SUPERFAMILY 1.75 HMM library and genome assignments server

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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 cancer0.901Moderately 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 nervous system physiology0.04695Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.06075Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.08133Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.09498Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1542Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1873Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.02236Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.041Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.09358Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.1107Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.1878Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.2738Moderately InformativeInherited
Phenotypic Abnormality (PA)Global developmental delay0.0007444InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.0008385InformativeDirect
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1472InformativeInherited
Phenotypic Abnormality (PA)Hernia0.1736InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4807InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the sense of smell0.0006618Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0008998Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.003667Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal form of the vertebral bodies0.647Highly 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 homeostasis0.3735Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.604Least InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.0004628Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.0006515Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.004123Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06074Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.0613Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.3619Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.3648Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7807Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.004748InformativeInherited
Mammalian Phenotype (MP)abnormal head morphology0.01085InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.03335InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.04143InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.06724InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.07237InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.1839InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.2595InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.2737InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.7146InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.0001096Highly InformativeDirect
Mammalian Phenotype (MP)edema0.0001938Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0005822Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.0005958Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.001803Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.002416Highly 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 variant0.0004158Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0008537Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001972Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0000106Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.00009284Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.02559Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.08594Moderately InformativeInherited
Worm Phenotype (WP)protruding vulva0.00000102InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.0000135InformativeDirect
Worm Phenotype (WP)epithelial system development variant0.05018InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.1536InformativeInherited
Worm Phenotype (WP)vulva development variant0.3779InformativeInherited
Worm Phenotype (WP)VPC competence variant0.7202InformativeInherited
Worm Phenotype (WP)gonad arm morphology variant0.0000009758Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.000104Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.005165Highly InformativeInherited
Worm Phenotype (WP)amphid phasmid sensillum morphology variant0.01767Highly InformativeInherited
Worm Phenotype (WP)amphid morphology variant0.02873Highly InformativeInherited
Worm Phenotype (WP)amphid phasmid morphology variant0.4019Highly 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)visible0.000944Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.04311Least InformativeInherited
Fly Anatomy (FA)adult0.04364Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)region of integument0.002753Moderately InformativeInherited
Fly Anatomy (FA)appendage0.006564Moderately InformativeInherited
Fly Anatomy (FA)thorax0.01194Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.02668Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.03095Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.05052Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.07968Moderately InformativeInherited
Zebrafish Anatomy (ZA)sensory system0.433Moderately InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.06901InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure0.117InformativeInherited
Zebrafish Anatomy (ZA)neurogenic placode0.01372Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial ganglion0.717Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.003889Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01278Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.05924Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.08903Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.5603Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00002903Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00004306Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00005377Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.004472Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.06105Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.233Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3185Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindbrain0.0000001193InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.000002856InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000003302InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000575InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0001285InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0001386InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0001628InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0002778InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0245InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.04037InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.05495InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.1218InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border0.00000001677Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.000001961Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000002758Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000009525Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.00003827Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0001397Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0007806Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.0009744Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.004551Highly InformativeInherited
Xenopus ANatomical entity (XAN)optic vesicle0.009491Highly 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 groups0.00000002491Moderately 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 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 ]