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Homeodomain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   Homeodomain-like [ 46689] (19)
Families:   Homeodomain [ 46690] (40)
  Recombinase DNA-binding domain [ 46728] (5)
  Myb/SANT domain [ 46739] (15)
  SLIDE domain [ 100998]
  GARP response regulators [ 81683]
  DNA-binding domain of telomeric protein [ 46745] (2)
  Paired domain [ 46748] (3)
  DNA-binding domain of rap1 [ 46753]
  Centromere-binding [ 46756] (2)
  FIS-like [ 100918] (4)
  AraC type transcriptional activator [ 46759] (2)
  Tetracyclin repressor-like, N-terminal domain [ 46764] (34)
  Middle operon regulator, Mor [ 109659]
  Psq domain [ 140213]
  Alr1493-like [ 140216]
  Nanomeric phage protein-like [ 140219]
  SWIRM domain [ 140222] (3)
  Cgl2762-like [ 158260]
  RpiR-like [ 158263]


Superfamily statistics
Genomes (2,989) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 218,252 1,101,933 207
Proteins 189,461 940,997 197


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)multicellular organismal process0.00000024660Least InformativeDirect
Biological Process (BP)biological regulation0.00000095910Least InformativeDirect
Biological Process (BP)single-organism cellular process0.19381Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.38331Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.38651Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.4751Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.49991Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.52161Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000000000000006150Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.000000000000037410Moderately InformativeDirect
Biological Process (BP)regulation of gene expression0.000000000000061980Moderately InformativeDirect
Biological Process (BP)cell differentiation0.0000000071340.0000008442Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000019640Moderately InformativeDirect
Biological Process (BP)reproduction0.00023510Moderately InformativeDirect
Biological Process (BP)regulation of developmental process0.00039260.00006038Moderately InformativeDirect
Biological Process (BP)animal organ development0.26070Moderately InformativeInherited
Biological Process (BP)anatomical structure morphogenesis0.3160.000000004281Moderately InformativeInherited
Biological Process (BP)tissue development0.11970.0000000008365Moderately InformativeInherited
Biological Process (BP)regulation of cell differentiation0.000013650.0000005068InformativeDirect
Biological Process (BP)single organism reproductive process0.0005310.00000001885InformativeDirect
Biological Process (BP)reproductive system development0.0013930.0008006InformativeInherited
Biological Process (BP)developmental process involved in reproduction0.014640.4472InformativeInherited
Biological Process (BP)central nervous system development0.19710InformativeInherited
Biological Process (BP)DNA metabolic process0.00083020.6451InformativeInherited
Biological Process (BP)animal organ morphogenesis0.36750InformativeInherited
Biological Process (BP)epithelium development0.95040.0713InformativeInherited
Biological Process (BP)forebrain development0.00058630Highly InformativeDirect
Biological Process (BP)sensory organ morphogenesis0.0041970.00001578Highly InformativeInherited
Biological Process (BP)DNA recombination0.00000077140.3758Highly InformativeInherited
Biological Process (BP)camera-type eye development0.00010210.1777Highly InformativeInherited
Biological Process (BP)epithelial cell differentiation0.010830.1481Highly InformativeInherited
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding00InformativeDirect

