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 (451) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,334 13,422 25
Proteins 10,365 11,426 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)cellular component organization or biogenesis0.00064761.562e-07Least InformativeDirect
Biological Process (BP)regulation of metabolic process0.001220Least InformativeInherited
Biological Process (BP)regulation of cellular process0.023714.833e-07Least InformativeInherited
Biological Process (BP)single-organism cellular process0.046914.032e-14Least InformativeInherited
Biological Process (BP)organelle organization9.707e-060.0001282Moderately InformativeDirect
Biological Process (BP)regulation of biosynthetic process2.677e-050Moderately InformativeDirect
Biological Process (BP)regulation of nitrogen compound metabolic process3.371e-050Moderately InformativeDirect
Biological Process (BP)regulation of gene expression3.505e-050Moderately InformativeDirect
Biological Process (BP)regulation of cellular metabolic process0.00032170Moderately InformativeDirect
Biological Process (BP)chromosome organization2.084e-100InformativeDirect
Molecular Function (MF)binding0.00015110Least InformativeDirect
Molecular Function (MF)heterocyclic compound binding0.00016670Moderately InformativeDirect
Molecular Function (MF)organic cyclic compound binding0.00024490Moderately InformativeDirect
Molecular Function (MF)structural molecule activity7.075e-050.7288Moderately InformativeInherited
Molecular Function (MF)DNA binding2.34e-120InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity9.817e-080InformativeDirect
Molecular Function (MF)chromatin binding9.629e-120Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.051350.09968Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.0034880.01023Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.39453.595e-06Least InformativeInherited
Cellular Component (CC)chromosome7.117e-092.482e-12InformativeDirect

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) cellular component organization or biogenesis 1.562e-07 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 4.833e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.032e-14 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 6.477e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 2.114e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 4.742e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0002488 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) localization 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.002399 Least Informative Inherited
Biological Process (BP) organelle organization 0.0001282 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0001938 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular 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 3.864e-14 Moderately Informative Direct
Biological Process (BP) tissue development 9.808e-10 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 1.84e-09 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 4.48e-06 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0001446 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002468 Moderately Informative Direct
Biological Process (BP) organ development 0.0004706 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.2777 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9178 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 0.04546 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.07104 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.001075 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.6898 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.7645 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9123 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.05041 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1766 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.5573 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.2452 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.1376 Moderately Informative Inherited
Biological Process (BP) system process 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) aromatic compound biosynthetic process 0.4933 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5133 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5656 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.7876 Moderately Informative Inherited
Biological Process (BP) gene expression 0.8219 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.3075 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4662 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) chordate embryonic development 0 Informative Direct
Biological Process (BP) negative regulation of developmental process 0 Informative Direct
Biological Process (BP) embryonic morphogenesis 2.076e-15 Informative Direct
Biological Process (BP) DNA metabolic process 2.076e-15 Informative Direct
Biological Process (BP) central nervous system development 4.008e-15 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 1.348e-14 Informative Direct
Biological Process (BP) embryonic organ development 7.993e-12 Informative Direct
Biological Process (BP) single organism reproductive process 9.599e-12 Informative Direct
Biological Process (BP) regulation of nervous system development 5.352e-11 Informative Direct
Biological Process (BP) cellular process involved in reproduction 1.2e-10 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 6.876e-10 Informative Direct
Biological Process (BP) positive regulation of gene expression 1.562e-09 Informative Direct
Biological Process (BP) organ morphogenesis 5.533e-09 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 3.961e-08 Informative Direct
Biological Process (BP) regulation of cell proliferation 4.024e-08 Informative Direct
Biological Process (BP) gland development 3.634e-07 Informative Direct
