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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 morphology0.1134Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1403Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1406Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.02226Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.08153Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.3148Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.8651Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1357InformativeInherited
Phenotypic Abnormality (PA)Hernia0.1804InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4983InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0009722Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal form of the vertebral bodies0.6561Highly 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 variant0.0008744Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001111Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.001771Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00002295Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0001753Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02504Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.08438Moderately InformativeInherited
Worm Phenotype (WP)protruding vulva0.000002096InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00001861InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.00141InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.04922InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1538InformativeInherited
Worm Phenotype (WP)vulva development variant0.3726InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.000001405Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001563Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.005008Highly InformativeInherited
Worm Phenotype (WP)amphid phasmid sensillum morphology variant0.01805Highly InformativeInherited
Worm Phenotype (WP)amphid morphology variant0.02924Highly InformativeInherited
Worm Phenotype (WP)amphid phasmid morphology variant0.3941Highly 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 system0.0584Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.09532Moderately InformativeInherited
Zebrafish Anatomy (ZA)sensory system0.3376Moderately InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.06228InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure0.1162InformativeInherited
Zebrafish Anatomy (ZA)neurogenic placode0.01305Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial ganglion0.7202Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.004358Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.0128Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.06154Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08842Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5597Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.0000401Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00005294Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00007824Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.004624Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.06536Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2361Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3189Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.000002654InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000006762InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.000007604InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002341InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0002594InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0002913InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0004215InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.02651InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.05295InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.05748InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.1405InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.00000001787Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0000003044Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.000001973Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000005435Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000009524Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.00006164Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0001479Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0009404Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.005047Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.01085Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.1359Highly 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 groups0.00000002499Moderately 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 ]