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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 cancer0.9011Moderately 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 system0.03503Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.04671Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.07349Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1821Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.31Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3173Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.03039Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.04631Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.05253Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.0724Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.1985Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.4711Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4766Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.0008872InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.005991InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.009247InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1261InformativeInherited
Phenotypic Abnormality (PA)Hernia0.166InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.2242InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5125InformativeInherited
Phenotypic Abnormality (PA)Congenital diaphragmatic hernia0.0002966Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the sense of smell0.000526Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.000542Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft palate0.0007928Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal form of the vertebral bodies0.6239Highly 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 phenotype0.02068Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3739Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.6037Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004645Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.0006556Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004143Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06048Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06144Moderately 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 regulation0.004763InformativeInherited
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 morphology0.06699InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.0725InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.1839InformativeInherited
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 morphology0.0001099Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001946Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0005822Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005958Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001807Highly 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 variant0.0003465Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0008811Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004509Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00001143Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02463Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.07997Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.1251Moderately InformativeInherited
Worm Phenotype (WP)maintenance of gene silencing variant0.00001811InformativeDirect
Worm Phenotype (WP)epithelial system development variant0.05053InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1586InformativeInherited
Worm Phenotype (WP)vulva development variant0.3962InformativeInherited
Worm Phenotype (WP)VPC competence variant0.7346InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.000001059Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001082Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.005348Highly 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 subdivision0.04259Least InformativeInherited
Fly Anatomy (FA)adult0.04845Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0.003218Moderately InformativeInherited
Fly Anatomy (FA)appendage0.007409Moderately InformativeInherited
Fly Anatomy (FA)adult thorax0.008268Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.03129Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.03226Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.5405Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.004271Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.03353Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.07127Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.3932Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.05897Moderately InformativeInherited
Zebrafish Anatomy (ZA)sensory system0.4742Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.5151Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.5431Moderately InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure0.07832InformativeInherited
Zebrafish Anatomy (ZA)skeletal system0.09539InformativeInherited
Zebrafish Anatomy (ZA)skeletal element0.1611InformativeInherited
Zebrafish Anatomy (ZA)ectoderm0.2986InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.3104InformativeInherited
Zebrafish Anatomy (ZA)pharyngeal arch0.3151InformativeInherited
Zebrafish Anatomy (ZA)neurogenic placode0.01277Highly InformativeInherited
Zebrafish Anatomy (ZA)chondral bone0.02416Highly InformativeInherited
Zebrafish Anatomy (ZA)pharyngeal arch 3-70.07127Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial ganglion0.7147Highly 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 system0.002158Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.002587Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01226Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.04821Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08548Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5436Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00005027Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00005975Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00009582Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.003911Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.1029Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2374Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3175Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindbrain0.000000147InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000003626InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00001397InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00001569InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.00004178InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.00007623InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0001439InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.01013InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.0213InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.04356InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.1732InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.0000001409Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000001686Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000008562Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.00001567Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.0001525Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0002803Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0006784Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0009184Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.004007Highly 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 groups0.00000002457Moderately 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 ]