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 (470)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	13,101	10,124	35
Proteins	10,803	8,052	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 term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Molecular Function (MF)	binding	0	0	Least Informative	Direct
Molecular Function (MF)	chromatin binding	0	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0	0	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0	0	Least Informative	Direct
Cellular Component (CC)	chromosome	0	0	Informative	Direct
Cellular Component (CC)	chromatin	0	1.948e-11	Highly Informative	Direct

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)	single-organism cellular process	3.303e-13	Least Informative	Direct
Biological Process (BP)	regulation of metabolic process	6.78e-13	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	4.316e-12	Least Informative	Direct
Biological Process (BP)	protein metabolic process	4.339e-06	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	5.283e-06	Least Informative	Direct
Biological Process (BP)	cellular aromatic compound metabolic process	1.249e-05	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	5.095e-05	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	5.22e-05	Least Informative	Direct
Biological Process (BP)	multicellular organismal process	0.1041	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	0.7245	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1	Least Informative	Inherited
Biological Process (BP)	developmental process	0.004511	Least Informative	Inherited
Biological Process (BP)	negative regulation of metabolic process	0	Moderately Informative	Direct
Biological Process (BP)	organelle organization	0	Moderately Informative	Direct
Biological Process (BP)	negative regulation of cellular process	1.158e-14	Moderately Informative	Direct
Biological Process (BP)	regulation of cellular metabolic process	1.515e-09	Moderately Informative	Direct
Biological Process (BP)	regulation of gene expression	7.618e-09	Moderately Informative	Direct
Biological Process (BP)	regulation of biosynthetic process	9.63e-08	Moderately Informative	Direct
Biological Process (BP)	reproduction	1.64e-07	Moderately Informative	Direct
Biological Process (BP)	regulation of nitrogen compound metabolic process	1.003e-06	Moderately Informative	Direct
Biological Process (BP)	cellular protein modification process	1.182e-06	Moderately Informative	Direct
Biological Process (BP)	cell differentiation	5.558e-06	Moderately Informative	Direct
Biological Process (BP)	macromolecular complex subunit organization	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of multicellular organismal process	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)	regulation of developmental process	1	Moderately Informative	Inherited
Biological Process (BP)	RNA metabolic process	0.6824	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular component organization	1	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	0.9174	Moderately Informative	Inherited
Biological Process (BP)	anatomical structure morphogenesis	0.8563	Moderately Informative	Inherited
Biological Process (BP)	cellular response to stress	0.002078	Moderately Informative	Inherited
Biological Process (BP)	negative regulation of biosynthetic process	0	Informative	Direct
Biological Process (BP)	chromosome organization	0	Informative	Direct
Biological Process (BP)	negative regulation of cellular metabolic process	0	Informative	Direct
Biological Process (BP)	negative regulation of nitrogen compound metabolic process	0	Informative	Direct
Biological Process (BP)	peptidyl-amino acid modification	2.787e-10	Informative	Direct
Biological Process (BP)	cellular process involved in reproduction	2.639e-09	Informative	Direct
Biological Process (BP)	developmental process involved in reproduction	5.621e-08	Informative	Direct
Biological Process (BP)	single organism reproductive process	2.82e-06	Informative	Direct
Biological Process (BP)	response to DNA damage stimulus	8.226e-05	Informative	Direct
Biological Process (BP)	sexual reproduction	0.0002127	Informative	Direct
Biological Process (BP)	DNA metabolic process	0.0005891	Informative	Direct
Biological Process (BP)	multicellular organismal reproductive process	0.0009835	Informative	Direct
Biological Process (BP)	negative regulation of developmental process	1	Informative	Inherited
