chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of human SUV39H1, a histone lysine methyltransferase (HMT) which catalyzes di- and tri-methylation of lysine 9 of histone H3 (H3K9me2/3), leading to heterochromatin formation and gene silencing. H3K9me2/3 represents a specific mark for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3, and/or CBX5) proteins to methylated histones. SUV39H1 mainly functions in heterochromatin regions. The human SUV39H1/2, histone H3K9 methyltransferases, are the mammalian homologs of Drosophila Su(var)3-9 and Schizosaccharomyces pombe Clr4. SUV39H1 contains a chromodomain at its N-terminus and a SET domain at its C-terminus. Although the SET domain performs the catalytic activity, the chromodomain of SUV39H1 is essential for the catalytic activity of SUV39H1. 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 8131952   43 YEVEYLCDYKVAK-VEYYLVKWKGWPDSTNTWEPLRNLRCPQLLRQFSD 90
Cdd:cd18639   1 YEVEYLCDYKKIReQEYYLVKWKGYPDSENTWEPRQNLKCSRLLKQFHK 49

chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of human SUV39H1, a histone lysine methyltransferase (HMT) which catalyzes di- and tri-methylation of lysine 9 of histone H3 (H3K9me2/3), leading to heterochromatin formation and gene silencing. H3K9me2/3 represents a specific mark for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3, and/or CBX5) proteins to methylated histones. SUV39H1 mainly functions in heterochromatin regions. The human SUV39H1/2, histone H3K9 methyltransferases, are the mammalian homologs of Drosophila Su(var)3-9 and Schizosaccharomyces pombe Clr4. SUV39H1 contains a chromodomain at its N-terminus and a SET domain at its C-terminus. Although the SET domain performs the catalytic activity, the chromodomain of SUV39H1 is essential for the catalytic activity of SUV39H1. 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 8131952   43 YEVEYLCDYKVAK-VEYYLVKWKGWPDSTNTWEPLRNLRCPQLLRQFSD 90
Cdd:cd18639   1 YEVEYLCDYKKIReQEYYLVKWKGYPDSENTWEPRQNLKCSRLLKQFHK 49

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 8131952     43 YEVEYLCDYKVAK--VEYYLVKWKGWPDSTNTWEPLRNL-RCPQLLRQFSD 90
Cdd:pfam00385   1 YEVERILDHRKDKggKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKD 51

Chromatin organization modifier domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 8131952      43 YEVEYLCDYKVAK--VEYYLVKWKGWPDSTNTWEPLRNL-RCPQLLRQFSDDKK 93
Cdd:smart00298   2 YEVEKILDHRWKKkgELEYLVKWKGYSYSEDTWEPEENLlNCSKKLDNYKKKER 55

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  159 DFYYINEYRPAPGISINSEATFGCSCT-DCFF--DKCCPAEAGVVLAYNKKQQIKIQPGTPIYECNSRCRCGPECPNRIV 235
Cdd:cd10542   2 NFQYINDYIPGDGVKIPEDFLVGCECTeDCHNnnPTCCPAESGVKFAYDKQGRLRLPPGTPIYECNSRCKCGPDCPNRVV 81

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 8131952  236 QKGTQYSLCIFKTNNGCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd10542  82 QRGRKVPLCIFRTSNGRGWGVKTLEDIKKGTFVMEYVGE 120

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  158 LDFYYINEYRPAPGISINSEATF--GCSCTD-CFFDKC-CPAEAGVVLAYNKKQQIK-IQPGTPIYECNSRCRCGPECPN 232
Cdd:cd10538   1 PSFTYIKDNIVGKNVQPFSNIIDsvGCKCKDdCLDSKCaCAAESDGIFAYTKNGLLRlNNSPPPIFECNSKCSCDDDCKN 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 8131952  233 RIVQKGTQYSLCIFKTNNGcGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd10538  81 RVVQRGLQARLQVFRTSKK-GWGVRSLEFIPKGSFVCEYVGE 121

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  159 DFYYINEYRPAPGISInSEATF--GCSCT---DCFFDKC-C---------PAEAGVVLAYNKKQQIK-------IQPGTP 216
Cdd:cd19473   2 DFRFIEKSILGEGVEL-ADEEFrsGCECTddeDCMYSGClClqdvdpdddRDPGKKKNAYHSSGAKKgclrghmLNSRLP 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 8131952  217 IYECNSRCRCGPECPNRIVQKGTQYSLCIFKTNNGCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd19473  81 IYECHEGCACSDDCPNRVVERGRKVPLQIFRTSDGRGWGVRSTVDIKRGQFVDCYVGE 138

