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Histone-fold superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Histone-fold [ 47112]
Superfamily:   Histone-fold [ 47113] (4)
Families:   Nucleosome core histones [ 47114] (5)
  Archaeal histone [ 47129]
  TBP-associated factors, TAFs [ 47134] (13)
  Bacterial histone-fold protein [ 101318] (2)


Superfamily statistics
Genomes (661) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,869 39,243 82
Proteins 27,440 38,669 81


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 biogenesis0.0000000000000061020.000000000003366Least InformativeDirect
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.19680.00001075Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0010530.0006119Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.16950.000002989Least InformativeInherited
Biological Process (BP)primary metabolic process0.75290.609Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)biological regulation0.75040.9164Least InformativeInherited
Biological Process (BP)biosynthetic process0.9060.0003974Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.06850.00000009129Least InformativeInherited
Biological Process (BP)response to stimulus0.0000018940.1627Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.066570.0000001515Least InformativeInherited
Biological Process (BP)immune system process0.000000000059950.000332Moderately InformativeDirect
Biological Process (BP)organelle organization0.00000000000088050Moderately InformativeDirect
Biological Process (BP)response to biotic stimulus0.00000000022960.00000007399Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.00036220.0000004277Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000026750.000000006823Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000032240Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0005520.000000001971Moderately InformativeDirect
Biological Process (BP)multi-organism process0.00000000001150.0000635Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.0031010.000007118Moderately InformativeInherited
Biological Process (BP)protein complex biogenesis11Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.51530.7787Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.000079670.00967Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.13830.02562Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.88491Moderately InformativeInherited
Biological Process (BP)cellular localization0.82071Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.0056210.1653Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.0097140.08157Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.36560.000000000001706Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.13040.000000000000001945Moderately InformativeInherited
Biological Process (BP)gene expression0.58430.000001054Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.050050.00008781Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.41710.000000009346Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.24840.00000000000001267Moderately InformativeInherited
Biological Process (BP)reproduction0.0093960.0955Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated0.000032120InformativeDirect
Biological Process (BP)regulation of transcription, DNA-templated0.000015250.0000007392InformativeDirect
Biological Process (BP)immune response0.000000000020030.00000001904InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.00012530.00001038InformativeDirect
Biological Process (BP)response to bacterium0.00000012610.00000002874InformativeDirect
Biological Process (BP)cell cycle process0.00000040690.000005516InformativeDirect
Biological Process (BP)interspecies interaction between organisms0.000006530.00001019InformativeDirect
Biological Process (BP)chromosome organization00InformativeDirect
Biological Process (BP)defense response to other organism0.000000026160.00000000001031InformativeDirect
Biological Process (BP)cellular protein complex assembly10.8443InformativeInherited
Biological Process (BP)organelle assembly10.9954InformativeInherited
Biological Process (BP)negative regulation of gene expression0.14730.8263InformativeInherited
Biological Process (BP)DNA metabolic process0.0000012860.003834InformativeInherited
Biological Process (BP)protein localization to organelle0.13110.02385InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.17680.0000237InformativeInherited
Biological Process (BP)single organism reproductive process0.00056940.009239InformativeInherited
Biological Process (BP)nuclear division0.000000078350.00000001383Highly InformativeDirect
Biological Process (BP)chromatin assembly or disassembly0.0000000000086960Highly InformativeDirect
Biological Process (BP)histone modification0.00031280.000000004963Highly InformativeDirect
Biological Process (BP)peptidyl-lysine modification0.00050970.0000000001292Highly InformativeDirect
Biological Process (BP)innate immune response0.00000000000033830.0000000004328Highly InformativeDirect
Biological Process (BP)defense response to Gram-positive bacterium0.0000000081540.00000000001095Highly InformativeDirect
Biological Process (BP)protein-DNA complex subunit organization00Highly InformativeDirect
Biological Process (BP)nuclear chromosome segregation0.00061350.00004415Highly InformativeDirect
Biological Process (BP)antimicrobial humoral response0.029350.01546Highly InformativeInherited
Biological Process (BP)regulation of gene expression, epigenetic0.0017430.01424Highly InformativeInherited
Biological Process (BP)DNA replication0.0000026780.006513Highly InformativeInherited
Biological Process (BP)transcription from RNA polymerase II promoter0.00430.00000002728Highly InformativeInherited
Biological Process (BP)meiotic cell cycle0.0019230.03357Highly InformativeInherited
Biological Process (BP)DNA recombination0.055880.1257Highly InformativeInherited
Molecular Function (MF)binding0.0000000018570.0000000004438Least InformativeDirect
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.93251Moderately InformativeInherited
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding0.0000000000016050InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.028650.07594InformativeInherited
Molecular Function (MF)transcription factor activity, transcription factor binding0.000066680.00000303Highly InformativeDirect
Molecular Function (MF)chromatin binding0.00000000010840.000003572Highly InformativeDirect
Molecular Function (MF)DNA-directed DNA polymerase activity0.0000095850.00009272Highly InformativeDirect
Cellular Component (CC)macromolecular complex00Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00.00000000000001208Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0017310.000007862Least InformativeInherited
Cellular Component (CC)extracellular region part0.0000000000040770.00000000372Moderately InformativeDirect
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00Moderately InformativeDirect
Cellular Component (CC)transferase complex00Moderately InformativeDirect
Cellular Component (CC)vesicle11Moderately InformativeInherited
Cellular Component (CC)extracellular space00.0000000000002356InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)protein-DNA complex00InformativeDirect
Cellular Component (CC)nucleoplasm part0.000035050.00000000000005685InformativeDirect
Cellular Component (CC)extracellular organelle0.18110.01746InformativeInherited
Cellular Component (CC)transferase complex, transferring phosphorus-containing groups0.96830.002255InformativeInherited
Cellular Component (CC)chromatin0.000011920.0003665Highly InformativeDirect
Cellular Component (CC)lipid particle0.000000000000039710Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.000000069130.0000000002283Highly InformativeDirect
Cellular Component (CC)nuclear chromosome part0.000000000021860.00002494Highly InformativeDirect
Cellular Component (CC)extracellular vesicle0.0000014760.00000004528Highly InformativeDirect
Cellular Component (CC)replisome0.019090.005862Highly InformativeInherited

