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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 (540) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,532 15,105 35
Proteins 11,860 12,118 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)
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)chromatin00Highly 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) biological regulation 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000009493 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00002478 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.01195 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.07288 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9454 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.009657 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02317 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000001746 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.00000000000007407 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000000000002973 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000000002272 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.00000000008681 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.000000002747 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0000001822 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.00001186 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.9343 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 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) RNA metabolic process 0.7561 Moderately Informative Inherited
Biological Process (BP) response to stress 0.01582 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1949 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) single organism reproductive process 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00000000000001582 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000000000004534 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.00000000000005973 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.0000000000005136 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00000000004468 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.000000001924 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.000002209 Informative Direct
Biological Process (BP) reproductive system development 0.000391 Informative Direct
Biological Process (BP) regulation of organelle organization 0.7289 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.8421 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.01803 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) epithelium development 0.003656 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.1186 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) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) generation of neurons 0.6118 Informative Inherited
Biological Process (BP) regulation of growth 0.3517 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.2354 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.6198 Informative Inherited
Biological Process (BP) behavior 0.1197 Informative Inherited
Biological Process (BP) system process 0.8201 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.9485 Informative Inherited
Biological Process (BP) post-embryonic development 0.08053 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.6034 Informative Inherited
Biological Process (BP) locomotion 0.4435 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 1 Informative Inherited
Biological Process (BP) cell development 0.00123 Informative Inherited
Biological Process (BP) immune response 0.2916 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 0 Highly Informative Direct
Biological Process (BP) chromosome organization 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) gene silencing 0.000000000000007239 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.0000000000002696 Highly Informative Direct
Biological Process (BP) germ cell development 0.00000000008114 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000006836 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.00000001166 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000005216 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.000001384 Highly Informative Direct
Biological Process (BP) pattern specification process 0.0001443 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0002334 Highly Informative Direct
Biological Process (BP) sex differentiation 0.164 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.1363 Highly Informative Inherited
Biological Process (BP) positive regulation of growth 0.001542 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.04931 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.001031 Highly Informative Inherited
Biological Process (BP) neuron development 1 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.6804 Highly Informative Inherited
Biological Process (BP) cell maturation 0.02061 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.02138 Highly Informative Inherited
Biological Process (BP) appendage development 0.04017 Highly Informative Inherited
Biological Process (BP) instar larval or pupal morphogenesis 0.003134 Highly Informative Inherited
Biological Process (BP) metamorphosis 0.01156 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.2106 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) cell migration 0.3658 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000000001549 Least Informative Direct
Molecular Function (MF) transferase activity 0.05021 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.03064 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000003238 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000493 Moderately Informative Direct
Molecular Function (MF) protein binding 0.3422 Moderately Informative Inherited
Molecular Function (MF) macromolecular complex binding 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000002464 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00004288 Informative Direct
Molecular Function (MF) DNA binding 0.0002076 Informative Direct
Molecular Function (MF) ATPase activity 0.01266 Informative Inherited
Molecular Function (MF) RNA binding 0.8714 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000001631 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.9251 Highly Informative Inherited
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.09906 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.001219 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000002081 Least Informative Direct
Cellular Component (CC) protein complex 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 0.0007511 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000000000001217 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.00002768 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.00002992 Informative Direct
Cellular Component (CC) chromatin 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) histone deacetylase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 0.00000001755 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.007526Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.05171Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.1601Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.8155Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.001005Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.0033Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny0.01575Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.08889Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.2518Moderately InformativeInherited
Worm Phenotype (WP)maintenance of gene silencing variant0.00000005989InformativeDirect
Worm Phenotype (WP)vulva development variant0.000002396InformativeDirect
Worm Phenotype (WP)VPC competence variant0.00001607InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000002243Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.000003705Highly InformativeDirect
Worm Phenotype (WP)apoptosis increased0.0007096Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7161Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)modifier of variegation0.00006657InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation0.00001761Highly InformativeDirect
Fly Phenotype (FP)suppressor of variegation0.00002329Highly InformativeDirect

Document: FP 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)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Moderately 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 system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least 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)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.002159Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides2.466e-16Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0003223Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0.0000000000008101Moderately InformativeDirect
Biological processDNA damage0.000008155Moderately InformativeDirect
Biological processBiological rhythms0.00000000000609InformativeDirect
Biological processWnt signaling pathway0.000001464InformativeDirect
Biological processGrowth regulation0.00000000002458Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat0.00000000001609Least InformativeDirect
DomainZinc-finger0.0000000000001886Moderately InformativeDirect
DomainANK repeat0.0006504InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionZinc0.00000000000000917Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0000002181InformativeDirect
Post-translational modificationTransferase0.001193Least InformativeInherited
Post-translational modificationHydrolase0.004413Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationAcyltransferase0.0000003282InformativeDirect
Post-translational modificationMethyltransferase0.00001026InformativeDirect
Post-translational modificationAcetylation0.0000000003039Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000003161Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000000004981Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00000238Moderately 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]