.835e-050Highly InformativeDirect
Cellular Component (CC)membrane4.963e-050Least InformativeDirect
Cellular Component (CC)plasma membrane0.00073620Moderately InformativeDirect
Cellular Component (CC)cell surface1.448e-080InformativeDirect
Cellular Component (CC)external side of plasma membrane0.00077890Highly 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 0.1399 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 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 0.3823 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) organ development 4.408e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 3.296e-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 6.39e-07 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0009182 Moderately Informative Direct
Biological Process (BP) regulation of localization 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 0.0261 Moderately Informative Inherited
Biological Process (BP) regulation of cellular 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) regulation of macromolecule biosynthetic 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 2.448e-09 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) response to bacterium 2.538e-13 Informative Direct
Biological Process (BP) defense response 0 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 cell activation 0 Informative Direct
Biological Process (BP) regulation of cytokine production 3.755e-15 Informative Direct
Biological Process (BP) regulation of defense response 2.458e-14 Informative Direct
Biological Process (BP) negative regulation of immune system process 8.229e-07 Informative Direct
Biological Process (BP) regulation of protein localization 0.0001455 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001914 Informative Direct
Biological Process (BP) regulation of secretion 0.0002292 Informative Direct
Biological Process (BP) protein oligomerization 0.185 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.5007 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.06363 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.1381 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.5733 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.8961 Informative Inherited
Biological Process (BP) leukocyte activation 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.3086 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 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) ear development 0 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 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) antigen processing and presentation 0 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte mediated immunity 5.378e-11 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte mediated cytotoxicity 1.474e-08 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 7.347e-15 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 1.121e-10 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 1.679e-10 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 6.843e-10 Highly Informative Direct
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 1.317e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 2.723e-06 Highly Informative Direct
Biological Process (BP) innate immune response 4.88e-06 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 8.232e-06 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 1.476e-05 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 2.853e-05 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.07497 Highly Informative Inherited
Biological Process (BP) immune response-activating signal transduction 0.004082 Highly Informative Inherited
Biological Process (BP) negative regulation of leukocyte activation 1 Highly Informative Inherited
Biological Process (BP) T cell differentiation 0.06183 Highly Informative Inherited
Biological Process (BP) positive regulation of defense response 0.7214 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.001559 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.004809 Highly Informative Inherited
Biological Process (BP) negative regulation of immune response 0.618 Highly Informative Inherited
Biological Process (BP) regulation of innate immune response 1 Highly Informative Inherited
Biological Process (BP) negative regulation of immune effector process 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 0.0001244 Informative Direct
Molecular Function (MF) lipid binding 0.958 Informative Inherited
Molecular Function (MF) receptor activity 0.01034 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.05175 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 0.4676 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 1.43e-08 Least Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 3.099e-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 0.7159 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) cytoplasmic vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 6.088e-15 Highly Informative Direct
Cellular Component (CC) late endosome 4.909e-11 Highly Informative Direct
Cellular Component (CC) anchored to membrane 0.159 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 disease2.748e-06Least InformativeDirect
Disease Ontology (DO)nervous system disease0.02431Least InformativeInherited
Disease Ontology (DO)organ system cancer0.09015Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease2.632e-08Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease4.7e-06Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism6.26e-06Moderately InformativeDirect
Disease Ontology (DO)skin disease3.918e-05Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.0001308Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.00026Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.00382Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.006508Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.01612Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.1068Moderately InformativeInherited
Disease Ontology (DO)syndrome0.1945Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.6136Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis1.99e-12InformativeDirect
Disease Ontology (DO)liver disease3.526e-08InformativeDirect
Disease Ontology (DO)Kawasaki disease7.052e-08InformativeDirect
Disease Ontology (DO)alopecia2.92e-05InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.0002969InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003383InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0005124InformativeDirect
Disease Ontology (DO)thyroid gland disease0.003054InformativeInherited
Disease Ontology (DO)arthropathy0.003755InformativeInherited
Disease Ontology (DO)autosomal recessive disease0.0201InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.02447InformativeInherited
Disease Ontology (DO)neuropathy0.03394InformativeInherited
Disease Ontology (DO)eye disease0.04538InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease6.766e-10Highly InformativeDirect
Disease Ontology (DO)Behcet's disease1.978e-08Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia8.916e-07Highly InformativeDirect
Disease Ontology (DO)spondylitis6.402e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus1.142e-05Highly InformativeDirect
Disease Ontology (DO)sarcoidosis1.596e-05Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis5.613e-05Highly InformativeDirect
Disease Ontology (DO)rheumatic fever0.0002038Highly InformativeDirect
Disease Ontology (DO)leprosy0.0004317Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001607Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.04061Highly 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 physiology0.4494Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07603Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.0238InformativeInherited
Phenotypic Abnormality (PA)Arrhythmia0.002575Highly 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 physiology3.092e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0003017Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune cell physiology0.09501Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.09984Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1103Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.1531Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.2458Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology4.421e-06InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte cell number1.266e-05InformativeDirect
Mammalian Phenotype (MP)abnormal antigen presentation8.031e-05InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.0005113InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.001329InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.2453InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6077InformativeInherited
Mammalian Phenotype (MP)decreased leukocyte cell number0.6851InformativeInherited
Mammalian Phenotype (MP)increased hematopoietic cell number0.7892InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.0004945Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0005782Highly InformativeDirect
Mammalian Phenotype (MP)increased lymphocyte cell number0.3256Highly InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.3577Highly InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell number0.5135Highly 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 reticulum9.641e-16Moderately InformativeDirect
Cellular componentGolgi apparatus2.793e-14Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Cellular componentGPI-anchor0.0007438InformativeDirect
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 ]