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  158 LDFYYINEYRPAPGISIN-SEATF-GCSC--TDCFFDKCcPAEAGVVLAYNKKQQIKIQPGT---PIYECNSRCRCGPEC 230
Cdd:cd10544   1 PDFQYTPENVPGPGADTDpNEITFpGCDCktSSCEPETC-SCLRKYGPNYDDDGCLLDFDGKysgPVFECNSMCKCSESC 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 8131952  231 PNRIVQKGTQYSLCIFKTNNGcGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd10544  80 QNRVVQNGLQFKLQVFKTPKK-GWGLRTLEFIPKGRFVCEYAGE 122

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  158 LDFYYINEYRPAPGIS-INSEATFGCSCTD---CFFD-----KCCPAEAGVVLAYNKKQQIKIQPGTPIYECNSRCRCGP 228
Cdd:cd20073   1 IDFEFITSYRYGLGIEpPDPLFISGCSCSKlggCDLNnpgscQCLEDSNEKSFAYDEYGRVRANTGSIIYECNENCDCGI 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 8131952  229 ECPNRIVQKGTQYSLCIFKTNNGcGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd20073  81 NCPNRVVQRGRKLPLEIFKTKHK-GWGLRCPRFIKAGTFIGVYLGE 125

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  159 DFYYINEYRPAPGISINSEATF--GCSCTD-CFFDKCCPAEAGVVLAYNK-----KQQIKIQPGTpIYECNSRCRCGPEC 230
Cdd:cd10543   2 DFLYVTENCETSPLNIDRNITSlqTCSCRDdCSSDNCVCGRLSVRCWYDKegrllPDFNKLDPPL-IFECNRACSCWRNC 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 8131952  231 PNRIVQKGTQYSLCIFKTnNGCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd10543  81 RNRVVQNGIRYRLQLFRT-RGMGWGVRALQDIPKGTFVCEYIGE 123

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 8131952   43 YEVEYLCDYKVAK-VEYYLVKWKGWPDSTNTWEPLRNLR-CPQLLRQF 88
Cdd:cd00024   1 YEVEKILDHRVRKgKLEYLVKWKGYPPEENTWEPEENLTnAPELIKEY 48

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 8131952     43 YEVEYLCDYKVAK--VEYYLVKWKGWPDSTNTWEPLRNL-RCPQLLRQFSD 90
Cdd:pfam00385   1 YEVERILDHRKDKggKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKD 51

N-terminal to some SET domains; A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952     145 IFVENTVDLEGPPLDFYYINEYRPAPGISINSEATF--GCSCT-DCFFDK--CCPAEAGVVLAYNKKQQIKIQPGTPIYE 219
Cdd:smart00468  13 VPLVNEVDEDPPPPDFEYISEYIYGQGVPIDRSPSPlvGCSCSgDCSSSNkcECARKNGGEFAYELNGGLRLKRKPLIYE 92

                   ....*.
gi 8131952     220 CNSRCR 225
Cdd:smart00468  93 CNSRCS 98

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  182 CSCTD-CFFDKCCPAEAGVVLAYNKKQQI-----KIQPGTpIYECNSRCRCGPECPNRIVQKGTQYSLCIFKTNNgCGWG 255
Cdd:cd10535  27 CVCIDdCSSSNCMCGQLSMRCWYDKDGRLlpefnMAEPPL-IFECNHACSCWRNCRNRVVQNGLRARLQLYRTRD-MGWG 104

                        90
                ....*....|....*....
gi 8131952  256 VKTLVKIKRMSFVMEYVGE 274
Cdd:cd10535 105 VRSLQDIPPGTFVCEYVGE 123

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8131952  170 PGISiNSEATFGCSCTDCFFD--KC------------CPAEAGVVLAYNKKQQIKIQPGTPIYECNSRCRCGPE-CPNRI 234
Cdd:cd10523  23 FDIS-NGAFVDSCDCTDGCIDilKCaclqltarafskSESSPSKGGRGYKYKRLQEPIPSGLYECNVSCKCNRMlCQNRV 101

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 8131952  235 VQKGTQYSLCIFKTNNGcGWGVKTLVKIKRMSFVMEYVG 273
Cdd:cd10523 102 VQHGLQVRLQVFKTEKK-GWGVRCLDDIDKGTFVCIYAG 139

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 8131952   43 YEVEYLCDYKV--AKVEYYLvKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18652   2 FVVEKVLDRRVvnGKVEYFL-KWKGFTDADNTWEPEENLDCPELIEAF 48

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 8131952   43 YEVEYLCDYKVAK--VEYyLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18650   2 YVVEKVLDRRVVKgkVEY-LLKWKGFSDEDNTWEPEENLDCPDLIAEF 48

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 8131952   43 YEVEYLCDYKVAKVEY-YLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18978   4 YEVEKIINHRGEKNRRkYLVKWKGYDDTDNSWVTQEDFNDKDMIDEY 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 8131952   43 YEVEYLCDYKVAKV--EYYLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18960   2 FVVERILDKRLGRNggEEFLIKWQGFPESDSSWEPRENLQCDEMLEEF 49