Biological Process (BP) reproductive system development 4.205e-07 Informative Direct
Biological Process (BP) developmental process involved in reproduction 5.443e-07 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 7.265e-07 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 9.416e-07 Informative Direct
Biological Process (BP) nucleocytoplasmic transport 5.444e-06 Informative Direct
Biological Process (BP) transcription, DNA-dependent 6.416e-06 Informative Direct
Biological Process (BP) regulation of secretion 8.617e-06 Informative Direct
Biological Process (BP) anatomical structure homeostasis 1.068e-05 Informative Direct
Biological Process (BP) cardiovascular system development 2.515e-05 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 2.928e-05 Informative Direct
Biological Process (BP) tube development 0.0001458 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.0002398 Informative Direct
Biological Process (BP) sexual reproduction 0.000395 Informative Direct
Biological Process (BP) cell proliferation 0.0004128 Informative Direct
Biological Process (BP) tissue morphogenesis 0.0004624 Informative Direct
Biological Process (BP) muscle structure development 0.0004847 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0005264 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0005578 Informative Direct
Biological Process (BP) sensory organ development 0.0007583 Informative Direct
Biological Process (BP) regulation of reproductive process 0.05872 Informative Inherited
Biological Process (BP) regulation of protein localization 0.8321 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.2168 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.9369 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.002085 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.1196 Informative Inherited
Biological Process (BP) cell cycle process 1 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.8424 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.06661 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.08156 Informative Inherited
Biological Process (BP) response to organic nitrogen 0.884 Informative Inherited
Biological Process (BP) response to external stimulus 0.5753 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.006427 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.002642 Informative Inherited
Biological Process (BP) growth 0.01243 Informative Inherited
Biological Process (BP) multicellular organismal homeostasis 0.01082 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01051 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.6636 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 1 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) regulation of growth 0.7432 Informative Inherited
Biological Process (BP) generation of neurons 0.06893 Informative Inherited
Biological Process (BP) regulation of cell development 0.02196 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.002161 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) cell activation 0.1851 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.00797 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) muscle tissue development 1 Informative Inherited
Biological Process (BP) protein transport 0.03782 Informative Inherited
Biological Process (BP) protein localization to organelle 0.001281 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) response to lipid 0.02289 Informative Inherited
Biological Process (BP) regulation of system process 1 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.5662 Informative Inherited
Biological Process (BP) regulation of locomotion 0.6382 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.9562 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.8065 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) localization of cell 0.001955 Informative Inherited
Biological Process (BP) locomotion 0.1322 Informative Inherited
Biological Process (BP) cellular component movement 0.9053 Informative Inherited
Biological Process (BP) biological adhesion 0.06942 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.6445 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.05049 Informative Inherited
Biological Process (BP) mitochondrion organization 0.6697 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) chromatin assembly or disassembly 1.389e-07 Highly Informative Direct
Biological Process (BP) spermatogenesis 0 Highly Informative Direct
Biological Process (BP) regulation of insulin secretion 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 1.716e-14 Highly Informative Direct
Biological Process (BP) endocrine system development 8.817e-12 Highly Informative Direct
Biological Process (BP) hair cycle process 1.173e-11 Highly Informative Direct
Biological Process (BP) regulation of stem cell proliferation 3.687e-11 Highly Informative Direct
Biological Process (BP) ossification 3.765e-11 Highly Informative Direct
Biological Process (BP) tube formation 6.255e-11 Highly Informative Direct
Biological Process (BP) gonad development 2.639e-10 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 5.572e-10 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 6.811e-10 Highly Informative Direct
Biological Process (BP) nuclear import 3.164e-09 Highly Informative Direct
Biological Process (BP) skeletal system development 4.098e-09 Highly Informative Direct
Biological Process (BP) connective tissue development 9.031e-09 Highly Informative Direct
Biological Process (BP) regulation of binding 9.264e-09 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 1.073e-08 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 2.819e-08 Highly Informative Direct
Biological Process (BP) negative regulation of signal transduction 4.528e-08 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 5.75e-08 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 6.884e-08 Highly Informative Direct
