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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 (657) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,695 39,243 82
Proteins 27,265 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 biogenesis0.000000000000011570.00000000003102Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.13850.01151Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.2960.000009Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)response to stimulus0.00000084910.08126Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.1180.0000001273Least InformativeInherited
Biological Process (BP)biological regulation0.018520.2006Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.24880.000002272Least InformativeInherited
Biological Process (BP)biosynthetic process0.99940.0007498Least InformativeInherited
Biological Process (BP)primary metabolic process10.9221Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.12110.00000008164Least InformativeInherited
Biological Process (BP)immune system process0.00000000010780.0002832Moderately InformativeDirect
Biological Process (BP)response to stress0.000000000034510.00003888Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0002860Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.000000000000070270Moderately InformativeDirect
Biological Process (BP)multi-organism process0.000000000015610.00002837Moderately InformativeDirect
Biological Process (BP)regulation of cellular metabolic process0.074390.0009207Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process0.0020320.0000002711Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.00010630.01617Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.0017050.868Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.84641Moderately InformativeInherited
Biological Process (BP)cellular localization0.72191Moderately InformativeInherited
Biological Process (BP)nucleobase-containing compound biosynthetic process0.0074880Moderately InformativeInherited
Biological Process (BP)organelle organization0.013690.1025Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.056540.009785Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.75730.96Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.062880.00001255Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.21880.515Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.084490.000000000008151Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.010020.000006987Moderately InformativeInherited
Biological Process (BP)gene expression0.13570.000000002498Moderately InformativeInherited
Biological Process (BP)reproduction0.0076920.1085Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated0.0000093280InformativeDirect
Biological Process (BP)regulation of transcription, DNA-templated0.00021540.0000345InformativeDirect
Biological Process (BP)immune response0.0000000000014910.000000003919InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.0000022230.000000249InformativeDirect
Biological Process (BP)response to bacterium00.000000000000007239InformativeDirect
Biological Process (BP)cell cycle process0.000067870.0003602InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly00.00000000001213InformativeDirect
Biological Process (BP)defense response to other organism0.00000000088010.0000000000005337InformativeDirect
Biological Process (BP)organelle assembly0.4810.2545InformativeInherited
Biological Process (BP)organelle fission0.027010.01624InformativeInherited
Biological Process (BP)single organism reproductive process0.0004240.01125InformativeInherited
Biological Process (BP)protein localization to organelle0.12170.01753InformativeInherited
Biological Process (BP)DNA metabolic process0.00000016430.00415InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0096150.00001748InformativeInherited
Biological Process (BP)negative regulation of gene expression0.029890.7044InformativeInherited
Biological Process (BP)internal protein amino acid acetylation0.00000089390Highly InformativeDirect
Biological Process (BP)gene silencing0.000078620.0009115Highly InformativeDirect
Biological Process (BP)histone modification0.0000079870.000000002621Highly InformativeDirect
Biological Process (BP)peptidyl-lysine modification0.00031210.00000000011Highly InformativeDirect
Biological Process (BP)defense response to bacterium0.00000000016490.0000000000009075Highly InformativeDirect
Biological Process (BP)innate immune response0.00000000000090340.000000000831Highly InformativeDirect
Biological Process (BP)chromosome organization00Highly InformativeDirect
Biological Process (BP)nuclear chromosome segregation0.000042940.000005399Highly InformativeDirect
Biological Process (BP)meiotic cell cycle process0.000064360.001448Highly InformativeInherited
Biological Process (BP)regulation of gene expression, epigenetic0.001070.01252Highly InformativeInherited
Biological Process (BP)DNA replication0.00038030.04672Highly InformativeInherited
Biological Process (BP)transcription from RNA polymerase II promoter0.0026340.0000000103Highly InformativeInherited
Biological Process (BP)DNA recombination0.20390.2744Highly InformativeInherited
Molecular Function (MF)binding0.0000000023460.00000003315Least InformativeDirect
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.91661Moderately InformativeInherited
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding0.000000000000075290InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.027850.07273InformativeInherited
Molecular Function (MF)macromolecular complex binding0.0006280.03366InformativeInherited
Molecular Function (MF)transcription factor activity, transcription factor binding0.000066240.000002285Highly InformativeDirect
Molecular Function (MF)chromatin binding0.0000000000002110.0000002638Highly InformativeDirect
Molecular Function (MF)DNA-directed DNA polymerase activity0.0000095570.00008363Highly InformativeDirect
Molecular Function (MF)transcription regulatory region DNA binding0.0001350.000118Highly InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00.000000000003402Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00044450.0000002974Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)protein complex10.003672Least InformativeInherited
Cellular Component (CC)extracellular region part0.0000000000011420.000000001183Moderately InformativeDirect
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00Moderately InformativeDirect
Cellular Component (CC)transferase complex00Moderately InformativeDirect
Cellular Component (CC)DNA-directed RNA polymerase complex0.000093450InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)lipid particle0.000000014670.00000000005653InformativeDirect
Cellular Component (CC)nucleoplasm part0.00000041390InformativeDirect
Cellular Component (CC)nuclear chromosome00.0000000007374Highly InformativeDirect
Cellular Component (CC)chromatin00Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.000000074150.0000000002093Highly InformativeDirect
Cellular Component (CC)replisome0.096770.014Highly 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 0.0000001273 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0007498 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000009 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000008164 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000000003102 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000002272 Least Informative Direct
Biological Process (BP) biological regulation 0.2006 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.01151 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.08126 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.9221 Least Informative Inherited
Biological Process (BP) immune system process 0.0002832 Moderately Informative Direct
