SUPERFAMILY 1.75 HMM library and genome assignments server

MIR domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-Trefoil [ 50352] (8)
Superfamily:   MIR domain [ 82109]
Families:   MIR domain [ 82110] (2)


Superfamily statistics
Genomes (576) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,231 3,855 2
Proteins 2,535 3,088 2


Functional annotation
General category Metabolism
Detailed category Transferases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Cellular Component (CC)intracellular membrane-bounded organelle0.11460.08611Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.11970.000000000001108Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.00010610Moderately 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) protein metabolic process 0.00000006816 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001539 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000001578 Least Informative Direct
Biological Process (BP) localization 0.0000000000001485 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000001763 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000001914 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001885 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0246 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.08056 Least Informative Inherited
Biological Process (BP) developmental process 0.0191 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.09391 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000000000003082 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0000000000006364 Moderately Informative Direct
Biological Process (BP) ion transport 0.00000000002016 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.000000007605 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0000000109 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.000004838 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00001831 Moderately Informative Direct
Biological Process (BP) organ development 0.0001083 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0005821 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.4485 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.05643 Moderately Informative Inherited
Biological Process (BP) tissue development 0.02156 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.4872 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3631 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1495 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.7843 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.004025 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.3892 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.006521 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2069 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.07467 Moderately Informative Inherited
Biological Process (BP) metal ion transport 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0 Informative Direct
Biological Process (BP) muscle system process 0.00000000001724 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0000000004595 Informative Direct
Biological Process (BP) muscle structure development 0.000000003262 Informative Direct
Biological Process (BP) cell wall organization or biogenesis 0.0000002506 Informative Direct
Biological Process (BP) cytoplasmic transport 0.000003245 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.00000467 Informative Direct
Biological Process (BP) cardiovascular system development 0.00001395 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001767 Informative Direct
Biological Process (BP) regulation of system process 0.00002478 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00003372 Informative Direct
Biological Process (BP) protein oligomerization 0.00008205 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0001282 Informative Direct
Biological Process (BP) response to inorganic substance 0.3782 Informative Inherited
Biological Process (BP) growth 0.001236 Informative Inherited
Biological Process (BP) organ morphogenesis 0.001762 Informative Inherited
Biological Process (BP) response to purine-containing compound 0 Highly Informative Direct
Biological Process (BP) calcium ion transport 0 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 0 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 0 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0 Highly Informative Direct
Biological Process (BP) protein glycosylation 0 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.000000000001192 Highly Informative Direct
Biological Process (BP) muscle organ development 0.00000000001341 Highly Informative Direct
Biological Process (BP) response to alkaloid 0.0000000005168 Highly Informative Direct
Biological Process (BP) response to calcium ion 0.000000001107 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0.0000001752 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.000003166 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.000009645 Highly Informative Direct
Biological Process (BP) ossification 0.0004876 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0005054 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0009154 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.01267 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.004617 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000003699 Least Informative Direct
Molecular Function (MF) binding 0.0018 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000002866 Moderately Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0 Informative Direct
Molecular Function (MF) receptor activity 0.000000000005601 Informative Direct
Molecular Function (MF) molecular transducer activity 0.00000000001289 Informative Direct
Molecular Function (MF) lipid binding 0.000000004012 Informative Direct
Molecular Function (MF) calcium ion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) gated channel activity 0 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 0 Highly Informative Direct
Molecular Function (MF) cation channel activity 0 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring hexosyl groups 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000001108 Least Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.0000003645 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000002575 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.6474 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.08611 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) membrane region 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.514 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.7931 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.007009 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.8441 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0 Informative Direct
Cellular Component (CC) contractile fiber part 0.0000004717 Informative Direct
Cellular Component (CC) nuclear envelope 0.0009894 Informative Direct
Cellular Component (CC) synapse 0.005917 Informative Inherited
Cellular Component (CC) sarcoplasmic reticulum 0 Highly Informative Direct
Cellular Component (CC) sarcomere 0.000000000009839 Highly Informative Direct
Cellular Component (CC) nuclear membrane 0.00003031 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)muscular disease0.005608Moderately 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 physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3032Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.3307Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle morphology0.05224Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0.1112Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of brain morphology0.1324Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.1469Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.004802InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the peripheral nervous system0.06013InformativeInherited
Phenotypic Abnormality (PA)Muscular dystrophy0.000001605Highly InformativeDirect
Phenotypic Abnormality (PA)Motor delay0.00002763Highly InformativeDirect
Phenotypic Abnormality (PA)Facial palsy0.00009552Highly InformativeDirect
Phenotypic Abnormality (PA)Myopathy0.0005888Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebellum1Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)muscle phenotype0.005791Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)behavior defective0.0004467InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)late embryo0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)nervous system0Least InformativeDirect
Drugbank ATC_code (DB)other analgesics and antipyretics0Moderately InformativeDirect
Drugbank ATC_code (DB)psychoanaleptics0Moderately InformativeDirect
Drugbank ATC_code (DB)paracetamol0InformativeDirect
Drugbank ATC_code (DB)xanthine derivatives0InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.000000000000001398Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processCalcium transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentSarcoplasmic reticulum0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane9.217e-16Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionCalmodulin-binding0InformativeDirect
Post-translational modificationTransferase0.006313Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationCalcium channel0Highly InformativeDirect
Post-translational modificationLigand-gated ion channel0Highly InformativeDirect
Post-translational modificationS-nitrosylation0.000000303InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein glycosylation0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR003608 SSF82109 Protein matches
Abstract This is a domain found in ryanodine, inositol trisphosphate receptor and protein O-mannosyltransferase. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules [PubMed1645727]. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) [PubMed7829078]. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.

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) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 MIR 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 2 hidden Markov models representing the MIR 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) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]