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Conserved domains on  [gi|478732990|ref|NP_956106|]
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uncharacterized protein LOC327494 [Danio rerio]

Protein Classification

chromo domain-containing protein( domain architecture ID 10032091)

chromo (chromatin organization modifier) domain-containing protein may bind methylated histone tails; similar to Caenorhabditis elegans cec-3 that specifically recognizes and binds methylated 'Lys-9' of histone H3 (H3K9me)

CATH:  2.40.50.40
Gene Ontology:  GO:0035064|GO:0003682
SCOP:  4000375

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
501-542 4.03e-04

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


:

Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 38.23  E-value: 4.03e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 478732990 501 FPVENILRWRNNKGKNEVRVKWLpctlcG-AKFQNTWEPAESF 542
Cdd:cd00024    1 YEVEKILDHRVRKGKLEYLVKWK-----GyPPEENTWEPEENL 38
 
Name Accession Description Interval E-value
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
501-542 4.03e-04

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 38.23  E-value: 4.03e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 478732990 501 FPVENILRWRNNKGKNEVRVKWLpctlcG-AKFQNTWEPAESF 542
Cdd:cd00024    1 YEVEKILDHRVRKGKLEYLVKWK-----GyPPEENTWEPEENL 38
 
Name Accession Description Interval E-value
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
501-542 4.03e-04

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 38.23  E-value: 4.03e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 478732990 501 FPVENILRWRNNKGKNEVRVKWLpctlcG-AKFQNTWEPAESF 542
Cdd:cd00024    1 YEVEKILDHRVRKGKLEYLVKWK-----GyPPEENTWEPEENL 38
CD_polycomb cd18644
chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG ...
499-540 2.21e-03

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.


Pssm-ID: 349291  Cd Length: 54  Bit Score: 36.29  E-value: 2.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 478732990 499 GVFPVENILRWRNNKGKNEVRVKWLPCTlcgaKFQNTWEPAE 540
Cdd:cd18644    2 LVYAAEKILKKRVRKGKVEYLVKWKGWS----NKHNTWEPEE 39
CD_Chp1_like cd18636
chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin ...
500-544 9.70e-03

chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of chromodomain-containing protein 1 (CHp1), and similar proteins. Chp1 is needed for RNA interference-dependent heterochromatin formation in fission yeast. Chp1 is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions. The chromodomain of the Chp1 component binds the histone H3 lysine 9 methylated tail (H3K9me) and the core of the nucleosome. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349286  Cd Length: 52  Bit Score: 34.73  E-value: 9.70e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 478732990 500 VFPVENILRWRNNK-GKNEVRVKWLPCTlcgaKFQNTWEPAESFPG 544
Cdd:cd18636    1 VYEVEDILADRVNKnGINEYYIKWAGYD----WYDNTWEPEQNLFG 42
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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