chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) 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. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a 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. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564374059 120 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 177
Cdd:cd18654    1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) 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. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a 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. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564374059 120 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 177
Cdd:cd18654    1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58

Chromo Shadow Domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564374059   119 RGFARGLEPERIIGATDSSGELMFLMKWKNsDEADLVPAKEANVKCPQVVISFYEERLTWHS 180
Cdd:smart00300   1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQS 61

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 564374059   27 LDRRVVK-GKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQS 70
Cdd:pfam00385   7 LDHRKDKgGKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKDR 52

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) 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. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a 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. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564374059 120 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 177
Cdd:cd18654    1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58

chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. 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 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. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564374059 120 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 177
Cdd:cd18656    1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 58

Chromo Shadow Domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564374059   119 RGFARGLEPERIIGATDSSGELMFLMKWKNsDEADLVPAKEANVKCPQVVISFYEERLTWHS 180
Cdd:smart00300   1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQS 61

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 564374059  20 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 69
Cdd:cd18650    1 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 50

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
                 ....*....|....*....|....*....|....*....|...
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 69
Cdd:cd18651    8 LDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMK 50

chromo shadow domain of insect heterochromatin protein 1a; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. 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 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. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CSD of Drosophila melanogaster HP1a.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564374059 124 GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERL 176
Cdd:cd18658    1 GLEAEKILGASDSNGGLTFLIQFKGVDQAEMVPASVANVKIPQMVIKFYEERL 53

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
                 ....*....|....*....|....*....|....*....|....
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQ 69
Cdd:cd00024    7 LDHRVRKGKLEYLVKWKGYPPEENTWEPEENLtNAPELIKEYEK 50

chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 69
Cdd:cd18627    7 LKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 49

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 564374059  28 DRRVVKGKVEYLLKWKGFSDEDNTWEPEENLD-CPDLIAEF 67
Cdd:cd18968   15 DAESRKKGWKYLVKWAGYPDEENTWEPEESFDgCDDLLERF 55

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL 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 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEF 67
Cdd:cd18975    7 LNSRLHRGKLQYLIQWKGYPLEEASWELEDNIKNPRLIEEF 47

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. 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 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLD--CPDLIAEF 67
Cdd:cd18976    7 LDRRKVRGQVQYLVKWRGFPRSEATWEPREELMrrCAELVAAY 49

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 564374059  27 LDRRVVK-GKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEF 67
Cdd:cd18960    8 LDKRLGRnGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEF 49

chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins; This subgroup includes the N-terminal CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 (HP1)-like protein from Entamoeba histolytica, and similar proteins. 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
                 ....*....|....*....|....*....|....*....|.
gi 564374059  29 RRVVKGKVEYLLKWKGFSDEDNTWEPEENLD--CPDLIAEF 67
Cdd:cd18638   10 KKTVKGGTEYFVKWKGYSAKENTWETEDNLEksYKEMIDEF 50

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAE 66
Cdd:cd18966    7 LAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKE 46

chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 6 (CBX6), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQK 72
Cdd:cd18648   10 IKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKER 55

chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 8 (CBX8), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, CBX8 for example promotes proliferation while suppressing metastasis, in colorectal carcinoma progression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEF 67
Cdd:cd18649   11 LKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAF 51

chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizopus microsporus putative DDE transposases, and similar proteins. 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 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 69
Cdd:cd18978   10 INHRGEKNRRKYLVKWKGYDDTDNSWVTQEDFNDKDMIDEYEN 52

