SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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)chromatin00.0000000000005334Highly 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 0.000000000000001931 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000007002 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000009547 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000002132 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000006346 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000001614 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00003496 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.07155 Least Informative Inherited
Biological Process (BP) developmental process 0.00256 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.001251 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 0.000000000000003741 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000001429 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000000002617 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000001368 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000002969 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000004323 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000124 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0005359 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 0.3559 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) single-organism developmental process 0.6733 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 0.6351 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9666 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 0.6962 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.04668 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 0.000000000000001931 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.00000000000004604 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000000000006223 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000000000005773 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.00000000002025 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000005333 Informative Direct
Biological Process (BP) DNA metabolic process 0.0000001106 Informative Direct
Biological Process (BP) sexual reproduction 0.000002998 Informative Direct
Biological Process (BP) reproductive system development 0.0000341 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.00003538 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0002004 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.0003859 Informative Direct
Biological Process (BP) regulation of organelle organization 0.3962 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.6764 Informative Inherited
Biological Process (BP) epithelium development 0.01358 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 0.008017 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.3386 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.00497 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.00467 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.9478 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.002352 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.003277 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.001199 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.001501 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1806 Informative Inherited
Biological Process (BP) cell cycle process 0.2522 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 0.000000000002575 Highly Informative Direct
Biological Process (BP) gene silencing 0.00000000001049 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000001595 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000003278 Highly Informative Direct
Biological Process (BP) gonad development 0.0000006931 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00004409 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.0000495 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0.00006539 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.0003625 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0.0005719 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0008085 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0009048 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.001404 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.1855 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.9248 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.001952 Highly Informative Inherited
Biological Process (BP) protein deacylation 0.004371 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.002781 Highly Informative Inherited
Biological Process (BP) mitosis 0.01739 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.08307 Least Informative Inherited
Molecular Function (MF) transferase activity 0.003402 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.000000002518 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00001147 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.0000000006013 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.000000001916 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.000002411 Informative Direct
Molecular Function (MF) DNA binding 0.0146 Informative Inherited
Molecular Function (MF) RNA binding 0.7584 Informative Inherited
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000000673 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.000000008594 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000006262 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.0004066 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 0.0005877 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.005437 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000009004 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000000003369 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.008384 Informative Inherited
Cellular Component (CC) chromatin 0.0000000000005334 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0000000000005371 Highly Informative Direct
Cellular Component (CC) spindle 0.211 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 variegation0.00008559InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation0.00002123Highly InformativeDirect
Fly Phenotype (FP)suppressor of variegation0.00003341Highly 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)Hydrolases0.001149Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0007785Moderately 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 processDifferentiation0.000000000000279Moderately InformativeDirect
Biological processDNA damage0.00001143Moderately InformativeDirect
Biological processBiological rhythms0.0000000000001453InformativeDirect
Biological processWnt signaling pathway0.000001248InformativeDirect
Biological processGrowth regulation0.00000000001072Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
DomainRepeat0.0000000000001031Least InformativeDirect
DomainZinc-finger0.000000004268Moderately InformativeDirect
DomainANK repeat0.0003136InformativeDirect
Molecular functionZinc0.00000000007644Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0000005138InformativeDirect
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 modificationAcyltransferase0.0000002151InformativeDirect
Post-translational modificationMethyltransferase0.00003823InformativeDirect
Post-translational modificationAcetylation0.00000000001709Least InformativeDirect
Post-translational modificationPhosphoprotein0.000002683Least 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 ]