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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd00024     1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  434 RRPSSLPAHPFDATAAPRSRAAAPSVLRARERLLAKPVKKVKDGEGKGHGPWGSRRGEEEQEEKAVAVVGKRVEPSGKTW 513
Cdd:COG3321    858 RRRVPLPTYPFQREDAAAALLAAALAAALAAAAALGALLLAALAAALAAALLALAAAAAAALALAAAALAALLALVALAA 937

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  514 YRVRWSGGRETEEPLTRLPASLHTPRGPLFAFEHRHPYPPVASFPTLRQAYARARVEGQRMWAAGRGTGRSRLYRMHGAE 593
Cdd:COG3321    938 AAAALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAALALLAAAALLLAAAAA 1017

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  594 EEDERMGKAGGWEGTGWGTGSDSDDEDESSEDEVVVGVQGEREDADDEAGDEAELEMGRSVSMRRLPGTPTSAIVGASAR 673
Cdd:COG3321   1018 AAALLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAAAALALALAALLLLAALAELALAAAALALAAALAAAALAL 1097

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  674 VDVDADGDvdmsGVEERAGRWEDDTHFAMSPASFRPPTPAGPGGAFGRMFSTSAIPVPTIPTATPLAPTSAAAISVFGIP 753
Cdd:COG3321   1098 ALAALAAA----LLLLALLAALALAAAAAALLALAALLAAAAAAAALAAAAAAAAALALAAAAAALAAALAAALLAAAAL 1173

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  754 LAPLPTSGGWDSDGSDDADRPTGPAAIEAQDLQDAEDEAEFERDGGDVSEDELKGLLEDAEEVGLEAFTPVEEGRGRRRR 833
Cdd:COG3321   1174 LLALALALAAALAAALAGLAALLLAALLAALLAALLALALAALAAAAAALLAAAAAAAALALLALAAAAAAVAALAAAAA 1253

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  834 ARSGLEVTERSEPAVSVVPVVALPAQSEGFQKDNSGDVEDVANEVVADAQLGNDGYDWTVDNGEQRPTELEPDKLVAVER 913
Cdd:COG3321   1254 ALLAALAALALLAAAAGLAALAAAAAAAAAALALAAAAAAAAAALAALLAAAAAAAAAAAAAAAAAALAAALLAAALAAL 1333

                          490
                   ....*....|....*...
gi 1001610236  914 IIDVDADEFEITAGAVDR 931
Cdd:COG3321   1334 AAAVAAALALAAAAAAAA 1351

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd00024     1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Chromatin organization modifier domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1001610236   57 EWEVEAIVDKRV-RKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQKRAD 110
Cdd:smart00298   1 EYEVEKILDHRWkKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKKER 55

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 120 SSAPPKPPTLRRSTQPGPAAPLVNPPRPPSQPAVTPAPTISTTQLSAPQpdtSRKRKPSPKPRSPTSFSSHRGSNPRLsp 199
Cdd:pfam03154 322 QQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQ---SHKHPPHLSGPSPFQMNSNLPPPPAL-- 396

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 200 NPQPQLKRAKPSSRHTHanilPFDVPSSDEdELVAAEAQPQFSSSRRPVPPEHAKellAARVLGTPATAAAGAKHALATK 279
Cdd:pfam03154 397 KPLSSLSTHHPPSAHPP----PLQLMPQSQ-QLPPPPAQPPVLTQSQSLPPPAAS---HPPTSGLHQVPSQSPFPQHPFV 468

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 280 PAGQTGTPARSGTPTSqigAGSGAPKVHPPSS--VSSKLPIAWVPSTASSKLVVSASIGVKPPAASMPVETPRSTTPSNT 357
Cdd:pfam03154 469 PGGPPPITPPSGPPTS---TSSAMPGIQPPSSasVSSSGPVPAAVSCPLPPVQIKEEALDEAEEPESPPPPPRSPSPEPT 545

                         250
                  ....*....|.
gi 1001610236 358 HSSTPLTRSGS 368
Cdd:pfam03154 546 VVNTPSHASQS 556

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd00024     1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPELIKEYEK 50

