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 21355721   8 FVVERIMDKRITSeGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKF 55
Cdd:cd18652   2 FVVEKVLDRRVVN-GKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 48

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma 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. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma 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 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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 21355721   8 FVVERIMDKRITSeGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKF 55
Cdd:cd18652   2 FVVEKVLDRRVVN-GKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 48

chromo shadow domain; 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. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. 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. 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21355721  85 LELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQKM 135
Cdd:cd00034   1 LEVEKILGATDSDGELMFLIKWKGSDEADLVPAKEANEKCPQIVIQFYESR 51

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 21355721    89 EIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:pfam01393   3 KIIGATDTRGELMFLMKWKNGEEADLVPSKEANQKCPQKVIKFYEE 48

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma 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. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma 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 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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 21355721   8 FVVERIMDKRITSeGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKF 55
Cdd:cd18652   2 FVVEKVLDRRVVN-GKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 48

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 21355721     8 FVVERIMDKRITSEGKVEYYIKWRGYTSADNTWEPEENC-DCPNLIQKFEES 58
Cdd:pfam00385   1 YEVERILDHRKDKGGKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKDR 52

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
                ....*....|....*....|....*....|....*....|....*...
gi 21355721   8 FVVERIMDKRITsEGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKF 55
Cdd:cd18650   2 YVVEKVLDRRVV-KGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEF 48

chromo shadow domain; 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. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. 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. 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21355721  85 LELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQKM 135
Cdd:cd00034   1 LEVEKILGATDSDGELMFLIKWKGSDEADLVPAKEANEKCPQIVIQFYESR 51

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 21355721   8 FVVERIMDKRITSEGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKFE 56
Cdd:cd18960   2 FVVERILDKRLGRNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFE 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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 21355721   8 FVVERIMDKRItSEGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKFEE 57
Cdd:cd18627   1 FAAECILKKRI-RKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 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        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21355721   8 FVVE-----RIMDKRITSEGKVEYYIKWRGYTSADNTWEPEENCD-CPNLIQKF 55
Cdd:cd18968   2 YEVEvilaaRVVKDAESRKKGWKYLVKWAGYPDEENTWEPEESFDgCDDLLERF 55

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.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 21355721   8 FVVERIMDKRITSEGKVEYYIKWRGYTSADNTWEPEEN 45
Cdd:cd18636   2 YEVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQN 39

chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 2 (CBX2), 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        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 21355721   5 EPNFVVERIMDKRiTSEGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKFEE 57
Cdd:cd18647   1 EQVFAAECILSKR-LRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 52

chromodomain of M-phase phosphoprotein 8; The chromodomain of M-phase phosphoprotein 8 (MPP8), a component of the RanBPM-containing large protein complex, binds methylated H3K9. This may in turn recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promoting tumor cell motility and invasion. 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 21355721   8 FVVERIMDKRiTSEGKVEYYIKWRGYTSADNTWEPEENC-DCPNLIQKFEE 57
Cdd:cd18633   2 FEVEKILDMK-TEGGKVLYKVRWKGYTSDDDTWEPEVHLeDCKEVLLEFRK 51

chromodomain of fission yeast Swi6, and similar proteins; Fission yeast Swi6 protein is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromeres, telomeres, and the silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. chromodomains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2). CSDs have only been found in proteins that also possess a chromodomain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 21355721   8 FVVERIMDKRITSEGK-VEYYIKWRGYTSA-DNTWEPEENCD-CPNLIQKFEE 57
Cdd:cd18637   2 YVVEKILKHRMARKGGgYEYLLKWEGYDDPsDNTWSSEADCAgCKDLIEAYWE 54

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 21355721  80 GYERGLELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:cd18654   1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEE 55

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 21355721    89 EIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:pfam01393   3 KIIGATDTRGELMFLMKWKNGEEADLVPSKEANQKCPQKVIKFYEE 48

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        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21355721   8 FVVERIMDKRITSE---GKVEYYIKWRGYTSADNTWEPEENC-DCPNLIQKFEE 57
Cdd:cd18964   1 FFVERIIGRRPSARdgpGKFLWLVKWDGYPIEDATWEPPENLgEHAKLIEDFEK 54