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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000008442 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00006038 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00000001889 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000005868 Moderately Informative Direct
Biological Process (BP) tissue development 0.0000000008365 Moderately Informative Direct
Biological Process (BP) animal organ development 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.000000004281 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0000000000001633 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0001378 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000003043 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00001129 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0005328 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00251 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1639 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) ion transport 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) defense response 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2291 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.02626 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.1359 Moderately Informative Inherited
Biological Process (BP) gene expression 0.5759 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.0000005068 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000001885 Informative Direct
Biological Process (BP) reproductive system development 0.0008006 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0000006168 Informative Direct
Biological Process (BP) central nervous system development 0 Informative Direct
Biological Process (BP) embryo development 0 Informative Direct
Biological Process (BP) animal organ morphogenesis 0 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.000000000000001925 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0000000001462 Informative Direct
Biological Process (BP) response to acid chemical 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) locomotion 0.00000003015 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.0000003168 Informative Direct
Biological Process (BP) behavior 0.000002131 Informative Direct
Biological Process (BP) localization of cell 0.000002976 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.8328 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) regulation of secretion 0.9964 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) regulation of system process 1 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.2759 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.07643 Informative Inherited
Biological Process (BP) negative regulation of cell death 1 Informative Inherited
Biological Process (BP) generation of neurons 0.0471 Informative Inherited
Biological Process (BP) regulation of cellular component movement 1 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 1 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.7121 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 1 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.2025 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.08327 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) regulation of locomotion 1 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.01986 Informative Inherited
Biological Process (BP) response to metal ion 1 Informative Inherited
Biological Process (BP) positive regulation of immune system process 1 Informative Inherited
Biological Process (BP) cell cycle process 1 Informative Inherited
Biological Process (BP) organelle localization 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 1 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) epithelium development 0.0713 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.4472 Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.2715 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.6809 Informative Inherited
Biological Process (BP) regulation of cell proliferation 1 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.6947 Informative Inherited
Biological Process (BP) DNA metabolic process 0.6451 Informative Inherited
Biological Process (BP) response to extracellular stimulus 1 Informative Inherited
Biological Process (BP) anion transport 1 Informative Inherited
Biological Process (BP) organic acid transport 1 Informative Inherited
Biological Process (BP) metal ion transport 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.04446 Informative Inherited
Biological Process (BP) cellular response to lipid 0.02805 Informative Inherited
Biological Process (BP) response to bacterium 1 Informative Inherited
Biological Process (BP) defense response to other organism 1 Informative Inherited
Biological Process (BP) immune response 1 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) post-embryonic development 0.05052 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) multicellular organism reproduction 1 Informative Inherited
Biological Process (BP) multi-organism reproductive process 1 Informative Inherited
Biological Process (BP) regulation of apoptotic process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 1 Informative Inherited
Biological Process (BP) regulation of proteolysis 1 Informative Inherited
Biological Process (BP) hemopoiesis 1 Informative Inherited
Biological Process (BP) circulatory system development 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.7867 Informative Inherited
Biological Process (BP) protein localization to organelle 1 Informative Inherited
Biological Process (BP) protein transport 1 Informative Inherited
Biological Process (BP) single-organism cellular localization 1 Informative Inherited
Biological Process (BP) intracellular transport 1 Informative Inherited
Biological Process (BP) forebrain development 0 Highly Informative Direct
Biological Process (BP) sensory organ morphogenesis 0.00001578 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.0000001157 Highly Informative Direct
Biological Process (BP) embryonic organ development 0 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.0000000000009364 Highly Informative Direct
Biological Process (BP) appendage development 0.0000000006572 Highly Informative Direct
Biological Process (BP) tube morphogenesis 0.000000001524 Highly Informative Direct
Biological Process (BP) regulation of binding 0.000000007757 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.00000000784 Highly Informative Direct
Biological Process (BP) kidney development 0.0000001528 Highly Informative Direct
Biological Process (BP) histone modification 0.0000005501 Highly Informative Direct
Biological Process (BP) response to alcohol 0.000001221 Highly Informative Direct
Biological Process (BP) cell proliferation 0.000001789 Highly Informative Direct
Biological Process (BP) response to water deprivation 0.00004605 Highly Informative Direct
Biological Process (BP) pigmentation 0.00004671 Highly Informative Direct
Biological Process (BP) response to retinoic acid 0.000053 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00005704 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.00007949 Highly Informative Direct
Biological Process (BP) demethylation 0.00009654 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0001914 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.0002077 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.0002238 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0006516 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0006733 Highly Informative Direct
Biological Process (BP) gene silencing 0.0006957 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0008258 Highly Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.2264 Highly Informative Inherited
Biological Process (BP) positive regulation of apoptotic process 1 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 1 Highly Informative Inherited
Biological Process (BP) positive regulation of secretion by cell 1 Highly Informative Inherited
Biological Process (BP) regulation of lipid localization 0.0336 Highly Informative Inherited
Biological Process (BP) regulation of endocrine process 0.003349 Highly Informative Inherited
Biological Process (BP) regulation of hormone secretion 0.02282 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 1 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.9918 Highly Informative Inherited
Biological Process (BP) regeneration 1 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription from RNA polymerase II promoter 0.007344 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic process 0.07502 Highly Informative Inherited
