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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 (544) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,635 15,105 35
Proteins 11,932 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)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)chromatin00.00000000005632Highly 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 component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) biological regulation 0.0000000000000109 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000003423 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0008562 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.003318 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.00541 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.002523 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.02257 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.001149 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000000000000001945 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0000000000000109 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000000000007551 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000000000002877 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00000000002026 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000002637 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000001183 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00000004728 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0000004936 Moderately Informative Direct
Biological Process (BP) immune system process 0.00007076 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0002517 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) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.6358 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.8341 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.946 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.000000000000001945 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000000000000003764 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000000003764 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0000000000007579 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.0000000001445 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000000002058 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000000002396 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.0000002585 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.7544 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.01079 Informative Inherited
Biological Process (BP) cell development 0.01277 Informative Inherited
Biological Process (BP) reproductive system development 0.005142 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.1077 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) regulation of growth 0.3445 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) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) embryo development 0.07723 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.02697 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.8197 Informative Inherited
Biological Process (BP) immune response 0.6382 Informative Inherited
Biological Process (BP) generation of neurons 0.1951 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.2842 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.6419 Informative Inherited
Biological Process (BP) behavior 0.1546 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) post-embryonic development 0.1418 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) tissue development 0.494 Informative Inherited
Biological Process (BP) locomotion 0.4433 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 1 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.000000000000007367 Highly Informative Direct
Biological Process (BP) gene silencing 0.0000000000001185 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.0000000000001311 Highly Informative Direct
Biological Process (BP) protein alkylation 0.0000000000002117 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.0000000000004998 Highly Informative Direct
Biological Process (BP) germ cell development 0.0000000002706 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.0000000005577 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000005478 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.000000923 Highly Informative Direct
Biological Process (BP) antimicrobial humoral response 0.00002426 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.00004837 Highly Informative Direct
Biological Process (BP) pattern specification process 0.0006947 Highly Informative Direct
Biological Process (BP) sex differentiation 0.1788 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.127 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.05107 Highly Informative Inherited
Biological Process (BP) positive regulation of growth 0.001112 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.001098 Highly Informative Inherited
Biological Process (BP) neuron development 1 Highly Informative Inherited
Biological Process (BP) chromatin assembly or disassembly 0.1856 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.7433 Highly Informative Inherited
Biological Process (BP) cell maturation 0.0453 Highly Informative Inherited
Biological Process (BP) neurological system process 0.02075 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.03284 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.2531 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) appendage development 0.04021 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.01383 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000000002503 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.04105 Least Informative Inherited
Molecular Function (MF) transferase activity 0.088 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000002902 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.000004262 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000003558 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00004983 Informative Direct
Molecular Function (MF) DNA binding 0.0001263 Informative Direct
Molecular Function (MF) ATPase activity 0.01105 Informative Inherited
Molecular Function (MF) RNA binding 0.941 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 8.425e-16 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000003771 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.2569 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 1 Highly Informative Inherited
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.1091 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.001756 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.000000000007131 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000005088 Least Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.0002699 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.000000000001492 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.00002648 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.007189 Informative Inherited
Cellular Component (CC) chromatin 0.00000000005632 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 chromosome part 0.000000002754 Highly Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 0.0000006794 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.0002039 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

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 integument0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.0077Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.06557Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.1871Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.843Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.001015Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.004623Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny0.01579Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.09064Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.1263Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.2541Moderately InformativeInherited
Worm Phenotype (WP)maintenance of gene silencing variant0.00000006318InformativeDirect
Worm Phenotype (WP)protein modification variant0.0006679InformativeDirect
Worm Phenotype (WP)gonad development variant0.2395InformativeInherited
Worm Phenotype (WP)vulva cell fate specification variant0.533InformativeInherited
Worm Phenotype (WP)organism UV hypersensitive0.00000002467Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.000004143Highly InformativeDirect
Worm Phenotype (WP)apoptosis increased0.0007497Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7062Highly 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 variegation0.0001259InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation0.00002594Highly InformativeDirect
Fly Phenotype (FP)suppressor of variegation0.00004879Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) 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 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)Hydrolases0.001982Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0002385Moderately 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 processDifferentiation0.000000000001111Moderately InformativeDirect
Biological processDNA damage0.000008079Moderately InformativeDirect
Biological processBiological rhythms0.000000000006385InformativeDirect
Biological processWnt signaling pathway0.000001432InformativeDirect
Biological processGrowth regulation0.00000000003001Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat0.00000000001842Least InformativeDirect
DomainZinc-finger0.000000000000206Moderately InformativeDirect
DomainANK repeat0.000662InformativeDirect
Molecular functionZinc0.00000000000005746Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0000004671InformativeDirect
Post-translational modificationTransferase0.008465Least InformativeInherited
Post-translational modificationHydrolase0.01484Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationAcyltransferase0.0000002977InformativeDirect
Post-translational modificationMethyltransferase0.000007839InformativeDirect
Post-translational modificationAcetylation0.0000000003353Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000003413Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000000004901Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000003428Moderately 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) · Human Phenotype (HP) · 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) · Human Phenotype (HP) · 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 ]