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        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 21355721   8 FVVERIMDKRITSEGKV-EYYIKWRGYTSADNTWEPEENCD-CPNLIQKFEE 57
Cdd:cd18640   1 EPVEKIVAKRFNPRKKTwEYLVKWENRSHHENTWEPMANLErCKYLLQMFEK 52

chromo shadow domain of heterochromatin protein 1 homolog alpha; Chromo shadow domain (CSD) 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. 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, 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 21355721  80 GYERGLELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:cd18655   1 GFERGLEPEKIIGATDSCGDLMFLMKWKDSDEADLVLAKEANVKCPQIVIAFYEE 55

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        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21355721   8 FVVERIMDKRiTSEGKVEYYIKWRGYTSADNTWEPEENCD--CPNLIQKFE 56
Cdd:cd18976   1 YIVESLLDRR-KVRGQVQYLVKWRGFPRSEATWEPREELMrrCAELVAAYD 50

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 21355721  80 GYERGLELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:cd18656   1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEE 55

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        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 21355721   5 EPNFVVERIMDKRItSEGKVEYYIKWRGYTSADNTWEPEENCDCPNLIQKFEE 57
Cdd:cd18646   2 EQVFAVESIRKKRV-RKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEE 53

chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. 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 21355721  10 VERIMDKRItSEGKVEYYIKWRGYTSADNTWEPEENC-DCPNLIQKFE 56
Cdd:cd18974   3 VEEIVDEKM-IDDELHYLVKWKGWPAEYNQWEPEDDMeNAPKAIQSYE 49

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 21355721  84 GLELAEIVGATDVTGDIKYLVRWQFCDEFDLVPSAQIVEKDPQMLIDYFQK 134
Cdd:cd18658   1 GLEAEKILGASDSNGGLTFLIQFKGVDQAEMVPASVANVKIPQMVIKFYEE 51

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        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21355721   8 FVVERIMDKRI-----TSEGKVEYYIKWRGYTSADNTWEPEENC-DCPNLIQKF 55
Cdd:cd18635   2 FEVEKLVGICYgdpkkTGERGLYFKVRWKGYGPEEDTWEPIEGLsNCPEKIKEF 55

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
                ....*....|....*....|....*....|....*...
gi 21355721   8 FVVERIMDKRITSeGKVEYYIKWRGYTSADNTWEPEEN 45
Cdd:cd18965   1 YIIEALLKKRQFN-RKLEYLVKWHGLPESENTWEREKD 37

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, 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 CHD3 and CHD4, and yeast protein CHD1. 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. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. 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 21355721  10 VERIMDKRITSEGKVEYYIKWRGYTSADNTWEPEENcDCPNLIQKFEE 57
Cdd:cd18662   6 IHRIINHRVDKDGNTWYLVKWRDLPYDQSTWESEDD-DIPDYEKHIQE 52

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
                ....*....|....*....|....*....|....*
gi 21355721   8 FVVERIMDKRITSEGKvEYYIKWRGYTSADNTWEP 42
Cdd:cd18970   1 FFVERILDERRRGRGW-QYLVRWLGYGPSDDSWLP 34

repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as yeast protein CHD1. 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.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 21355721   9 VVERIMDKRITSEG----KVEYYIKWRGYTSADNTWE 41
Cdd:cd18664   4 VVERIIASQRASLEdgtsQLQYLVKWRRLNYDECTWE 40

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 21355721   9 VVERIMDKR-ITSEGKVEYYIKWrgYTSADNTWEPEENCDcPNLIQKFE 56
Cdd:cd18628   5 VAESVIGKRvGDDGKTIEYLVKW--TDMSDATWEPQDNVD-STLVLLYQ 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.

                        10        20
                ....*....|....*....|....
gi 21355721  21 EGKVEYYIKWRGYTSADNTWEPEE 44
Cdd:cd18666  44 ETEIQYLIKWKGWSHIHNTWESEE 67