SUPERFAMILY 1.75 HMM library and genome assignments server


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)chromatin05.23e-13Highly 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 7.377e-15 Least Informative Direct
Biological Process (BP) single-organism cellular process 3.644e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.662e-07 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 3.717e-07 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 9.732e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.535e-06 Least Informative Direct
Biological Process (BP) protein metabolic process 2.66e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.06256 Least Informative Inherited
Biological Process (BP) developmental process 0.002109 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.001233 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 biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.635e-14 Moderately Informative Direct
Biological Process (BP) reproduction 1.085e-10 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 3.658e-10 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 4.489e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.152e-06 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0004481 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
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 0.3666 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 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) organic cyclic compound catabolic process 0.7529 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9518 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) organ development 0.6941 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.04351 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 4.463e-14 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 5.118e-14 Informative Direct
Biological Process (BP) negative regulation of gene expression 4.926e-13 Informative Direct
Biological Process (BP) developmental process involved in reproduction 2.154e-11 Informative Direct
Biological Process (BP) single organism reproductive process 5.895e-10 Informative Direct
Biological Process (BP) DNA metabolic process 2.42e-07 Informative Direct
Biological Process (BP) sexual reproduction 3.293e-06 Informative Direct
Biological Process (BP) reproductive system development 3.334e-05 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 3.555e-05 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0001841 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.000403 Informative Direct
Biological Process (BP) regulation of organelle organization 0.3882 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.6922 Informative Inherited
Biological Process (BP) epithelium development 0.01321 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 0.007936 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.3385 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.004514 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004202 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 1 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.002068 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.002885 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.001076 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.001327 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1828 Informative Inherited
Biological Process (BP) cell cycle process 0.2577 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 1.849e-12 Highly Informative Direct
Biological Process (BP) gene silencing 1.098e-11 Highly Informative Direct
Biological Process (BP) spermatogenesis 1.411e-08 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 3.086e-08 Highly Informative Direct
Biological Process (BP) gonad development 6.806e-07 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 3.913e-05 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 4.678e-05 Highly Informative Direct
Biological Process (BP) ATP metabolic process 5.869e-05 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.0003707 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0.0005163 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0007297 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0008146 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.001341 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.1887 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.9296 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.001996 Highly Informative Inherited
Biological Process (BP) protein deacylation 0.00443 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.002867 Highly Informative Inherited
Biological Process (BP) mitosis 0.01693 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.08576 Least Informative Inherited
Molecular Function (MF) transferase activity 0.003305 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 2.338e-09 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1.173e-05 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 5.685e-10 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 1.636e-09 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 2.338e-06 Informative Direct
Molecular Function (MF) DNA binding 0.01492 Informative Inherited
Molecular Function (MF) RNA binding 0.7565 Informative Inherited
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 6.29e-09 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 6.894e-09 Highly Informative Direct
Molecular Function (MF) transcription factor binding 6.207e-06 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.0003664 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 0.000597 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.005817 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.423e-12 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 2.372e-10 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.008156 Informative Inherited
Cellular Component (CC) chromatin 5.23e-13 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 4.07e-13 Highly Informative Direct
Cellular Component (CC) spindle 0.2102 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 anhydrides1.708e-12Least 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)Methyltransferases3.649e-10Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)DNA (cytosine-5-)-methyltransferase1.535e-09Highly 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 hypersensitive1.098e-08Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene1.828e-06Highly 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 variegation8.551e-05InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation2.134e-05Highly InformativeDirect
Fly Phenotype (FP)suppressor of variegation3.356e-05Highly 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)Hydrolases0.001069Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0007794Moderately 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 processDifferentiation2.79e-13Moderately InformativeDirect
Biological processDNA damage1.143e-05Moderately InformativeDirect
Biological processBiological rhythms1.453e-13InformativeDirect
Biological processWnt signaling pathway1.248e-06InformativeDirect
Biological processGrowth regulation1.072e-11Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat1.031e-13Least InformativeDirect
DomainZinc-finger4.268e-09Moderately InformativeDirect
DomainANK repeat0.0003136InformativeDirect
Molecular functionZinc7.644e-11Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine5.138e-07InformativeDirect
Post-translational modificationTransferase0.0005535Least InformativeDirect
Post-translational modificationHydrolase0.006481Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationAcyltransferase2.151e-07InformativeDirect
Post-translational modificationMethyltransferase3.823e-05InformativeDirect
Post-translational modificationAcetylation1.709e-11Least InformativeDirect
Post-translational modificationPhosphoprotein2.683e-06Least InformativeDirect
Post-translational modificationIsopeptide bond0.0006872Moderately 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 ]