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 (539) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,486 15,105 35
Proteins 11,830 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)binding0.012890Least InformativeInherited
Molecular Function (MF)chromatin binding0.000000000078120InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.67780.0009687Least InformativeInherited
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) regulation of metabolic process 0 Least Informative Direct
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) heterocycle metabolic process 0.0000001018 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000002289 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000006316 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000001789 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00001298 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00004038 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.001649 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.07555 Least Informative Inherited
Biological Process (BP) developmental process 0.00706 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5683 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism organelle organization 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000000000000007248 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000000000009016 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000000001071 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000001752 Moderately Informative Direct
Biological Process (BP) reproductive process 0.0000000001209 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000004138 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000001396 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000007332 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0001554 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0003464 Moderately Informative Direct
Biological Process (BP) organ development 0.652 Moderately Informative Inherited
Biological Process (BP) tissue development 0.1276 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.5094 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 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) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.5406 Moderately Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.000000000000001913 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.000000000000001913 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000000003427 Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.0000000001372 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.000007864 Informative Direct
Biological Process (BP) sexual reproduction 0.0001087 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0005465 Informative Direct
Biological Process (BP) epithelium development 0.000573 Informative Direct
Biological Process (BP) DNA repair 0.0007148 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.6437 Informative Inherited
Biological Process (BP) reproductive structure development 0.00393 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.006701 Informative Inherited
Biological Process (BP) negative regulation of developmental process 1 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.007535 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.4122 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.003384 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.002837 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.9291 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.3524 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.05418 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.009707 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.005725 Informative Inherited
Biological Process (BP) cell division 0.03754 Informative Inherited
Biological Process (BP) cell cycle process 0.1063 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.6063 Informative Inherited
Biological Process (BP) organelle fission 1 Informative Inherited
Biological Process (BP) protein methylation 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0 Highly Informative Direct
Biological Process (BP) gene silencing 0.00000000000009141 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.000000000004288 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.000000002523 Highly Informative Direct
Biological Process (BP) germ cell development 0.00000000412 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000001338 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000002473 Highly Informative Direct
Biological Process (BP) gonad development 0.000001362 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.00003971 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00004893 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.00006135 Highly Informative Direct
Biological Process (BP) negative regulation of chromosome organization 0.0005521 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.0006971 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.0007521 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0009819 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.04556 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.9301 Highly Informative Inherited
Biological Process (BP) columnar/cuboidal epithelial cell differentiation 0.009352 Highly Informative Inherited
Biological Process (BP) protein deacylation 0.004375 Highly Informative Inherited
Biological Process (BP) purine ribonucleotide catabolic process 0.001097 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.004051 Highly Informative Inherited
Biological Process (BP) nuclear division 0.06656 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.06504 Least Informative Inherited
Molecular Function (MF) transferase activity 0.01246 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.000006648 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000004146 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.000000000969 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0000008671 Informative Direct
Molecular Function (MF) DNA binding 0.00144 Informative Inherited
Molecular Function (MF) RNA binding 0.8662 Informative Inherited
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000000005394 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.00000001388 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000007368 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.00007517 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.4358 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 0.0009687 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 0.00000000000006118 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) transferase complex 0.3801 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000000000000158 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.00002204 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.01055 Informative Inherited
Cellular Component (CC) chromatin 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.000000000006145 Highly Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 0.000008613 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.00006405 Highly Informative Direct
Cellular Component (CC) spindle 0.4487 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 ]