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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 cancer0.9017Moderately 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 the genitourinary system0.002171Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.01225Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.0156Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.02324Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.05514Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.07194Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.08481Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.08957Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1991Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.007979Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02606Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.04121Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.04471Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.1002Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.1016Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1647Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.3476Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.3585Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5022Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.5794Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebrum0.9285Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.00009691InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.002871InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.007757InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.08372InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral subcortex0.1276InformativeInherited
Phenotypic Abnormality (PA)Hernia0.165InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.2173InformativeInherited
Phenotypic Abnormality (PA)Vascular skin abnormality0.4463InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5052InformativeInherited
Phenotypic Abnormality (PA)Congenital diaphragmatic hernia0.0001155Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft palate0.0001304Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0001848Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the sense of smell0.0002141Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0007873Highly InformativeDirect
Phenotypic Abnormality (PA)Cutis marmorata0.0008973Highly InformativeDirect
Phenotypic Abnormality (PA)Hypogonadism0.2137Highly 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 homeostasis0.3739Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.6037Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004642Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.0006553Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004142Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06049Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06145Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.3618Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.363Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7808Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.004762InformativeInherited
Mammalian Phenotype (MP)abnormal head morphology0.01088InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.03361InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.0417InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.067InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.07252InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.184InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.2602InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.2742InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.7144InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.0001098Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001945Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.000582Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005955Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001806Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.002417Highly 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 variant0.0003404Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0008267Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004413Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00001148Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02498Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.07419Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.126Moderately InformativeInherited
Worm Phenotype (WP)maintenance of gene silencing variant0.00001783InformativeDirect
Worm Phenotype (WP)epithelial system development variant0.05014InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1535InformativeInherited
Worm Phenotype (WP)vulva development variant0.3955InformativeInherited
Worm Phenotype (WP)VPC competence variant0.7411InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.000001015Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001076Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.005452Highly 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 Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)visible0.0009718InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.04207Least InformativeInherited
Fly Anatomy (FA)adult0.04878Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0.003247Moderately InformativeInherited
Fly Anatomy (FA)appendage0.00728Moderately InformativeInherited
Fly Anatomy (FA)adult thorax0.008155Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.03108Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.03182Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.54Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.004482Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.03333Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.07052Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.3924Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.05534Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.5126Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.5592Moderately InformativeInherited
Zebrafish Anatomy (ZA)skeletal system0.1004InformativeInherited
Zebrafish Anatomy (ZA)skeletal element0.1625InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.3143InformativeInherited
Zebrafish Anatomy (ZA)pharyngeal arch0.3228InformativeInherited
Zebrafish Anatomy (ZA)ganglion0.0005502Highly InformativeDirect
Zebrafish Anatomy (ZA)chondral bone0.02261Highly 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 system0.002137Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.002575Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01221Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.04785Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08512Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5424Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00004616Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00004658Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00008631Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.003656Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.104Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2347Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3188Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindbrain0.0000001165InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000002571InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00001299InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.0000134InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.00002913InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.00006132InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0001316InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0008948InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.009356InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.01896InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.04471InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.0000001019Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000001281Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000007676Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.00001267Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.0001347Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0002344Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0005499Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0008251Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.004289Highly InformativeInherited
Xenopus ANatomical entity (XAN)non-neural ectoderm0.005542Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.01803Highly 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 cell0.00000000002198Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.0007545Highly 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 groups0.00000002537Moderately 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 Phenotype (FP) · 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 16 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 16 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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]