Biological Process (BP)	negative regulation of response to stimulus	0.7306	Informative	Inherited
Biological Process (BP)	negative regulation of signaling	0.7566	Informative	Inherited
Biological Process (BP)	negative regulation of cell communication	0.8932	Informative	Inherited
Biological Process (BP)	regulation of organelle organization	0.01017	Informative	Inherited
Biological Process (BP)	anatomical structure formation involved in morphogenesis	0.2011	Informative	Inherited
Biological Process (BP)	peptidyl-lysine modification	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of RNA metabolic process	0	Highly Informative	Direct
Biological Process (BP)	protein methylation	0	Highly Informative	Direct
Biological Process (BP)	histone modification	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of cellular macromolecule biosynthetic process	0	Highly Informative	Direct
Biological Process (BP)	internal protein amino acid acetylation	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of gene expression	1.152e-13	Highly Informative	Direct
Biological Process (BP)	regulation of gene expression, epigenetic	1.247e-08	Highly Informative	Direct
Biological Process (BP)	DNA packaging	6.203e-06	Highly Informative	Direct
Biological Process (BP)	pattern specification process	9.478e-05	Highly Informative	Direct
Biological Process (BP)	nuclear division	0.0001558	Highly Informative	Direct
Biological Process (BP)	regulation of Ras protein signal transduction	0.0006109	Highly Informative	Direct
Biological Process (BP)	protein deacylation	0.0008707	Highly Informative	Direct
Biological Process (BP)	negative regulation of multicellular organismal process	0.1403	Highly Informative	Inherited
Biological Process (BP)	negative regulation of signal transduction	0.002705	Highly Informative	Inherited
Biological Process (BP)	female gamete generation	0.08378	Highly Informative	Inherited
Molecular Function (MF)	binding	0	Least Informative	Direct
Molecular Function (MF)	transferase activity	0.0005091	Least Informative	Direct
Molecular Function (MF)	hydrolase activity	0.3164	Least Informative	Inherited
Molecular Function (MF)	protein binding	0.5591	Moderately Informative	Inherited
Molecular Function (MF)	transferase activity, transferring acyl groups	2.635e-08	Informative	Direct
Molecular Function (MF)	nucleoside-triphosphatase activity	4.825e-08	Informative	Direct
Molecular Function (MF)	transferase activity, transferring one-carbon groups	2.294e-06	Informative	Direct
Molecular Function (MF)	chromatin binding	0	Highly Informative	Direct
Molecular Function (MF)	acetyltransferase activity	0	Highly Informative	Direct
Molecular Function (MF)	methyltransferase activity	3.534e-09	Highly Informative	Direct
Molecular Function (MF)	transcription factor binding	2.409e-05	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0	Least Informative	Direct
Cellular Component (CC)	protein complex	0.001609	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.05718	Least Informative	Inherited
Cellular Component (CC)	nuclear part	0	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	2.717e-08	Moderately Informative	Direct
Cellular Component (CC)	cytoskeleton	1	Moderately Informative	Inherited
Cellular Component (CC)	chromosome	0	Informative	Direct
Cellular Component (CC)	nucleoplasm part	1.408e-07	Informative	Direct
Cellular Component (CC)	microtubule cytoskeleton	0.001319	Informative	Inherited
Cellular Component (CC)	chromatin	1.948e-11	Highly Informative	Direct
Cellular Component (CC)	histone deacetylase complex	0	Highly Informative	Direct
Cellular Component (CC)	nuclear chromosome part	9.669e-12	Highly Informative	Direct
Cellular Component (CC)	microtubule organizing center	0.0002189	Highly Informative	Direct
Cellular Component (CC)	spindle	0.1536	Highly Informative	Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on acid anhydrides	1.708e-12	Least Informative	Direct
Enzyme Commission (EC)	Transferring one-carbon groups	0.0007915	Least Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	0	Moderately Informative	Direct
Enzyme Commission (EC)	Transferring groups other than amino-acyl groups	0	Moderately Informative	Direct
Enzyme Commission (EC)	Methyltransferases	3.649e-10	Moderately Informative	Direct
Enzyme Commission (EC)	Histone-lysine N-methyltransferase	0	Informative	Direct
Enzyme Commission (EC)	Histone acetyltransferase	0	Informative	Direct
Enzyme Commission (EC)	DNA (cytosine-5-)-methyltransferase	1.535e-09	Highly Informative	Direct

