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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18859937 233 WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLA-CDALIEKFMR 281
Cdd:cd00024   1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTnAPELIKEYEK 50

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18859937 233 WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLA-CDALIEKFMR 281
Cdd:cd00024   1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTnAPELIKEYEK 50

Chromatin organization modifier domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 18859937    233 WEVEKILDHVATKEGD-MFKIRWKKYGPKDDSWEPSKNLA-CDALIEKFMRKQA 284
Cdd:smart00298   2 YEVEKILDHRWKKKGElEYLVKWKGYSYSEDTWEPEENLLnCSKKLDNYKKKER 55

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18859937 233 WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLA-CDALIEKFMR 281
Cdd:cd00024   1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTnAPELIKEYEK 50

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; uncharacterized subgroup; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 18859937 235 VEKILDHVATKEG-DMFKIRWKKYGPKDDSWEPSKNLACDALIEKFMR 281
Cdd:cd18960   4 VERILDKRLGRNGgEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFEK 51

chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Trichosporon asahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins. 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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 18859937 230 EKQWEVEKILDHVAT---KEGDMFKIRWKKYGPKDDSWEPSKNL 270
Cdd:cd18980   1 QPEYEVEAILDHKVDrryRDPNFYLVRWRGYGPSHDSWEPTSAL 44

chromodomain of Hypsizygus marmoreus TY3B-I_0 protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Hypsizygus marmoreus TY3B-I_0 protein, a putative TY3/gypsy retrotransposon polyprotein, and similar proteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and 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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 18859937 233 WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLA-CDAL 275
Cdd:cd18970   1 FFVERILDERRRGRGWQYLVRWLGYGPSDDSWLPRRELEeCEAL 44

chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18859937 232 QWEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLACDALIEKFMR 281
Cdd:cd18651   1 EYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMK 50

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18859937 232 QWEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLACDALIEKFMR 281
Cdd:cd18650   1 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 50

chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 18859937 233 WEVEKILDHVATKEGDM-FKIRWKKYGPKDDSWEPSKNL-ACDALIEKFMR 281
Cdd:cd18634   2 YEVERIVDKRKNKKGKTeYLVRWKGYDSEDDTWEPEQHLlNCEEFIHDFNR 52

N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of cryptic loci regulator 4 (Clr4), a histone H3 lysine methyltransferase which targets H3K9. Clr4 regulates silencing and switching at the mating-type loci and affects chromatin structure at centromeres. Clr4 is a catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18859937 233 WEVEKILD---HVATKEgDMFKIRWKKYGPKDDSWEPSKNLA-CDALIEKFMRKQ 283
Cdd:cd18632   2 YEVEKIVDektDRNTAE-PLYLVRWKNYSKNHDTWEPAENLSgCQAVLEKWKRKK 55

chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and 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.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 18859937 233 WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNL 270
Cdd:cd18973   1 YVVEAILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENL 38

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18859937 232 QWEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLACDALIEKFM 280
Cdd:cd18631   1 EYVVEKVLDRRVVKGKVEYLLKWKGYPDEDNTWEPEENLDCPDLIAEFE 49

chromodomain of a putative Coemansia reversa NRRL 1564 methyltransferase, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Coemansia reversa NRRL 1564 SET (Su(var)3-9, enhancer-of-zeste, trithorax) domain-containing protein, and similar proteins. The SU(VAR)3-9 protein is the main chromocenter-specific histone H3-K9 methyltransferase (HMTase) in Drosophila where it plays a role in heterochromatic gene silencing. 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 18859937 230 EKQWEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLACDALIEKFMR 281
Cdd:cd18962   1 EGHYVVEAIVNDVLIDGKHMYEVKWEGYPSDHNNWVAEWDLNDKEILRKYNK 52

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18859937 235 VEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNLACDALIEKFMRKQ 283
Cdd:cd18644   6 AEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIFERTN 54

chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Rhizoctonia solani AG-3 Rhs1AP, a putative Ty3/Gypsy polyprotein/retrotransposon which includes a protease, a reverse transcriptase, a ribonuclease H, and an integrase domain, in that order, with a chromodomain at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and 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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 18859937 232 QWEVEKILDHVATKEGD----MFKIRWKKYGPKDDSWEPSKNL 270
Cdd:cd18977   3 EYEVEKIVGEKWKKRKNrrvkLYKVRFKGYGPEEDEWLTKEEL 45