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 (575) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,228 3,855 2
Proteins 2,532 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)cytoplasmic part0.083621.061e-11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.084850.2293Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum2.252e-050Moderately 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 3.877e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0002006 Least Informative Direct
Biological Process (BP) response to stimulus 1.478e-08 Least Informative Direct
Biological Process (BP) localization 6.223e-14 Least Informative Direct
Biological Process (BP) biosynthetic process 1.387e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.583e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 7.927e-05 Least Informative Direct
Biological Process (BP) developmental process 0.01914 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.06402 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.01823 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 1.083e-14 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.632e-13 Moderately Informative Direct
Biological Process (BP) ion transport 6.961e-13 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 6.543e-09 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1.357e-08 Moderately Informative Direct
Biological Process (BP) cellular localization 7.646e-08 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 4.559e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 1.371e-05 Moderately Informative Direct
Biological Process (BP) system process 2.42e-05 Moderately Informative Direct
Biological Process (BP) organ development 0.0001022 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.07292 Moderately Informative Inherited
Biological Process (BP) tissue development 0.02121 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.4557 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1626 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3836 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.9064 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.117 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.004363 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.3677 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.0516 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.006599 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.206 Moderately Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0 Informative Direct
Biological Process (BP) metal ion transport 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0 Informative Direct
Biological Process (BP) muscle system process 5.657e-13 Informative Direct
Biological Process (BP) intracellular signal transduction 1.119e-10 Informative Direct
Biological Process (BP) muscle structure development 4.962e-10 Informative Direct
Biological Process (BP) cytoplasmic transport 1.161e-06 Informative Direct
Biological Process (BP) muscle tissue development 2.183e-06 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 4.379e-06 Informative Direct
Biological Process (BP) regulation of system process 6.615e-06 Informative Direct
Biological Process (BP) cardiovascular system development 1.342e-05 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.914e-05 Informative Direct
Biological Process (BP) protein oligomerization 7.381e-05 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0001294 Informative Direct
Biological Process (BP) organ morphogenesis 0.0005756 Informative Direct
Biological Process (BP) transmembrane transport 0.0007805 Informative Direct
Biological Process (BP) response to inorganic substance 0.3729 Informative Inherited
Biological Process (BP) growth 0.001238 Informative Inherited
Biological Process (BP) calcium ion transport 0 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 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) protein glycosylation 0 Highly Informative Direct
Biological Process (BP) heart morphogenesis 1.103e-12 Highly Informative Direct
Biological Process (BP) response to alkaloid 5.738e-10 Highly Informative Direct
Biological Process (BP) muscle organ development 7.457e-10 Highly Informative Direct
Biological Process (BP) response to calcium ion 1.052e-09 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 9.296e-07 Highly Informative Direct
Biological Process (BP) response to hypoxia 2.156e-06 Highly Informative Direct
Biological Process (BP) protein homooligomerization 8.844e-06 Highly Informative Direct
Biological Process (BP) developmental maturation 6.59e-05 Highly Informative Direct
Biological Process (BP) ossification 0.000402 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0004184 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0008867 Highly Informative Direct
Biological Process (BP) skeletal system development 0.004423 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.1951 Highly Informative Inherited
Molecular Function (MF) transferase activity 5.7e-07 Least Informative Direct
Molecular Function (MF) binding 0.001481 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.218e-09 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) receptor activity 9.345e-12 Informative Direct
Molecular Function (MF) molecular transducer activity 2.079e-11 Informative Direct
Molecular Function (MF) lipid binding 3.899e-09 Informative Direct
Molecular Function (MF) calcium ion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) ion gated channel activity 0 Highly Informative Direct
Molecular Function (MF) cation channel activity 0 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 0 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring hexosyl groups 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1.061e-11 Least Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.947e-05 Least Informative Direct
Cellular Component (CC) protein complex 0.000168 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.2293 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.4298 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.00329 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.7579 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.02786 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.7977 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0 Informative Direct
Cellular Component (CC) contractile fiber part 1.661e-07 Informative Direct
Cellular Component (CC) integral to membrane 7.621e-07 Informative Direct
Cellular Component (CC) synapse part 0.0002311 Informative Direct
Cellular Component (CC) nuclear envelope 0.0002428 Informative Direct
Cellular Component (CC) sarcoplasmic reticulum 0 Highly Informative Direct
Cellular Component (CC) sarcomere 8.867e-12 Highly Informative Direct
Cellular Component (CC) nuclear membrane 7.337e-06 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 disease0.005708Moderately 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 morphology0.3024Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.331Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle morphology0.05223Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0.1113Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of brain morphology0.1319Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.004833InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the peripheral nervous system0.06043InformativeInherited
Phenotypic Abnormality (PA)Muscular dystrophy1.634e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Motor delay2.804e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Facial palsy9.679e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Myopathy0.0005946Highly 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 phenotype0.005562Moderately 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 defective0.0004473InformativeDirect

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1.399e-15Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processCalcium transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentSarcoplasmic reticulum0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane9.229e-16Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionCalmodulin-binding0InformativeDirect
Post-translational modificationTransferase0.006318Least 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-nitrosylation3.055e-07InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]