SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 morphology0.09428Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1111Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.116Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.1264Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2358Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.2416Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.2523Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.3072Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.01618Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.04501Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.04918Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.06738Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.109Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.16Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.2324Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.2626Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.2852Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.5237Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.5623Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.822Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.008201InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.04845InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.06904InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.1015InformativeInherited
Phenotypic Abnormality (PA)Hernia0.1138InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.1337InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nail0.1638InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.1722InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1771InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.4503InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5783InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic fifth fingernail0.00000962Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplastic fifth toenail0.00001427Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0001183Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0001723Highly InformativeDirect
Phenotypic Abnormality (PA)Cutis marmorata0.0003825Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft palate0.0005934Highly InformativeDirect
Phenotypic Abnormality (PA)Lacrimation abnormality0.0007153Highly InformativeDirect
Phenotypic Abnormality (PA)Slow-growing hair0.0009214Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.002007Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of toe0.004809Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the 5th toe0.02625Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.04249Highly 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 phenotype0.02064Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3728Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.6039Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004616Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.000654Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004087Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06072Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06128Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1247Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.3648Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7798Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.004735InformativeInherited
Mammalian Phenotype (MP)abnormal head morphology0.01085InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.03335InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.04142InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.06725InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.07194InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.1838InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.2596InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.2738InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.7138InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.0001094Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001934Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0005455Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005945Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001796Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.002405Highly 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 variant0.0008511Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001755Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.002044Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.2603Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.00002457Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0007776Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02371Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.09301Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.2057Moderately InformativeInherited
Worm Phenotype (WP)protruding vulva0.00000236InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00002038InformativeDirect
Worm Phenotype (WP)anesthetic response variant0.000164InformativeDirect
Worm Phenotype (WP)male gonad development variant0.000565InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.001885InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.04874InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1452InformativeInherited
Worm Phenotype (WP)vulva development variant0.4045InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.000001427Highly InformativeDirect
Worm Phenotype (WP)postembryonic cell lineage variant0.00005388Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001711Highly InformativeDirect

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)visible0.0009797InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.03399Least InformativeInherited
Fly Anatomy (FA)adult0.0348Least InformativeInherited
Fly Anatomy (FA)organism subdivision0.06853Least InformativeInherited
Fly Anatomy (FA)region of integument0.001569Moderately InformativeInherited
Fly Anatomy (FA)appendage0.002011Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.007744Moderately InformativeInherited
Fly Anatomy (FA)thorax0.01208Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.03318Moderately InformativeInherited
Fly Anatomy (FA)adult tagma0.203Moderately InformativeInherited
Fly Anatomy (FA)wing0.00009246InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.05826Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.09606Moderately InformativeInherited
Zebrafish Anatomy (ZA)sensory system0.3272Moderately InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.06639InformativeInherited
Zebrafish Anatomy (ZA)neurogenic placode0.01548Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial ganglion0.7331Highly 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 system0.002936Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.004327Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01306Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.06139Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08776Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5578Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00004021Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00006612Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000791Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.004618Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.05263Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2332Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3183Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.000002635InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000007328InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.000008032InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002666InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0002732InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0003089InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0003573InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.0007232InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.02488InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.03921InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.04897InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.1459InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.00000001839Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0000003334Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.000001915Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000006681Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000009116Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.000143Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.0002595Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0009197Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.004937Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.009257Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.1348Highly 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 groups0.000003707Moderately InformativeDirect

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 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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]