SUPERFAMILY 1.75 HMM library and genome assignments server


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 (496) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,017 17,707 25
Proteins 10,964 15,165 24


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)regulation of metabolic process7.151e-050Least InformativeDirect
Biological Process (BP)regulation of cellular process0.0033561.599e-06Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0015735.537e-08Least InformativeInherited
Biological Process (BP)single-organism cellular process0.031465.124e-13Least InformativeInherited
Biological Process (BP)regulation of biosynthetic process2.831e-070Moderately InformativeDirect
Biological Process (BP)regulation of gene expression3.398e-070Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process3.452e-070Moderately InformativeDirect
Biological Process (BP)organelle organization5.941e-050.0007358Moderately InformativeDirect
Biological Process (BP)chromosome organization6.19e-100InformativeDirect
Molecular Function (MF)binding0.00070380Least InformativeDirect
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.00010940.6893Moderately InformativeInherited
Molecular Function (MF)chromatin binding2.17e-090InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity1.924e-070InformativeDirect
Molecular Function (MF)DNA binding0.0076350InformativeInherited
Molecular Function (MF)sequence-specific DNA binding transcription factor activity5.795e-080Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.024530.007767Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.039880.002731Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.66722.801e-07Least InformativeInherited
Cellular Component (CC)chromosome2.446e-102.434e-10InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 5.537e-08 Least Informative Direct
Biological Process (BP) regulation of cellular process 1.599e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 5.124e-13 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 2.648e-06 Least Informative Direct
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.6598 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0007358 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 3.827e-11 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 3.722e-15 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 5.25e-10 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 6.876e-09 Moderately Informative Direct
Biological Process (BP) tissue development 8.702e-07 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1.604e-05 Moderately Informative Direct
Biological Process (BP) cellular response to stress 4.789e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0001261 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0002248 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0004263 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.2758 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.1092 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.009217 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.2377 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5888 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8093 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.03009 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1459 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.6394 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.8708 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.04377 Moderately Informative Inherited
Biological Process (BP) organ development 0.005882 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4904 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) embryonic morphogenesis 0 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1.922e-15 Informative Direct
Biological Process (BP) negative regulation of developmental process 3.722e-15 Informative Direct
Biological Process (BP) central nervous system development 3.424e-14 Informative Direct
Biological Process (BP) embryonic organ development 5.358e-12 Informative Direct
Biological Process (BP) cellular process involved in reproduction 5.754e-11 Informative Direct
Biological Process (BP) single organism reproductive process 3.082e-10 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 3.217e-10 Informative Direct
Biological Process (BP) regulation of nervous system development 4.136e-10 Informative Direct
Biological Process (BP) growth 8.735e-09 Informative Direct
Biological Process (BP) organ morphogenesis 1.049e-08 Informative Direct
Biological Process (BP) positive regulation of gene expression 1.163e-08 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 7.104e-08 Informative Direct
Biological Process (BP) hexose metabolic process 1.327e-07 Informative Direct
Biological Process (BP) regulation of cell proliferation 2.305e-07 Informative Direct
Biological Process (BP) gland development 2.456e-07 Informative Direct
Biological Process (BP) DNA metabolic process 1.268e-06 Informative Direct
Biological Process (BP) regulation of secretion 1.664e-06 Informative Direct
Biological Process (BP) reproductive system development 2.682e-06 Informative Direct
Biological Process (BP) developmental process involved in reproduction 2.753e-06 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 3.036e-06 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 7.88e-06 Informative Direct
Biological Process (BP) tube development 1.101e-05 Informative Direct
Biological Process (BP) organelle localization 2.419e-05 Informative Direct
Biological Process (BP) cardiovascular system development 8.939e-05 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0001003 Informative Direct
Biological Process (BP) leukocyte activation 0.0001692 Informative Direct
Biological Process (BP) muscle structure development 0.0002593 Informative Direct
Biological Process (BP) tissue morphogenesis 0.0002866 Informative Direct
Biological Process (BP) sensory organ development 0.0002915 Informative Direct
Biological Process (BP) localization of cell 0.0004333 Informative Direct
Biological Process (BP) regulation of cell development 0.0005208 Informative Direct
Biological Process (BP) sexual reproduction 0.0006151 Informative Direct
Biological Process (BP) protein localization to organelle 0.0007072 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.1066 Informative Inherited
Biological Process (BP) regulation of locomotion 0.1399 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.01215 Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0.01151 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.2998 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.6447 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.001637 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.005618 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.4191 Informative Inherited
Biological Process (BP) cell cycle process 1 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.7632 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.0872 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.09515 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.9334 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.005878 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.02921 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.004069 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.001816 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) regulation of growth 0.8525 Informative Inherited
Biological Process (BP) generation of neurons 0.04865 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.001551 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.02984 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.01369 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) muscle tissue development 0.8922 Informative Inherited
Biological Process (BP) protein transport 0.01881 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) response to lipid 0.0106 Informative Inherited
Biological Process (BP) regulation of system process 1 Informative Inherited
Biological Process (BP) cell-cell signaling 0.1823 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.69 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) locomotion 0.04347 Informative Inherited
Biological Process (BP) cellular component movement 1 Informative Inherited
Biological Process (BP) biological adhesion 0.03527 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.9136 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.2969 Informative Inherited
Biological Process (BP) response to nutrient levels 0.002859 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1401 Informative Inherited