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564374059  28 DRRVVKGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQ 69
Cdd:cd18964   12 SARDGPGKFLWLVKWDGYPIEDATWEPPENLgEHAKLIEDFEK 54

chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 7 (CBX7), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX7 has been shown to function as a tumor suppressor in lung carcinoma and an oncogene in gastric cancer and lymphoma.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 564374059  29 RRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQK 72
Cdd:cd18646   13 KRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 56

chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier (chromo) domain of DNA (cytosine-5)-methyltransferase chromomethylase 3 (CMT3, EC:2.1.1.37), and similar proteins. CMT3 is primarily a CHG (where H is either A, T or C) methyltransferase and is predominantly expressed in actively replicating cells. The protein is involved in preferentially methylating transposon-related sequences, reducing their mobility. Studies suggest that in order to target DNA methylation, CMT3 associates with H3K9me2-containing nucleosomes through binding of its BAH- and chromo-domains to H3K9me2. 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
                 ....*....|....*....|....*....|....*...
gi 564374059  33 KGKVEYLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQ 69
Cdd:cd18635   20 ERGLYFKVRWKGYGPEEDTWEPIEGLsNCPEKIKEFVQ 57

chromodomain of Drosophila melanogaster chromator chromodomain protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in chromodomain of Drosophila melanogaster chromator (also known as Chriz/Chro) chromodomain protein, and similar proteins. Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. 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
                 ....*....|....*....|....*....|..
gi 564374059  37 EYLLKWKGFSDEDNTWEPEENLD-CPDLIAEF 67
Cdd:cd18640   19 EYLVKWENRSHHENTWEPMANLErCKYLLQMF 50

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.

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gi 564374059  28 DRRVVKGKVE-YLLKWKGFSDEDNTWEPEENL-DCPDLIAEFLQ 69
Cdd:cd18632   10 EKTDRNTAEPlYLVRWKNYSKNHDTWEPAENLsGCQAVLEKWKR 53

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

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gi 564374059  27 LDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL 58
Cdd:cd18965    7 LKKRQFNRKLEYLVKWHGLPESENTWEREKDI 38

chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Moniliophthora perniciosa FA553 putative retrotelement polyprotein, which includes domains in the following order: 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

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                 ....*....|....*....|....*....|....
gi 564374059  37 EYLLKWKGFSDEDNTWEPEENLD-CPDLIAEFLQ 69
Cdd:cd18972   17 QFLVSWLGYDSSHNEWKQKEELEnARELLQDYLK 50

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. 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.

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                 ....*....|....*....|....*.
gi 564374059  33 KGKVEYLLKWKGFSDEDNTWEPEENL 58
Cdd:cd18666   44 ETEIQYLIKWKGWSHIHNTWESEESL 69

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. 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.

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gi 564374059  38 YLLKWKGFSDEDNTWEPEENLDcPDLIAEF 67
Cdd:cd18663   27 YLVKWCSLPYEDSTWELEEDVD-PAKIEEF 55

chromodomain of Caenorhabditis elegans chromodomain protein 4, and similar proteins; CHRomatin Organization Modifier (chromo) domain of Caenorhabditis elegans CEC-4, and similar proteins. CEC-4 is a perinuclear heterochromatin anchor, it mediates the anchoring of H3K9 methylation-bearing chromatin at the nuclear periphery in early to mid-stage embryos. It is necessary for anchoring, but does not affect transcriptional repression. CEC-4 contributes to the efficiency with which muscle differentiation is induced following ectopic expression of the master regulator, HLH-1 (MyoD in mammals). 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.

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                 ....*....|....*....|....*....|....*....|...
gi 564374059  27 LDRRVVKGKVEYLLKWKGFSD-EDNTWEPEENL-DCPDLIAEF 67
Cdd:cd18961    7 LSHRIVNGKPLYLVMWVGYPGpVENSEMWEEDLkNCGELLKAY 49

chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 3 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.

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gi 564374059  27 LDRRVVKG--KVEYLLKWkgFSDEDNTWEPEENLDcPDLIAEF 67
Cdd:cd18628   10 IGKRVGDDgkTIEYLVKW--TDMSDATWEPQDNVD-STLVLLY 49

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

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gi 564374059  38 YLLKWKGFSDEdnTWEPEENLDCPDLIAEF 67
Cdd:cd18967   26 YLTKWEGFPDE--TWEPAESFDDRKILHDY 53

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal 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. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

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gi 564374059  27 LDRRVVKGKVEYLLKWKGFS 46
Cdd:cd18963   10 IKRRVRKGRIEYLVKWKGWA 29