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Chromo domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   Chromo domain-like [ 54160] (3)
Families:   "Histone-like" proteins from archaea [ 54161]
  Chromo domain [ 54165] (7)
  Chromo barrel domain [ 117157] (3)


Superfamily statistics
Genomes (545) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 14,654 34,257 35
Proteins 11,948 27,086 33


Functional annotation
General category Information
Detailed category DNA replication/repair

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 biogenesis0.00034530Least InformativeDirect
Biological Process (BP)organelle organization0.0000076760Moderately InformativeDirect
Biological Process (BP)chromosome organization0.000000015970InformativeDirect
Molecular Function (MF)binding0.018180.0000000000003504Least InformativeInherited
Molecular Function (MF)chromatin binding0.00000000001780Highly InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)chromatin00.00000000004912Highly 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 0.0006798 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000006497 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000004731 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0005057 Least Informative Direct
Biological Process (BP) biological regulation 0.0000000000001894 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.002184 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.003043 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.003544 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.03456 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) immune system process 0.00001873 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000000000002679 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0000000000408 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000001422 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000002027 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000000009264 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000000000002076 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0004197 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000001079 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0000001375 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.1929 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) RNA metabolic process 0.5399 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.5154 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.8826 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9529 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0000000002107 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000000000000007296 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000000004911 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) hemopoiesis 0.00000000000181 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.000000000000007296 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.00000000000203 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000000003734 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000000002667 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.7531 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.01343 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.1021 Informative Inherited
Biological Process (BP) epithelium development 0.002369 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) regulation of growth 0.367 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) generation of neurons 0.1771 Informative Inherited
Biological Process (BP) embryo development 0.02347 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.02417 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.7762 Informative Inherited
Biological Process (BP) immune response 0.6606 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.2777 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.6415 Informative Inherited
Biological Process (BP) reproductive system development 0.004915 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) behavior 0.1853 Informative Inherited
Biological Process (BP) post-embryonic development 0.1513 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) cell development 0.0161 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 1 Informative Inherited
Biological Process (BP) locomotion 0.2654 Informative Inherited
Biological Process (BP) localization of cell 0.298 Informative Inherited
Biological Process (BP) myeloid cell homeostasis 0.00001498 Highly Informative Direct
Biological Process (BP) germ cell development 0.0000000004215 Highly Informative Direct
Biological Process (BP) protein alkylation 0.0000000000001326 Highly Informative Direct
Biological Process (BP) gene silencing 0.00000000000008258 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) antimicrobial humoral response 0.00002609 Highly Informative Direct
Biological Process (BP) myeloid cell differentiation 0.0005262 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.0000009703 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.0000000009109 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000003337 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.0000000000001264 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.0000000000003114 Highly Informative Direct
Biological Process (BP) embryonic organ development 0.01986 Highly Informative Inherited
Biological Process (BP) nervous system process 0.02978 Highly Informative Inherited
Biological Process (BP) positive regulation of growth 0.001237 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.05149 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.1219 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.001097 Highly Informative Inherited
Biological Process (BP) cell maturation 0.0491 Highly Informative Inherited
Biological Process (BP) neuron development 1 Highly Informative Inherited
Biological Process (BP) anatomical structure maturation 0.001712 Highly Informative Inherited
Biological Process (BP) chromatin assembly or disassembly 0.1667 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.7502 Highly Informative Inherited
Biological Process (BP) sex differentiation 0.1696 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.04077 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.01552 Highly Informative Inherited
Biological Process (BP) appendage development 0.04867 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.1811 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000000003504 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.05391 Least Informative Inherited
Molecular Function (MF) transferase activity 0.1131 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.000005763 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000004632 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0001754 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00004608 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000006852 Informative Direct
Molecular Function (MF) ATPase activity 0.01133 Informative Inherited
Molecular Function (MF) RNA binding 0.9123 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.000000000000003188 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000001067 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.3094 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 1 Highly Informative Inherited
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.1078 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.002161 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000008245 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 0.4176 Least Informative Inherited
Cellular Component (CC) membrane 1 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) transferase complex 0.0000861 Moderately Informative Direct
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.00003024 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000000000451 Informative Direct
Cellular Component (CC) side of membrane 0.02021 Informative Inherited
Cellular Component (CC) neuron projection 0.5674 Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.3894 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.009247 Informative Inherited
Cellular Component (CC) histone deacetylase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 0.0000006419 Highly Informative Direct
Cellular Component (CC) chromatin 0.00000000004912 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.0002513 Highly Informative Direct
Cellular Component (CC) growth cone 0.0002129 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.000000004052 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)Acting on acid anhydrides0.000000000001708Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0007915Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0.0000000003649Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)DNA (cytosine-5-)-methyltransferase0.000000001535Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0.000000000001125Moderately InformativeDirect
Biological processDNA damage0.000007884Moderately InformativeDirect
Biological processBiological rhythms0.000000000006367InformativeDirect
Biological processDNA repair0.0000004572InformativeDirect
Biological processWnt signaling pathway0.000001431InformativeDirect
Biological processGrowth regulation0.00000000003108Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat0.00000000001757Least InformativeDirect
DomainZinc-finger0.0000000000001869Moderately InformativeDirect
DomainANK repeat0.0006505InformativeDirect
Molecular functionZinc0.00000000000008972Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.00000003189InformativeDirect
Post-translational modificationTransferase0.004098Least InformativeInherited
Post-translational modificationHydrolase0.01804Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationAcyltransferase0.0000005625InformativeDirect
Post-translational modificationMethyltransferase0.000001036InformativeDirect
Post-translational modificationAcetylation0.0000000002802Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000002839Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000000004369Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000003261Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 21 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 Chromo domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 21 hidden Markov models representing the Chromo domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]