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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 (664) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 28,154 0 82
Proteins 27,725 0 81


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

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)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the head0.1792Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.3248Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.06976Moderately InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)embryo phenotype0.1611Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo morphology0.02043Highly 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 variant8.886e-16Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000000000005556Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000001673Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.00002921Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.001461Least InformativeInherited
Worm Phenotype (WP)cell development variant0.05244Least 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 variant0.000006725Moderately InformativeDirect
Worm Phenotype (WP)cell component morphology variant0.00001014Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.00005542Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0001015Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.04785Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.05532Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.07539Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant1Moderately 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 variant0.000000000001019InformativeDirect
Worm Phenotype (WP)organism pathogen response variant0.000000004714InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.000001545InformativeDirect
Worm Phenotype (WP)protruding vulva0.000009195InformativeDirect
Worm Phenotype (WP)mitosis variant0.02099InformativeInherited
Worm Phenotype (WP)body width variant0.2549InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2653InformativeInherited
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)no induction of antimicrobial peptide expression after infection0Highly InformativeDirect
Worm Phenotype (WP)lysosome-related organelle morphology variant0.00000000000001948Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant0.0000000000000283Highly InformativeDirect
Worm Phenotype (WP)dauer lifespan extended0.000000000003289Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.00000000000888Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant0.0000007134Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.000003922Highly InformativeDirect
Worm Phenotype (WP)alimentary system morphology variant0.01627Highly 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 progression0.002351InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase0.00008405Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002194Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0.4123Least InformativeInherited
Fly Anatomy (FA)embryo0.634Least InformativeInherited
Fly Anatomy (FA)late embryo0.4382Moderately InformativeInherited
Fly Anatomy (FA)embryonic/larval fat body0.0001165Highly InformativeDirect

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 system0.01848Least InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.0001052Highly 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 regulation0.000000000008696Moderately InformativeDirect
Biological processDNA damage0.0000004777Moderately InformativeDirect
Biological processCell cycle0.3767Moderately InformativeInherited
Biological processMitosis0.00000002414InformativeDirect
Biological processDNA repair0.0000001879InformativeDirect
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 modificationNucleotidyltransferase0.488Moderately InformativeInherited
Post-translational modificationAntimicrobial0.0000000005897InformativeDirect
Post-translational modificationChromatin regulator0.00000002656InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.000228InformativeDirect
Post-translational modificationDNA-directed DNA polymerase2.247e-16Highly InformativeDirect
Post-translational modificationAntibiotic0.0000000000000413Highly 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 modificationHydroxylation0InformativeDirect
Post-translational modificationADP-ribosylation0.00000000000004377InformativeDirect
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 · 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

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 · 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 ]