Biological Process (BP) response to stress 0.00003888 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.000006987 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000002498 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00001255 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000000008151 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.0009207 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0000002711 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00002837 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3604 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.01617 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.868 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 component assembly 0.009785 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.96 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.515 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) signaling 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1025 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1085 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.0000345 Informative Direct
Biological Process (BP) immune response 0.000000003919 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.000000249 Informative Direct
Biological Process (BP) response to bacterium 0.000000000000007239 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.00001748 Informative Direct
Biological Process (BP) cell cycle process 0.0003602 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.00000000001213 Informative Direct
Biological Process (BP) defense response to other organism 0.0000000000005337 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.3749 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.0238 Informative Inherited
Biological Process (BP) organelle assembly 0.2545 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.1091 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) organelle fission 0.01624 Informative Inherited
Biological Process (BP) single organism reproductive process 0.01125 Informative Inherited
Biological Process (BP) protein localization to organelle 0.01753 Informative Inherited
Biological Process (BP) DNA metabolic process 0.00415 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.7044 Informative Inherited
Biological Process (BP) response to acid chemical 0.1237 Informative Inherited
Biological Process (BP) cellular response to lipid 0.2208 Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.0000000103 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0 Highly Informative Direct
Biological Process (BP) gene silencing 0.0009115 Highly Informative Direct
Biological Process (BP) histone modification 0.000000002621 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00000000011 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.0000000000009075 Highly Informative Direct
Biological Process (BP) innate immune response 0.000000000831 Highly Informative Direct
Biological Process (BP) chromosome organization 0 Highly Informative Direct
Biological Process (BP) nuclear chromosome segregation 0.000005399 Highly Informative Direct
Biological Process (BP) response to alcohol 0.1315 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle process 0.001448 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.01252 Highly Informative Inherited
Biological Process (BP) DNA replication 0.04672 Highly Informative Inherited
Biological Process (BP) cellular response to acid chemical 0.008436 Highly Informative Inherited
Biological Process (BP) hormone-mediated signaling pathway 0.002147 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.2744 Highly Informative Inherited
Molecular Function (MF) binding 0.00000003315 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) protein binding 0.8965 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 0.003761 Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.07273 Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.03366 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.000002285 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0000002638 Highly Informative Direct
Molecular Function (MF) DNA-directed DNA polymerase activity 0.00008363 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000004587 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.000002473 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000118 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000000003402 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000002974 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 0.003672 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.000000001183 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) DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) lipid particle 0.00000000005653 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) extracellular organelle 0.01283 Informative Inherited
Cellular Component (CC) nuclear chromosome 0.0000000007374 Highly Informative Direct
Cellular Component (CC) kinetochore 0.0001735 Highly Informative Direct
Cellular Component (CC) chromatin 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.0000000002093 Highly Informative Direct
Cellular Component (CC) replisome 0.014 Highly Informative Inherited
Cellular Component (CC) condensed chromosome 1 Highly Informative Inherited
Cellular Component (CC) peptidase complex 0.002215 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 phenotype0.1392Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo morphology0.02059Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000000000003217Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000002367Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.02374Least InformativeInherited
Worm Phenotype (WP)cell development variant0.04909Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.6294Least 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)cell component morphology variant0.000002067Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.000005376Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.00004993Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.00009256Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000256Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0004687Moderately InformativeDirect
Worm Phenotype (WP)movement variant0.06409Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.07153Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.13Moderately 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 variant0.000000000001009InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.000000232InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.000001628InformativeDirect
Worm Phenotype (WP)protruding vulva0.000008703InformativeDirect
Worm Phenotype (WP)mitosis variant0.03661InformativeInherited
Worm Phenotype (WP)body width variant0.2606InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2682InformativeInherited
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)pharyngeal development variant0.00000000000002388Highly InformativeDirect
Worm Phenotype (WP)lysosome-related organelle morphology variant0.0000000000004555Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.000000000002229Highly InformativeDirect
Worm Phenotype (WP)dauer lifespan extended0.000000000002784Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant0.0000005635Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.000004257Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)cell cycle progression0.00233InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase0.0000862Highly InformativeDirect
Yeast Phenotype (YP)budding0.000221Highly 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)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0.008058Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.008827Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0009914InformativeDirect
Xenopus ANatomical entity (XAN)oocyte0.0000758Highly 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 regulation0.000000000005741Moderately InformativeDirect
Biological processDNA damage0.000001026Moderately InformativeDirect
Biological processCell cycle0.3209Moderately InformativeInherited
Biological processMitosis0.00000001391InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentKinetochore0Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.4905Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationAntimicrobial0.0000000006029InformativeDirect
Post-translational modificationChromatin regulator0.000000004078InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.0001162InformativeDirect
Post-translational modificationAntibiotic0.0000000000003639Highly 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 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 ]