Biological Process (BP) protein import 1.225e-07 Highly Informative Direct
Biological Process (BP) retina development in camera-type eye 1.845e-07 Highly Informative Direct
Biological Process (BP) epithelial tube morphogenesis 2.759e-07 Highly Informative Direct
Biological Process (BP) organelle localization 7.276e-07 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 1.282e-06 Highly Informative Direct
Biological Process (BP) lymphocyte differentiation 3.151e-06 Highly Informative Direct
Biological Process (BP) regulation of neurological system process 3.441e-06 Highly Informative Direct
Biological Process (BP) photoreceptor cell differentiation 9.378e-06 Highly Informative Direct
Biological Process (BP) T cell activation 9.802e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 1.214e-05 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 1.597e-05 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 2.26e-05 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 3.223e-05 Highly Informative Direct
Biological Process (BP) kidney development 4.004e-05 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 4.101e-05 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 4.554e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 5.847e-05 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 9.202e-05 Highly Informative Direct
Biological Process (BP) digestion 9.334e-05 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 9.928e-05 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0001843 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.0002165 Highly Informative Direct
Biological Process (BP) histone modification 0.000518 Highly Informative Direct
Biological Process (BP) signal transduction by p53 class mediator 0.0005476 Highly Informative Direct
Biological Process (BP) inner ear development 0.0005987 Highly Informative Direct
Biological Process (BP) signal transduction in response to DNA damage 0.0006494 Highly Informative Direct
Biological Process (BP) DNA packaging 0.0007336 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.2367 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.01004 Highly Informative Inherited
Biological Process (BP) cellular response to growth factor stimulus 0.03697 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.04375 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.009966 Highly Informative Inherited
Biological Process (BP) developmental growth 0.127 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.002008 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.01881 Highly Informative Inherited
Biological Process (BP) regulation of protein stability 0.002997 Highly Informative Inherited
Biological Process (BP) gastrulation 0.8593 Highly Informative Inherited
Biological Process (BP) positive regulation of secretion 0.1133 Highly Informative Inherited
Biological Process (BP) regulation of protein complex assembly 0.07157 Highly Informative Inherited
Biological Process (BP) regulation of neuron differentiation 1 Highly Informative Inherited
Biological Process (BP) epidermis development 0.002234 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.8421 Highly Informative Inherited
Biological Process (BP) post-embryonic development 1 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.6863 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.6843 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.004158 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.6508 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.02288 Highly Informative Inherited
Biological Process (BP) cell adhesion 0.5646 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.01635 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.05558 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.006305 Highly Informative Inherited
Biological Process (BP) nucleus organization 0.009821 Highly Informative Inherited
Biological Process (BP) germ cell development 0.8042 Highly Informative Inherited
Biological Process (BP) DNA repair 0.9748 Highly Informative Inherited
Biological Process (BP) cell growth 0.07326 Highly Informative Inherited
Biological Process (BP) cardiocyte differentiation 0.0156 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.01126 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.994 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.7288 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0791 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.1084 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 1.551e-12 Highly Informative Direct
Molecular Function (MF) transcription factor binding 3.733e-07 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 4.894e-06 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.07515 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.2775 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 3.595e-06 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.09968 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01023 Least Informative Inherited
Cellular Component (CC) protein complex 0.7302 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 3.382e-11 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.4035 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.2662 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.06118 Moderately Informative Inherited
Cellular Component (CC) chromosome 2.482e-12 Informative Direct
Cellular Component (CC) nucleoplasm part 4.063e-08 Informative Direct
Cellular Component (CC) transcription factor complex 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 6.064e-09 Highly Informative Direct