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 aromatic compound metabolic process 0.0000001515 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0003974 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00001075 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0006119 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000009129 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000000000003366 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000002989 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.609 Least Informative Inherited
Biological Process (BP) biological regulation 0.9164 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1627 Least Informative Inherited
Biological Process (BP) immune system process 0.000332 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.00000007399 Moderately Informative Direct
Biological Process (BP) gene expression 0.000001054 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00008781 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000004277 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000009346 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00000000000001267 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000006823 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000000000000001945 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000007118 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000001971 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0000635 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000000000001706 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.6935 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.623 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.7787 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.00967 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.02562 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1653 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.08157 Moderately Informative Inherited
Biological Process (BP) reproduction 0.0955 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.0000007392 Informative Direct
Biological Process (BP) immune response 0.00000001904 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00001038 Informative Direct
Biological Process (BP) response to bacterium 0.00000002874 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0000237 Informative Direct
Biological Process (BP) cell cycle process 0.000005516 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.00001019 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) defense response to other organism 0.00000000001031 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.4577 Informative Inherited
Biological Process (BP) cellular protein complex assembly 0.8443 Informative Inherited
Biological Process (BP) organelle assembly 0.9954 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.1219 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.7344 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.8263 Informative Inherited
Biological Process (BP) DNA metabolic process 0.003834 Informative Inherited
Biological Process (BP) protein localization to organelle 0.02385 Informative Inherited
Biological Process (BP) response to acid chemical 0.07731 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.03416 Informative Inherited
Biological Process (BP) cellular response to lipid 0.2882 Informative Inherited
Biological Process (BP) single organism reproductive process 0.009239 Informative Inherited
Biological Process (BP) nuclear division 0.00000001383 Highly Informative Direct
Biological Process (BP) chromatin assembly or disassembly 0 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.00000002728 Highly Informative Direct
Biological Process (BP) histone modification 0.000000004963 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.0000000001292 Highly Informative Direct
Biological Process (BP) innate immune response 0.0000000004328 Highly Informative Direct
Biological Process (BP) defense response to Gram-positive bacterium 0.00000000001095 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0 Highly Informative Direct
Biological Process (BP) nuclear chromosome segregation 0.00004415 Highly Informative Direct
Biological Process (BP) antimicrobial humoral response 0.01546 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.01424 Highly Informative Inherited
Biological Process (BP) DNA replication 0.006513 Highly Informative Inherited
Biological Process (BP) cellular response to acid chemical 0.01144 Highly Informative Inherited
Biological Process (BP) response to alcohol 0.1747 Highly Informative Inherited
Biological Process (BP) hormone-mediated signaling pathway 0.003041 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 0.03357 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.1257 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000004438 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.004318 Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.07594 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.00000303 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.000003572 Highly Informative Direct
Molecular Function (MF) DNA-directed DNA polymerase activity 0.00009272 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000001135 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.000004087 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0009364 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.00000000000001208 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000007862 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) extracellular region part 0.00000000372 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) extracellular space 0.0000000000002356 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) protein-DNA complex 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000000000005685 Informative Direct
Cellular Component (CC) extracellular organelle 0.01746 Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0.002255 Informative Inherited
Cellular Component (CC) kinetochore 0.0002345 Highly Informative Direct
Cellular Component (CC) chromatin 0.0003665 Highly Informative Direct
Cellular Component (CC) lipid particle 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.0000000002283 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.00002494 Highly Informative Direct