Biological Process (BP) regulation of cellular ketone metabolic process 0.9413 Highly Informative Inherited
Biological Process (BP) nuclear chromosome segregation 0.7857 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 1 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 1 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.7701 Highly Informative Inherited
Biological Process (BP) cellular response to acid chemical 0.003546 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.7834 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 1 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 1 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.02898 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell proliferation 1 Highly Informative Inherited
Biological Process (BP) striated muscle cell development 1 Highly Informative Inherited
Biological Process (BP) muscle tissue development 1 Highly Informative Inherited
Biological Process (BP) heart development 1 Highly Informative Inherited
Biological Process (BP) negative regulation of locomotion 1 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular component movement 1 Highly Informative Inherited
Biological Process (BP) sex differentiation 0.02727 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.258 Highly Informative Inherited
Biological Process (BP) ceramide metabolic process 0.007797 Highly Informative Inherited
Biological Process (BP) regulation of hemopoiesis 0.06548 Highly Informative Inherited
Biological Process (BP) establishment or maintenance of cell polarity 1 Highly Informative Inherited
Biological Process (BP) nuclear division 0.9493 Highly Informative Inherited
Biological Process (BP) establishment of organelle localization 1 Highly Informative Inherited
Biological Process (BP) response to ketone 0.1444 Highly Informative Inherited
Biological Process (BP) negative regulation of homeostatic process 1 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3666 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 1 Highly Informative Inherited
Biological Process (BP) myeloid cell differentiation 1 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 1 Highly Informative Inherited
Biological Process (BP) chromatin assembly or disassembly 0.8557 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) cellular response to extracellular stimulus 1 Highly Informative Inherited
Biological Process (BP) dicarboxylic acid transport 0.06989 Highly Informative Inherited
Biological Process (BP) transition metal ion transport 0.7889 Highly Informative Inherited
Biological Process (BP) regulation of carbohydrate biosynthetic process 1 Highly Informative Inherited
Biological Process (BP) regulation of cellular carbohydrate metabolic process 1 Highly Informative Inherited
Biological Process (BP) cell wall biogenesis 0.8473 Highly Informative Inherited
Biological Process (BP) regulation of cell division 0.2308 Highly Informative Inherited
Biological Process (BP) innate immune response 1 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.00698 Highly Informative Inherited
Biological Process (BP) nervous system process 0.01346 Highly Informative Inherited
Biological Process (BP) neuron development 0.05014 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.9985 Highly Informative Inherited
Biological Process (BP) germ cell development 1 Highly Informative Inherited
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0.05735 Highly Informative Inherited
Biological Process (BP) positive regulation of proteolysis 0.6431 Highly Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.3758 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.1481 Highly Informative Inherited
Biological Process (BP) leukocyte differentiation 1 Highly Informative Inherited
Biological Process (BP) multi-organism behavior 0.005642 Highly Informative Inherited
Biological Process (BP) camera-type eye development 0.1777 Highly Informative Inherited
Biological Process (BP) cell maturation 0.7181 Highly Informative Inherited
Biological Process (BP) anatomical structure maturation 0.4789 Highly Informative Inherited
Biological Process (BP) gastrulation 0.7517 Highly Informative Inherited
Biological Process (BP) protein localization to nucleus 0.04493 Highly Informative Inherited
Biological Process (BP) single-organism nuclear import 0.1988 Highly Informative Inherited
Biological Process (BP) protein import 0.5307 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 1 Moderately Informative Inherited
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.00005816 Informative Direct
Molecular Function (MF) receptor binding 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 1 Informative Inherited
Molecular Function (MF) identical protein binding 0.02608 Informative Inherited
Molecular Function (MF) enzyme activator activity 1 Informative Inherited
Molecular Function (MF) molecular transducer activity 1 Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.3298 Informative Inherited
Molecular Function (MF) signal transducer activity 1 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.000000000000006264 Highly Informative Direct
Molecular Function (MF) deacetylase activity 0.00000007313 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.00001882 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.08749 Highly Informative Inherited
Molecular Function (MF) kinase regulator activity 0.2219 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.08511 Highly Informative Inherited
Molecular Function (MF) double-stranded DNA binding 0.001034 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.7382 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00000000002904 Moderately Informative Direct
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.6572 Moderately Informative Inherited
Cellular Component (CC) protein-DNA complex 0 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) histone deacetylase complex 0.000000000001248 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.000008107 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0.000009125 Highly Informative Direct
Cellular Component (CC) peptidase complex 1 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)Phosphotransferases with an alcohol group as accep0.0000000007689Moderately InformativeDirect
Enzyme Commission (EC)Glucokinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processNitrogen fixation0.0000003484InformativeDirect
Biological processBiological rhythms0.00003016InformativeDirect
Biological processWnt signaling pathway0.00009996InformativeDirect
Biological processSensory transduction0.001732InformativeInherited
Biological processFlowering0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processVision0.0000000000002246Highly InformativeDirect
Biological processDNA integration0.00000000001157Highly InformativeDirect
Biological processOsteogenesis0.00000000185Highly InformativeDirect
Biological processMyogenesis0.0000001623Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.00000000072InformativeDirect
Cellular componentSpliceosome0.00001295InformativeDirect
Cellular componentTelomere0.000000000000001304Highly InformativeDirect
DiseaseDisease mutation0.000006022Least InformativeDirect
DiseaseDwarfism0.0006387InformativeDirect
DiseaseMicrophthalmia0.000001733Highly InformativeDirect
DomainLIM domain0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009057 SSF46689 Protein matches
Abstract

Homeodomain proteins are transcription factors that share a related DNA binding homeodomain [PubMed10377888]. The homeodomain was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well conserved in many other animals, including vertebrates. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure. Many proteins contain homeodomains, including Drosophila Engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and HOX proteins.

The homeodomain motif is very similar in sequence and structure to domains in a wide range of DNA-binding proteins, including recombinases, Myb proteins, GARP response regulators, human telomeric proteins (hTRF1), paired domain proteins (PAX), yeast RAP1, centromere-binding proteins CENP-B and ABP-1, transcriptional regulators (TyrR), AraC-type transcriptional activators, and tetracycline repressor-like proteins (TetR, QacR, YcdC) [PubMed12215502, PubMed9739097, PubMed7707374].


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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 137 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 Homeodomain-like 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 137 hidden Markov models representing the Homeodomain-like 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) · UniProtKB KeyWords (KW) · Internal database links ]