SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (538) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,470 15,105 35
Proteins 11,817 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)
Molecular Function (MF)binding00Least InformativeDirect
Molecular Function (MF)chromatin binding00InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)chromatin00.0000000000003375Highly 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) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.00000000000001086 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000007593 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000009568 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000002148 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000006393 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000001632 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00003685 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0724 Least Informative Inherited
Biological Process (BP) developmental process 0.002576 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.001202 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 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) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000000000001938 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000000001953 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000005424 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000001443 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000003334 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000004372 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000001279 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0005908 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.348 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9653 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.6963 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.000000000000001938 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.00000000000004773 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000000000005099 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000000000004747 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.00000000002271 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000005916 Informative Direct
Biological Process (BP) DNA metabolic process 0.0000001054 Informative Direct
Biological Process (BP) sexual reproduction 0.000003464 Informative Direct
Biological Process (BP) reproductive system development 0.00003401 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.00003541 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0001851 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.0003582 Informative Direct
Biological Process (BP) epithelium development 0.01396 Informative Inherited
Biological Process (BP) negative regulation of developmental process 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) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.007903 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.4082 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.3468 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.005046 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004743 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.9481 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.002396 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.003313 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.001523 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.0471 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.181 Informative Inherited
Biological Process (BP) cell cycle process 0.2507 Informative Inherited
Biological Process (BP) peptidyl-lysine modification 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) internal protein amino acid acetylation 0 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.00000000000224 Highly Informative Direct
Biological Process (BP) gene silencing 0.00000000001117 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000001755 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000002864 Highly Informative Direct
Biological Process (BP) gonad development 0.0000006857 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00004023 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.00005041 Highly Informative Direct
Biological Process (BP) purine ribonucleoside monophosphate metabolic process 0.000119 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.0003566 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.0005826 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.0006291 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0008225 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0009198 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 0.0009642 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.001453 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.1855 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.9318 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.002388 Highly Informative Inherited
Biological Process (BP) protein deacylation 0.004555 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.002722 Highly Informative Inherited
Biological Process (BP) mitosis 0.01709 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.08242 Least Informative Inherited
Molecular Function (MF) transferase activity 0.003383 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00001105 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.0000000005889 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.000000001971 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00000265 Informative Direct
Molecular Function (MF) DNA binding 0.01571 Informative Inherited
Molecular Function (MF) RNA binding 0.7457 Informative Inherited
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000009077 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.000000009584 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000005774 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.00006141 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 0.0006206 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.005626 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000007957 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000000003238 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.008268 Informative Inherited
Cellular Component (CC) chromatin 0.0000000000003375 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0000000000007463 Highly Informative Direct
Cellular Component (CC) spindle 0.2117 Highly Informative Inherited

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)organism environmental stimulus response variant0.07005Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.8729Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.01405Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.2632Moderately InformativeInherited
Worm Phenotype (WP)somatic gonad development variant0.0002128InformativeDirect
Worm Phenotype (WP)organism stress response variant0.001625InformativeInherited
Worm Phenotype (WP)vulva development variant0.01119InformativeInherited
Worm Phenotype (WP)VPC competence variant0.1666InformativeInherited
Worm Phenotype (WP)organism UV hypersensitive0.00000001098Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.000001828Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7496Highly 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 variegation0.00008548InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation0.00002121Highly InformativeDirect
Fly Phenotype (FP)suppressor of variegation0.00003337Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA 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)Hydrolases0.001139Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0007604Moderately 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 processDifferentiation0.0000000000003135Moderately InformativeDirect
Biological processDNA damage0.00001141Moderately InformativeDirect
Biological processBiological rhythms0.0000000000005202InformativeDirect
Biological processWnt signaling pathway0.000001245InformativeDirect
Biological processGrowth regulation0.0000000000107Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat0.0000000000001082Least InformativeDirect
DomainZinc-finger0.000000004157Moderately InformativeDirect
DomainANK repeat0.0003105InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionZinc0.00000000009332Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0000005121InformativeDirect
Post-translational modificationTransferase0.0005518Least InformativeDirect
Post-translational modificationHydrolase0.006781Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationAcyltransferase0.0000002211InformativeDirect
Post-translational modificationMethyltransferase0.00003816InformativeDirect
Post-translational modificationAcetylation0.0000000000172Least InformativeDirect
Post-translational modificationPhosphoprotein0.000002785Least InformativeDirect
Post-translational modificationIsopeptide bond0.0007274Moderately 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) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]