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	tumorigenesis	0.004226	Moderately Informative	Inherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	organism environmental stimulus response variant	0.07005	Least Informative	Inherited
Worm Phenotype (WP)	organism metabolism processing variant	0.8729	Least Informative	Inherited
Worm Phenotype (WP)	organ system development variant	0.01405	Moderately Informative	Inherited
Worm Phenotype (WP)	pattern of transgene expression variant	0.2632	Moderately Informative	Inherited
Worm Phenotype (WP)	somatic gonad development variant	0.0002128	Informative	Direct
Worm Phenotype (WP)	organism stress response variant	0.001625	Informative	Inherited
Worm Phenotype (WP)	vulva development variant	0.01119	Informative	Inherited
Worm Phenotype (WP)	VPC competence variant	0.1666	Informative	Inherited
Worm Phenotype (WP)	organism UV hypersensitive	1.098e-08	Highly Informative	Direct
Worm Phenotype (WP)	ectopic expression transgene	1.828e-06	Highly Informative	Direct
Worm Phenotype (WP)	transgene silencing variant	0.7496	Highly Informative	Inherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)

	YP term	FDR (all)	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	resistance to chemicals	0	Least Informative	Direct

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)

	FP term	FDR (all)	SDFP level	Annotation (direct or inherited)
Fly Phenotype (FP)	modifier of variegation	0.001283	Informative	Inherited
Fly Phenotype (FP)	suppressor of variegation	0.000662	Highly Informative	Direct

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	shoot apex	0	Least Informative	Direct
Plant ANatomical entity (PAN)	shoot internode	0	Least Informative	Direct
Plant ANatomical entity (PAN)	plant embryo	0	Least Informative	Direct
Plant ANatomical entity (PAN)	seed	0	Least Informative	Direct
Plant ANatomical entity (PAN)	stem	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Hydrolases	0.01802	Least Informative	Inherited
Enzyme Commission (EC)	Acyltransferases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	1.3e-12	Moderately Informative	Direct
Enzyme Commission (EC)	Transferring one-carbon groups	0.0008082	Moderately Informative	Direct
Enzyme Commission (EC)	Histone-lysine N-methyltransferase	0	Informative	Direct
Enzyme Commission (EC)	DNA helicase	0	Informative	Direct
Enzyme Commission (EC)	Histone acetyltransferase	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Transcription regulation	0	Moderately Informative	Direct
Biological process	Differentiation	1.722e-10	Moderately Informative	Direct
Biological process	DNA damage	6.489e-06	Moderately Informative	Direct
Biological process	Wnt signaling pathway	9.119e-07	Informative	Direct
Biological process	Growth regulation	2.235e-12	Highly Informative	Direct
Cellular component	Nucleus	0	Least Informative	Direct
Cellular component	Chromosome	0	Informative	Direct
Cellular component	Centromere	0	Highly Informative	Direct
Coding sequence diversity	Alternative splicing	0.0003754	Least Informative	Direct
Domain	Repeat	2.218e-14	Least Informative	Direct
Domain	ANK repeat	9.982e-05	Informative	Direct
Molecular function	Zinc	0.0005651	Least Informative	Direct
Molecular function	Metal-binding	1	Least Informative	Inherited
Molecular function	Nucleotide-binding	1	Least Informative	Inherited
Molecular function	DNA-binding	0	Moderately Informative	Direct
Molecular function	Zinc-finger	4.182e-11	Moderately Informative	Direct
Molecular function	Helicase	0	Informative	Direct
Molecular function	S-adenosyl-L-methionine	5.443e-08	Informative	Direct
Post-translational modification	Transferase	0.0002736	Least Informative	Direct
Post-translational modification	Activator	0	Moderately Informative	Direct
Post-translational modification	Repressor	0	Moderately Informative	Direct
Post-translational modification	Chromatin regulator	0	Informative	Direct
Post-translational modification	Acyltransferase	4.378e-08	Informative	Direct
Post-translational modification	Methyltransferase	0.0001499	Informative	Direct
Post-translational modification	Phosphoprotein	7.081e-08	Least Informative	Direct
Post-translational modification	Acetylation	8.882e-16	Moderately Informative	Direct
Post-translational modification	Isopeptide bond	0.0004865	Moderately Informative	Direct

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 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.

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Chromo domain-like superfamily