Biological Process (BP) mitochondrion organization 0.6682 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.1223 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.04483 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.08787 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) spermatogenesis 0 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0 Highly Informative Direct
Biological Process (BP) cell fate commitment 0 Highly Informative Direct
Biological Process (BP) stem cell development 0 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0 Highly Informative Direct
Biological Process (BP) diencephalon development 1.136e-13 Highly Informative Direct
Biological Process (BP) energy reserve metabolic process 1.117e-12 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 1.364e-12 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 1.893e-12 Highly Informative Direct
Biological Process (BP) endocrine system development 5.212e-12 Highly Informative Direct
Biological Process (BP) ossification 3.247e-10 Highly Informative Direct
Biological Process (BP) nuclear import 4.189e-10 Highly Informative Direct
Biological Process (BP) gonad development 4.378e-10 Highly Informative Direct
Biological Process (BP) connective tissue development 5.729e-10 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 1.23e-09 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 1.331e-09 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 1.574e-09 Highly Informative Direct
Biological Process (BP) regulation of binding 4.173e-09 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 5.866e-09 Highly Informative Direct
Biological Process (BP) skeletal system development 1.17e-08 Highly Informative Direct
Biological Process (BP) protein import 2.039e-08 Highly Informative Direct
Biological Process (BP) hair follicle development 3.468e-08 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 3.699e-08 Highly Informative Direct
Biological Process (BP) mesenchyme development 4.887e-08 Highly Informative Direct
Biological Process (BP) T cell differentiation 1.64e-07 Highly Informative Direct
Biological Process (BP) epithelial tube formation 2.231e-07 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 1.094e-06 Highly Informative Direct
Biological Process (BP) retina development in camera-type eye 1.326e-06 Highly Informative Direct
Biological Process (BP) protein-DNA complex assembly 6.551e-06 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 1.154e-05 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 1.635e-05 Highly Informative Direct
Biological Process (BP) photoreceptor cell differentiation 2.302e-05 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 2.622e-05 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 3.468e-05 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 6.444e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 8.347e-05 Highly Informative Direct
Biological Process (BP) digestion 8.971e-05 Highly Informative Direct
Biological Process (BP) sensory perception 0.0001054 Highly Informative Direct
Biological Process (BP) inner ear development 0.0001936 Highly Informative Direct
Biological Process (BP) histone modification 0.000371 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.000492 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0005032 Highly Informative Direct
Biological Process (BP) chromatin assembly 0.0005839 Highly Informative Direct
Biological Process (BP) cellular response to starvation 0.000665 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.0006953 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.0009743 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.05318 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.3045 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.01203 Highly Informative Inherited
Biological Process (BP) cellular response to growth factor stimulus 0.007815 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.004945 Highly Informative Inherited
Biological Process (BP) renal system development 0.005114 Highly Informative Inherited
Biological Process (BP) developmental growth 0.1957 Highly Informative Inherited
Biological Process (BP) tissue homeostasis 0.03398 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.001263 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.00798 Highly Informative Inherited
Biological Process (BP) regulation of protein stability 0.003214 Highly Informative Inherited
Biological Process (BP) negative regulation of growth 0.07059 Highly Informative Inherited
Biological Process (BP) regulation of protein complex assembly 0.07012 Highly Informative Inherited
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.009995 Highly Informative Inherited
Biological Process (BP) regulation of cellular ketone metabolic process 0.02558 Highly Informative Inherited
Biological Process (BP) DNA modification 0.00747 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.2362 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.9054 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.6411 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.6519 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.00677 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.6012 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.04254 Highly Informative Inherited
Biological Process (BP) cell adhesion 0.506 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.01393 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.01475 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.04065 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.02526 Highly Informative Inherited
Biological Process (BP) nucleus organization 0.007699 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.7942 Highly Informative Inherited
Biological Process (BP) cell growth 0.1062 Highly Informative Inherited
Biological Process (BP) cardiocyte differentiation 0.02421 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.02346 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.6893 Moderately Informative Inherited
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 6.253e-13 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.08292 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 4.964e-13 Highly Informative Direct
Molecular Function (MF) transcription factor binding 1.134e-06 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.0564 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 2.801e-07 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.007767 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.002731 Least Informative Inherited
Cellular Component (CC) protein complex 0.9693 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 4.759e-13 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.2696 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.1725 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.05105 Moderately Informative Inherited
Cellular Component (CC) chromosome 2.434e-10 Informative Direct
Cellular Component (CC) nucleoplasm part 2.15e-07 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.723 Informative Inherited
Cellular Component (CC) transcription factor complex 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 5.016e-09 Highly Informative Direct
Cellular Component (CC) SWI/SNF superfamily-type complex 1.839e-08 Highly Informative Direct
Cellular Component (CC) kinetochore 0.0002372 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.001413 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups2.056e-08Least InformativeDirect
Enzyme Commission (EC)Methyltransferases2.065e-09Moderately 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 cancer0.7894Moderately InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.6674Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.7155Least InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.06623Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1673Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.4853Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.008232InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.1952InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.2488InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.3337InformativeInherited
Mammalian Phenotype (MP)abnormal telencephalon development0.1039Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hindlimb morphology0.3821Highly InformativeInherited
Mammalian Phenotype (MP)abnormal erythrocyte morphology0.4528Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.4935Highly InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.6447Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)reproductive system morphology variant7.098e-05Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.005194Moderately InformativeInherited
Worm Phenotype (WP)protruding vulva1.634e-05InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0001076InformativeDirect