Cellular Component (CC) extracellular vesicle 0.00000004528 Highly Informative Direct
Cellular Component (CC) replisome 0.005862 Highly Informative Inherited
Cellular Component (CC) peptidase complex 0.03936 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)embryo phenotype0.1615Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo morphology0.02026Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant4.342e-16Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000000000004733Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000007774Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.001393Least InformativeInherited
Worm Phenotype (WP)cell development variant0.0503Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.711Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.000006005Moderately InformativeDirect
Worm Phenotype (WP)cell component morphology variant0.000008163Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.00005656Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.00008957Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.04792Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.06215Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.07405Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1933Moderately InformativeInherited
Worm Phenotype (WP)avoids bacterial lawn0InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0InformativeDirect
Worm Phenotype (WP)endosome morphology variant0InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0.0000000000008194InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.000000451InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.000001319InformativeDirect
Worm Phenotype (WP)protruding vulva0.000008528InformativeDirect
Worm Phenotype (WP)mitosis variant0.02508InformativeInherited
Worm Phenotype (WP)body width variant0.2563InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2626InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0Highly InformativeDirect
Worm Phenotype (WP)recycling endosome localization variant0Highly InformativeDirect
Worm Phenotype (WP)lysosome-related organelle morphology variant0.00000000000002248Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant0.0000000000000242Highly InformativeDirect
Worm Phenotype (WP)dauer lifespan extended0.000000000002735Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.000000000005478Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant0.0000005734Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.000004825Highly InformativeDirect
Worm Phenotype (WP)alimentary system morphology variant0.01647Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)cell cycle progression0.00235InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase0.00008403Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002194Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0.007949Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.00904Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0009681InformativeDirect
Xenopus ANatomical entity (XAN)oocyte0.00007408Highly 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)root system0.2388Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.7063Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8924Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.9374Least InformativeInherited
Plant ANatomical entity (PAN)primordium0.0008934InformativeDirect
Plant ANatomical entity (PAN)root tip0.01296InformativeInherited
Plant ANatomical entity (PAN)lateral root primordium0.000006491Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root0.00001517Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.00007883Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.0001123Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.0005858Highly InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage0.0000002539InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.000000000007009Moderately InformativeDirect
Biological processDNA damage0.0000004927Moderately InformativeDirect
Biological processCell cycle0.3243Moderately InformativeInherited
Biological processMitosis0.00000001573InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentKinetochore0Highly InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.4892Moderately InformativeInherited
Post-translational modificationAntimicrobial0.000000003632InformativeDirect
Post-translational modificationChromatin regulator0.00000002684InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.0002321InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationAntibiotic0.0000000000004381Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationADP-ribosylation0.00000000000001204InformativeDirect
Post-translational modificationCitrullination0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009072 SSF47113 Protein matches
Abstract

Histones mediate DNA organisation and plays a dominant role in regulating eukaryotic transcription. The histone-fold consists of a core of three helices, where the long middle helix is flanked at each end by shorter ones. Proteins displaying this structure include the nucleosome core histones, which form octomers composed of two copies of each of the four histones, H2A, H2B, H3 and H4; archaeal histone, which possesses only the core domain part of eukaryotic histone; and the TATA-box binding protein (TBP)-associated factors (TAF), where the histone fold is a common motif for mediating TAF-TAF interactions. TAF proteins include TAF(II)18 and TAF(II)28, which form a heterodimer, TAF(II)42 and TAF(II)62, which form a heterotetramer similar to (H3-H4)2, and the negative cofactor 2 (NC2) alpha and beta chains, which form a heterodimer. The TAF proteins are a component of transcription factor IID (TFIID), along with the TBP protein. TFIID forms part of the pre-initiation complex on core promoter elements required for RNA polymerase II-dependent transcription. The TAF subunits of TFIID mediate transcriptional activation of subsets of eukaryotic genes. The NC2 complex mediates the inhibition of TATA-dependent transcription through interactions with TBP.


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 32 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 Histone-fold 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 32 hidden Markov models representing the Histone-fold 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) · Human Phenotype (HP) · 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 ]