SUPERFAMILY 1.75 HMM library and genome assignments server


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 (655) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,761 39,243 82
Proteins 27,324 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 aromatic compound metabolic process3.724e-090Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process8.697e-061.355e-11Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process5.945e-093.594e-10Least InformativeDirect
Biological Process (BP)heterocycle metabolic process3.083e-090Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis4.2e-141.467e-11Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process1.021e-071.772e-14Least InformativeDirect
Biological Process (BP)regulation of metabolic process0.16162.431e-05Least InformativeInherited
Biological Process (BP)response to stimulus0.092031Least InformativeInherited
Biological Process (BP)localization11Least InformativeInherited
Biological Process (BP)regulation of cellular process0.82960.264Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.91133.262e-05Least InformativeInherited
Biological Process (BP)single-organism cellular process9.334e-070.01942Least InformativeInherited
Biological Process (BP)organelle organization00Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process2.527e-058.97e-09Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00021291.735e-12Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process9.614e-054.718e-05Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00020992.781e-10Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.060910.001131Moderately InformativeInherited
Biological Process (BP)multi-organism process0.017110.1738Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.78661Moderately InformativeInherited
Biological Process (BP)cellular localization11Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.00012510.006762Moderately InformativeInherited
Biological Process (BP)immune system process0.40691Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.50941Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.75591.213e-08Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.75886.672e-12Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.57134.035e-12Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.69852.236e-12Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.85415.212e-10Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0087880Moderately InformativeInherited
Biological Process (BP)gene expression0.7855.978e-08Moderately InformativeInherited
Biological Process (BP)reproduction0.0057180.2821Moderately InformativeInherited
Biological Process (BP)DNA metabolic process01.122e-10InformativeDirect
Biological Process (BP)transcription, DNA-dependent6.428e-050InformativeDirect
Biological Process (BP)response to DNA damage stimulus3.418e-076.309e-07InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly00InformativeDirect
Biological Process (BP)chromosome organization00InformativeDirect
Biological Process (BP)organelle assembly0.52680.3707InformativeInherited
Biological Process (BP)protein localization to organelle0.057220.08283InformativeInherited
Biological Process (BP)response to other organism0.12130.7283InformativeInherited
Biological Process (BP)defense response0.81550.7505InformativeInherited
Biological Process (BP)immune response0.33370.9901InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.013340.001783InformativeInherited
Biological Process (BP)cell cycle process0.07240.1053InformativeInherited
Biological Process (BP)cellular process involved in reproduction1.128e-050.05035InformativeInherited
Biological Process (BP)internal protein amino acid acetylation1.076e-062.319e-12Highly InformativeDirect
Biological Process (BP)chromosome segregation4.556e-062.061e-12Highly InformativeDirect
Biological Process (BP)histone modification2.411e-058.055e-07Highly InformativeDirect
Biological Process (BP)peptidyl-lysine modification2.944e-056.169e-10Highly InformativeDirect
Biological Process (BP)defense response to bacterium5.399e-050.000131Highly InformativeDirect
Biological Process (BP)DNA replication0.019490.5636Highly InformativeInherited
Biological Process (BP)humoral immune response0.0035810.01309Highly InformativeInherited
Biological Process (BP)transcription from RNA polymerase II promoter0.0068152.086e-05Highly InformativeInherited
Biological Process (BP)innate immune response0.30370.5177Highly InformativeInherited
Biological Process (BP)meiosis0.0028880.01184Highly InformativeInherited
Biological Process (BP)DNA recombination11Highly InformativeInherited
Molecular Function (MF)binding1.771e-112.079e-10Least InformativeDirect
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.89571Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity00InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)chromatin binding9.193e-070.0001269InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.019540.0405InformativeInherited
Molecular Function (MF)protein binding transcription factor activity0.00014922.913e-08Highly InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity00Highly InformativeDirect
Molecular Function (MF)DNA polymerase activity1.513e-059.918e-05Highly InformativeDirect
Molecular Function (MF)transcription regulatory region DNA binding2.781e-081.178e-07Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle2.126e-089.619e-05Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.033320.003169Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00Moderately InformativeDirect
Cellular Component (CC)vesicle11Moderately InformativeInherited
Cellular Component (CC)extracellular region part0.00095510.009559Moderately InformativeInherited
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)nucleoplasm part1.925e-053.092e-15InformativeDirect
Cellular Component (CC)extracellular membrane-bounded organelle0.10130.02861InformativeInherited
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex0.98344.251e-10InformativeInherited
Cellular Component (CC)chromatin6.453e-071.85e-05Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex3.761e-088.212e-12Highly InformativeDirect
Cellular Component (CC)nuclear chromosome part1.104e-080.0001554Highly InformativeDirect