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) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)digestive system4.293e-05Least InformativeDirect
Zebrafish Anatomy (ZA)portion of tissue0.005321Least InformativeInherited
Zebrafish Anatomy (ZA)cavitated compound organ0.006274Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.01683Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.06719Least InformativeInherited
Zebrafish Anatomy (ZA)head0.1645Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.4344Least InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure8.591e-05Moderately InformativeDirect
Zebrafish Anatomy (ZA)electrically signaling cell0.0009248Moderately InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch0.0009557Moderately InformativeDirect
Zebrafish Anatomy (ZA)suspensorium0.002102Moderately InformativeInherited
Zebrafish Anatomy (ZA)surface structure0.00731Moderately InformativeInherited
Zebrafish Anatomy (ZA)cartilage element0.2609Moderately InformativeInherited
Zebrafish Anatomy (ZA)eye0.2863Moderately InformativeInherited
Zebrafish Anatomy (ZA)electrically responsive cell1Moderately InformativeInherited
Zebrafish Anatomy (ZA)scapulocoracoid2.105e-06InformativeDirect
Zebrafish Anatomy (ZA)pectoral fin endoskeletal disc4.268e-06InformativeDirect
Zebrafish Anatomy (ZA)ceratobranchial 5 bone5.212e-06InformativeDirect
Zebrafish Anatomy (ZA)intramembranous bone9.675e-06InformativeDirect
Zebrafish Anatomy (ZA)amacrine cell1.284e-05InformativeDirect
Zebrafish Anatomy (ZA)ethmoid cartilage1.417e-05InformativeDirect
Zebrafish Anatomy (ZA)iridophore1.771e-05InformativeDirect
Zebrafish Anatomy (ZA)Muller cell0.0001381InformativeDirect
Zebrafish Anatomy (ZA)retroarticular0.0002037InformativeDirect
Zebrafish Anatomy (ZA)sphenoid region0.0002079InformativeDirect
Zebrafish Anatomy (ZA)basal plate cartilage0.0003264InformativeDirect
Zebrafish Anatomy (ZA)occipital arch cartilage0.0003264InformativeDirect
Zebrafish Anatomy (ZA)orbital region0.0007231InformativeDirect
Zebrafish Anatomy (ZA)dermatocranium0.0009364InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0.04658Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.101Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.1068Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.36Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.5277Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure3.074e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.01207Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.07641Moderately InformativeInherited
Xenopus ANatomical entity (XAN)forebrain2.24e-05InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain4.053e-05InformativeDirect
Xenopus ANatomical entity (XAN)neural plate4.278e-05InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0002324InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0009701InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.002929InformativeInherited
Xenopus ANatomical entity (XAN)neural plate border1.333e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)sensorial layer of neurectoderm1.5e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field1.693e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary2.64e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0001764Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0002865Highly InformativeDirect
Xenopus ANatomical entity (XAN)diencephalon0.0003856Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural fold0.0004408Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0004695Highly InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.0005273Highly InformativeDirect
Xenopus ANatomical entity (XAN)olfactory system0.0007735Highly InformativeDirect
Xenopus ANatomical entity (XAN)zygote0.0009017Highly InformativeDirect

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 cell2.191e-11Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.0007389Highly 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 groups2.159e-08Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDNA damage0.0002551Moderately InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processNeurogenesis6.003e-10InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentChromosome0InformativeDirect
DomainRepeat4.692e-05Least InformativeDirect
DomainCoiled coil1.077e-07Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionCalmodulin-binding0InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator3.666e-14InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond8.727e-15Moderately InformativeDirect

Document: KW 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

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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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · 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) · UniProtKB KeyWords (KW) · Internal database links ]