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HMG-box superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   HMG-box [ 47094]
Superfamily:   HMG-box [ 47095]
Families:   HMG-box [ 47096] (9)


Superfamily statistics
Genomes (516) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 14,117 44,963 25
Proteins 11,839 38,049 24


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0.00000002056Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0.000000002065Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)cell type cancer0.9009Moderately 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 skeletal morphology0.09404Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1113Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1162Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.1261Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2355Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.2411Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.2518Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.3068Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.01611Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.04482Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.04897Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.06734Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.1085Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1597Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.2325Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.262Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.2844Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.523Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.5621Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.8218Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.008192InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.04811InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.06856InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.1015InformativeInherited
Phenotypic Abnormality (PA)Hernia0.1138InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.1342InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nail0.1627InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.1722InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1776InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.4512InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5782InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic fifth fingernail0.000009627Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplastic fifth toenail0.00001428Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0001184Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0001726Highly InformativeDirect
Phenotypic Abnormality (PA)Cutis marmorata0.0003827Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft palate0.0005942Highly InformativeDirect
Phenotypic Abnormality (PA)Lacrimation abnormality0.0007171Highly InformativeDirect
Phenotypic Abnormality (PA)Slow-growing hair0.0009216Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.002006Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of toe0.004848Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the 5th toe0.02641Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.04133Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal form of the vertebral bodies0.6604Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0.02067Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3724Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.6041Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004621Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.0006555Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004089Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06052Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06133Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1248Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.3647Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7798Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.004736InformativeInherited
Mammalian Phenotype (MP)abnormal head morphology0.01084InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.03334InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.04156InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.0668InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.07196InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.1838InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.2598InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.274InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.7138InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.0001095Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001935Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0005458Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005945Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001796Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.002404Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.0007779Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001469Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.002007Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00002467Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0007672Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02383Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.09143Moderately InformativeInherited
Worm Phenotype (WP)protruding vulva0.000002389InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00001956InformativeDirect
Worm Phenotype (WP)male gonad development variant0.0005612InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.00179InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.04863InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.148InformativeInherited
Worm Phenotype (WP)vulva development variant0.3875InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.00000141Highly InformativeDirect
Worm Phenotype (WP)postembryonic cell lineage variant0.00004893Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001652Highly InformativeDirect
Worm Phenotype (WP)amphid phasmid sensillum morphology variant0.01951Highly InformativeInherited
Worm Phenotype (WP)amphid morphology variant0.03099Highly InformativeInherited
Worm Phenotype (WP)amphid phasmid morphology variant0.4031Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.04358Least InformativeInherited
Fly Anatomy (FA)adult0.04756Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)region of integument0.001985Moderately InformativeInherited
Fly Anatomy (FA)appendage0.002081Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.009541Moderately InformativeInherited
Fly Anatomy (FA)thorax0.01242Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.03293Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.05818Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.09487Moderately InformativeInherited
Zebrafish Anatomy (ZA)sensory system0.3355Moderately InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.06424InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure0.1161InformativeInherited
Zebrafish Anatomy (ZA)neurogenic placode0.01464Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial ganglion0.7214Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0.002713Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.004442Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01258Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.06277Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08804Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5635Least InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.00003542Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.00004217Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00008544Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.004655Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.05386Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2351Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3183Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.000002787InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000007466InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.000007916InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002557InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0002631InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0003363InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0003575InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.0007136InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0253InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.0495InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.05636InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.1443InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.00000001781Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0000003609Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.000001877Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000006266Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000009228Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0001449Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0009076Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.004999Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.01053Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.1324Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)cultured plant cell0.00000000002208Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.0007582Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0.0000000246Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009071 SSF47095 Protein matches
Abstract

High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.

HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors [PubMed12920151]; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation [PubMed10890911]; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor [PubMed11779632]; yeast transcription factors lxr1, Rox1, Nhp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi [PubMed12781674]; and the YABBY plant-specific transcription factors.


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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 28 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 HMG-box 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 28 hidden Markov models representing the HMG-box 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]