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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 system0.001959Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.01211Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.0228Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.0523Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.08312Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.08644Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.09165Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.2004Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.007402Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02668Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.03703Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1619Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.2979Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.3512Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.4755Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4965Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.592Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.6475Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.00008641InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the hypothalamus-pituitary axis0.006093InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.006859InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.04729InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.09659InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral subcortex0.1252InformativeInherited
Phenotypic Abnormality (PA)Hernia0.1713InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.2157InformativeInherited
Phenotypic Abnormality (PA)Vascular skin abnormality0.4649InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5234InformativeInherited
Phenotypic Abnormality (PA)Congenital diaphragmatic hernia0.0001127Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the sense of smell0.0001231Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft palate0.0001244Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.000179Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0008412Highly InformativeDirect
Phenotypic Abnormality (PA)Cutis marmorata0.0009397Highly InformativeDirect
Phenotypic Abnormality (PA)Hypogonadism0.2157Highly 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 phenotype0.02062Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3742Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.6034Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004651Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.000651Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004148Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06031Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06121Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.362Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.3635Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7813Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.004764InformativeInherited
Mammalian Phenotype (MP)abnormal head morphology0.0108InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.03359InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.04183InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.06727InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.07255InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.184InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.2606InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.2746InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.7144InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.0001099Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001948Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0005823Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005966Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001809Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.002418Highly 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 variant0.0003282Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0008246Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004532Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00001158Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02478Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.07272Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.1284Moderately InformativeInherited
Worm Phenotype (WP)maintenance of gene silencing variant0.00001838InformativeDirect
Worm Phenotype (WP)epithelial system development variant0.05007InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1538InformativeInherited
Worm Phenotype (WP)vulva development variant0.3941InformativeInherited
Worm Phenotype (WP)VPC competence variant0.741InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.000001073Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001081Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.005506Highly 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)visible0.0009285Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.04724Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.08774Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)appendage0.00751Moderately InformativeInherited
Fly Anatomy (FA)thorax0.0135Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.03089Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.03197Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.5414Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.004654Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.03347Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.0716Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.398Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.05427Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.511Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.5524Moderately InformativeInherited
Zebrafish Anatomy (ZA)skeletal system0.1016InformativeInherited
Zebrafish Anatomy (ZA)skeletal element0.1594InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.3115InformativeInherited
Zebrafish Anatomy (ZA)pharyngeal arch0.3205InformativeInherited
Zebrafish Anatomy (ZA)ganglion0.0005275Highly InformativeDirect
Zebrafish Anatomy (ZA)chondral bone0.02211Highly 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 system0.002098Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.002264Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01225Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.04382Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08531Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5412Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.00002776Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.00004233Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00007853Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.003433Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.1017Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2416Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3187Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindbrain0.00000006311InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000001529InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00001213InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00001241InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.00005076InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0001011InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0007409InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.007677InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.01833InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.04391InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.00000009618Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000006809Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.00001098Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.00001269Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary0.00001306Highly InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.00001869Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.0001248Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0001524Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0004791Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0007704Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.003925Highly InformativeInherited
Xenopus ANatomical entity (XAN)non-neural ectoderm0.005659Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.01691Highly 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 groups0.00000002553Moderately 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 ]