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 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.355e-11 Least Informative Direct
Biological Process (BP) biosynthetic process 3.262e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 2.431e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.594e-10 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1.467e-11 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.772e-14 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.264 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01942 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) gene expression 5.978e-08 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 1.934e-06 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 8.97e-09 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1.213e-08 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 6.672e-12 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1.735e-12 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 4.035e-12 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 4.718e-05 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.781e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 2.236e-12 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 5.212e-10 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.001131 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1738 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 response to stress 0.006762 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.2821 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 1.122e-10 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 6.309e-07 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) organelle assembly 0.3707 Informative Inherited
Biological Process (BP) protein localization to organelle 0.08283 Informative Inherited
Biological Process (BP) response to other organism 0.7283 Informative Inherited
Biological Process (BP) defense response 0.7505 Informative Inherited
Biological Process (BP) immune response 0.9901 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.001783 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.05035 Informative Inherited
Biological Process (BP) cell cycle process 0.1053 Informative Inherited
Biological Process (BP) RNA processing 1 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1232 Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 2.086e-05 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 2.319e-12 Highly Informative Direct
Biological Process (BP) chromosome segregation 2.061e-12 Highly Informative Direct
Biological Process (BP) histone modification 8.055e-07 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 6.169e-10 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.000131 Highly Informative Direct
Biological Process (BP) DNA replication 0.5636 Highly Informative Inherited
Biological Process (BP) humoral immune response 0.01309 Highly Informative Inherited
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.06213 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.002747 Highly Informative Inherited
Biological Process (BP) innate immune response 0.5177 Highly Informative Inherited
Biological Process (BP) meiosis 0.01184 Highly Informative Inherited
Biological Process (BP) DNA recombination 1 Highly Informative Inherited
Biological Process (BP) RNA splicing 0.0877 Highly Informative Inherited
Biological Process (BP) mitosis 0.1368 Highly Informative Inherited
Molecular Function (MF) binding 2.079e-10 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) enzyme regulator activity 0.48 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) chromatin binding 0.0001269 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.099 Informative Inherited
Molecular Function (MF) GTPase regulator activity 0.03123 Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.0405 Informative Inherited
Molecular Function (MF) protein binding transcription factor activity 2.913e-08 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0006566 Highly Informative Direct
Molecular Function (MF) transcription factor binding 4.346e-10 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 9.918e-05 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 1.178e-07 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.001783 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.003148 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 9.619e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.003169 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.009559 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 3.092e-15 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 4.251e-10 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.02861 Informative Inherited
Cellular Component (CC) kinetochore 3.722e-05 Highly Informative Direct
Cellular Component (CC) chromatin 1.85e-05 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 8.212e-12 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0001554 Highly Informative Direct

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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo development0.05625InformativeInherited
Mammalian Phenotype (MP)abnormal blastocyst morphology0.007589Highly 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)organism environmental stimulus response variant0.5346Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant3.072e-11Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant5.892e-05Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0002031Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.012Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.01602Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.4618Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant7.995e-13InformativeDirect
Worm Phenotype (WP)alimentary system development variant2.643e-07InformativeDirect
Worm Phenotype (WP)protruding vulva3.745e-05InformativeDirect
Worm Phenotype (WP)cell corpse number variant0.005489InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.01066InformativeInherited
Worm Phenotype (WP)organism stress response variant0.08471InformativeInherited
Worm Phenotype (WP)body width variant0.2544InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2832InformativeInherited
Worm Phenotype (WP)body elongation variant0Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant1.717e-14Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest2.499e-13Highly InformativeDirect
Worm Phenotype (WP)stress induced lethality increased1.048e-07Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant2.574e-06Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant1.192e-05Highly InformativeDirect
Worm Phenotype (WP)pathogen susceptibility increased6.252e-05Highly 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 progression0.002128InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase8.715e-05Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002804Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least 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 system0.2379Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.7048Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8912Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.9364Least InformativeInherited
Plant ANatomical entity (PAN)primordium0.0008924InformativeDirect
Plant ANatomical entity (PAN)root tip0.01274InformativeInherited
Plant ANatomical entity (PAN)lateral root primordium6.482e-06Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root1.515e-05Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex7.867e-05Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.0001122Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.000585Highly InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage2.424e-07InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-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 regulation9.051e-12Moderately InformativeDirect
Biological processDNA damage1.959e-05Moderately InformativeDirect
Biological processCell cycle0.4046Moderately InformativeInherited
Biological processMitosis5.191e-08InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentKinetochore0Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.4814Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationAntimicrobial3.805e-10InformativeDirect
Post-translational modificationChromatin regulator2.493e-09InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.0007047InformativeDirect
Post-translational modificationAntibiotic2.309e-13Highly 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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]