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 8131952   43 YEVEYLCDYKV--AKVEYyLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18644   4 YAAEKILKKRVrkGKVEY-LVKWKGWSNKHNTWEPEENILDRRLIEIF 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
                ....*....|....*....|....*....|....*
gi 8131952   54 AKVEYyLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18627  14 GKVEY-LVKWKGWSQKYNTWEPEENILDPRLLAAF 47

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
                ....*....|....*....|....*....|....*....|....*....
gi 8131952   41 NNYEVE-YLCDYKVAKVEYYLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18962   2 GHYVVEaIVNDVLIDGKHMYEVKWEGYPSDHNNWVAEWDLNDKEILRKY 50

chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 4 (CBX4), 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. In addition to a chromodomain with H3K27me3-binding activity, Cbx4 contains two SUMO-interacting motifs responsible for its small ubiquitin-related modifier (SUMO) E3 ligase activity. 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. CBX4 may serve as a tumor suppressor in colorectal carcinoma, and has been shown to be an oncogene in osteosarcoma and breast cancer.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 8131952   59 YLVKWKGWPDSTNTWEPLRNLRCPQLLRQFSDDKK 93
Cdd:cd18645  21 YLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRER 55

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 8131952   59 YLVKWKGWPDSTNTWEPLRNL-RCPQLLRQF 88
Cdd:cd18640  20 YLVKWENRSHHENTWEPMANLeRCKYLLQMF 50

chromodomain of Drosophila melanogaster Rhino, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of Drosophila melanogaster Rhino (also known as heterochromatin protein 1-like), and similar proteins. Rhino is a female-specific protein that affects chromosome structure and egg polarity that is required for germline PIWI-interacting RNA (piRNA) production. In Drosophila the RDC (rhino, deadlock, and cutoff) complex, composed of rhino, the protein deadlock (Del) and the Rai1-like transcription termination cofactor cutoff (Cuff) binds to chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is anchored to H3K9me3-marked chromatin in part via the H3K9me3-binding activity of Rhino, and is required for transcription of piRNA precursors. 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 8131952   59 YLVKWKGWPDSTNTWEPLRNL-RCPQLLRQF 88
Cdd:cd18630  19 VLVKWSGFPNENNTWEPLENLgNCMKLVADY 49

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 8131952   54 AKVEYyLVKWKGWPDSTNTWEPLRNLRCPQLLRQFSDDKK 93
Cdd:cd18646  18 GKVEY-LVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 56

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).

                        10        20
                ....*....|....*....|....*....
gi 8131952  246 FKTNNgCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd19174   5 FRTED-KGWGVRTKEPIKAGQFIIEYVGE 32

chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Magnaporthe grisea putative retrotransposon polyprotein which includes 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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 8131952   43 YEVEYLCDYKVAKVEY----YLVKWKGWPDStnTWEPLRNLRCPQLLRQF 88
Cdd:cd18971   1 YEVEEILAARRRRIRGkgreVLVKWVGYAEP--TWEPLDNLADTAALDRF 48

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
                ....*....|....*....|....*....|
gi 8131952   59 YLVKWKGWPDSTNTWEPLRNLRCPQLLRQF 88
Cdd:cd18649  22 YLVKWKGWSQKYSTWEPEENILDARLLAAF 51

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues

                           10        20        30
                   ....*....|....*....|....*....|....
gi 8131952     241 YSLCIFKTNnGCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:smart00317   1 NKLEVFKSP-GKGWGVRATEDIPKGEFIGEYVGE 33

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.

                        10        20        30
                ....*....|....*....|....*....|
gi 8131952  245 IFKTNNGcGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd19173   6 PFKTGDR-GWGLRTKRDIKKGDFVIEYVGE 34

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
                ....*....|....*....|....*....|....*
gi 8131952   59 YLVKWKGWPDSTNTWEPLRNLRCPQLLRQFSDDKK 93
Cdd:cd18648  21 YLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKER 55

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).

                        10        20        30
                ....*....|....*....|....*....|
gi 8131952  245 IFKTNNgCGWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd19175   4 LVKTEK-CGWGLVADEDINAGEFIIEYVGE 32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.

                        10        20
                ....*....|....*....|..
gi 8131952  253 GWGVKTLVKIKRMSFVMEYVGE 274
Cdd:cd19172  13 GWGLRAAEDLPKGTFVIEYVGE 34

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        40
                ....*....|....*....|....*....|....*....|
gi 8131952   43 YEVEYLCDYKV---AKVEYYlVKWKGWPDSTNTWEPLRNL 79
Cdd:cd18636   2 YEVEDILADRVnknGINEYY-IKWAGYDWYDNTWEPEQNL 40