Cellular Component (CC) kinetochore 0.0002464 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.001531 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 cancer0.8033Moderately InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.06492Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.226Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.02638InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.08339InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.09452InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage development0.05569Highly 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)portion of tissue0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)cell0.05725Least InformativeInherited
Zebrafish Anatomy (ZA)head0.1892Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.5552Least InformativeInherited
Zebrafish Anatomy (ZA)digestive system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)skeletal element4.601e-06Moderately InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch3.715e-05Moderately InformativeDirect
Zebrafish Anatomy (ZA)cranium4.432e-05Moderately InformativeDirect
Zebrafish Anatomy (ZA)surface structure0.0007122Moderately InformativeDirect
Zebrafish Anatomy (ZA)anatomical cluster0.006891Moderately InformativeInherited
Zebrafish Anatomy (ZA)eye0.3944Moderately InformativeInherited
Zebrafish Anatomy (ZA)intramembranous bone5.619e-06InformativeDirect
Zebrafish Anatomy (ZA)endochondral bone0.0001507InformativeDirect
Zebrafish Anatomy (ZA)paired fin0.001762InformativeInherited
Zebrafish Anatomy (ZA)ventral mandibular arch0.009098InformativeInherited
Zebrafish Anatomy (ZA)median fin fold0.01392InformativeInherited
Zebrafish Anatomy (ZA)pharyngeal arch 3-70.1176InformativeInherited
Zebrafish Anatomy (ZA)occipital region0.1259InformativeInherited
Zebrafish Anatomy (ZA)retinal neural layer0.1651InformativeInherited
Zebrafish Anatomy (ZA)electrically responsive cell1InformativeInherited
Zebrafish Anatomy (ZA)scapulocoracoid3.954e-07Highly InformativeDirect
Zebrafish Anatomy (ZA)ceratobranchial 5 bone3.407e-06Highly InformativeDirect
Zebrafish Anatomy (ZA)pectoral fin endoskeletal disc6.059e-06Highly InformativeDirect
Zebrafish Anatomy (ZA)iridophore8.731e-06Highly InformativeDirect
Zebrafish Anatomy (ZA)ethmoid cartilage1.149e-05Highly InformativeDirect
Zebrafish Anatomy (ZA)embryonic structure1.851e-05Highly InformativeDirect
Zebrafish Anatomy (ZA)amacrine cell1.851e-05Highly InformativeDirect
Zebrafish Anatomy (ZA)sphenoid region2.587e-05Highly InformativeDirect
Zebrafish Anatomy (ZA)Muller cell8.639e-05Highly InformativeDirect
Zebrafish Anatomy (ZA)orbital region0.0002137Highly InformativeDirect
Zebrafish Anatomy (ZA)retroarticular0.0003055Highly InformativeDirect
Zebrafish Anatomy (ZA)basal plate cartilage0.0005603Highly InformativeDirect
Zebrafish Anatomy (ZA)occipital arch cartilage0.0005603Highly InformativeDirect
Zebrafish Anatomy (ZA)maxilla0.0005859Highly InformativeDirect
Zebrafish Anatomy (ZA)fin fold actinotrichium0.0007122Highly InformativeDirect

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 system0.04274Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.0923Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.1008Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.3443Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.5076Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure1.116e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.007703Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.06791Moderately InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.1219Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate7.275e-06InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0002463InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0003343InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.0009298InformativeDirect
Xenopus ANatomical entity (XAN)forebrain2.961e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain6.248e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary1.227e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)sensorial layer of neurectoderm1.335e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural plate border1.8e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field4.866e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate5.755e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain0.0001002Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.0001677Highly InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.0002397Highly InformativeDirect
Xenopus ANatomical entity (XAN)olfactory system0.0003122Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0004854Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic vesicle0.0004897Highly InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0007806Highly InformativeDirect
Xenopus ANatomical entity (XAN)hyoid crest0.0007868Highly InformativeDirect
Xenopus ANatomical entity (XAN)non-neural ectoderm0.00524Highly 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)plant cell0.7826Least InformativeInherited
Plant ANatomical entity (PAN)cultured plant cell2.746e-11Highly 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 groups2.085e-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 damage0.000212Moderately InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processNeurogenesis2.509e-10InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentChromosome0InformativeDirect
DomainRepeat1.792e-05Least InformativeDirect
DomainCoiled coil7.027e-08Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionCalmodulin-binding0InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator2.488e-14InformativeDirect
Post-translational modificationPhosphoprotein4.66e-11Least InformativeDirect
Post-translational modificationIsopeptide bond4.414e-10Moderately InformativeDirect
Post-translational modificationAcetylation2.631e-09Moderately InformativeDirect
Post-translational modificationUbl conjugation1.023e-08Moderately InformativeDirect
Post-translational modificationADP-ribosylation0InformativeDirect

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 ]