Chromatin organization modifier domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1001610236   57 EWEVEAIVDKRV-RKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQKRAD 110
Cdd:smart00298   1 EYEVEKILDHRWkKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKKER 55

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 1001610236  60 VEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHaTALLEAFQKR 108
Cdd:cd18644     6 AEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILD-RRLIEIFERT 53

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 1001610236  60 VEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATaLLEAFQK 107
Cdd:cd18627     3 AECILKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPR-LLAAFES 49

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1001610236  57 EWEVEAIVDKRV-RKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd18634     1 LYEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLLNCEEFIHDFNR 52

chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. 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. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1001610236  57 EWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHL 95
Cdd:cd18653     1 EYAVEKICDRRVRKGKVEYYLKWKGYPETENTWEPEENL 39

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 1001610236  60 VEAIVDKRVRKGKTEYLVKWLGWSPAENTWE---PVDHLSHATALLEAFQ 106
Cdd:cd18965     3 IEALLKKRQFNRKLEYLVKWHGLPESENTWErekDIKHVSHWKQLLKDLR 52

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        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1001610236  55 EQEWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATaLLEAFQKR 108
Cdd:cd18645     1 EHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPR-LLIAFQNR 53

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 1001610236  55 EQEWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHL 95
Cdd:cd18646     2 EQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHI 42

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 1001610236  58 WEVEAIVD---KRVRKGKTEYLVKWLGWspAENTWEPVDHLShATALLEAFQK 107
Cdd:cd18971     1 YEVEEILAarrRRIRGKGREVLVKWVGY--AEPTWEPLDNLA-DTAALDRFEA 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        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1001610236  60 VEAIV----DKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd18964     3 VERIIgrrpSARDGPGKFLWLVKWDGYPIEDATWEPPENLGEHAKLIEDFEK 54

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 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLE 103
Cdd:cd18966     1 YEVERILAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKE 46

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 1001610236  57 EWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLShATALLEAF 105
Cdd:cd18652     1 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD-CPELIEAF 48

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 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd18633     2 FEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEVHLEDCKEVLLEFRK 51

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        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1001610236  58 WEVEAIVDKRVRK-GKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd18636     2 YEVEDILADRVNKnGINEYYIKWAGYDWYDNTWEPEQNLFGAEKVLKKWKK 52

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        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001610236  57 EWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQ 106
Cdd:cd18630     1 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENLGNCMKLVADYE 50

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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1001610236  55 EQEWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATaLLEAFQKR 108
Cdd:cd18648     1 ERVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSR-LIAAFEQK 53

N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of cryptic loci regulator 4 (Clr4), a histone H3 lysine methyltransferase which targets H3K9. Clr4 regulates silencing and switching at the mating-type loci and affects chromatin structure at centromeres. Clr4 is a catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1001610236  57 EWEVEAIVD-KRVRK-GKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQKR 108
Cdd:cd18632     1 EYEVEKIVDeKTDRNtAEPLYLVRWKNYSKNHDTWEPAENLSGCQAVLEKWKRK 54

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 1001610236  55 EQEWEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWE 90
Cdd:cd18963     1 ERVFAAECIIKRRVRKGRIEYLVKWKGWASKERERE 36

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members of this subgroup, the chromodomain is followed by a chromo shadow domain; 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. For the majority of members of this subgroup, the chromodomain is followed by a chromo shadow domain (CSD).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1001610236  55 EQEWEVEAIVD---KRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATALLEAFQK 107
Cdd:cd18969     1 EEEYEIEEILDvkkGGFEDGKLAYFVKWKGYPSSENSWVTEEDAANAQEMIEEYWK 56

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  120 SSAPPKPPTLRRSTQPGPAAPLVNPPRPPSQPAVtPAPTISTTQLSAPqPDTSRKRKPSPKPRS-----PTSFSSHRGSN 194
Cdd:PHA03247  2655 DPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAA-RPTVGSLTSLADP-PPPPPTPEPAPHALVsatplPPGPAAARQAS 2732

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  195 PRLSPNPQPQLKRAKPSsrhthanilpfdVPSSDedelvaaeaqpqfssSRRPVPPEHAkellaarvlgtpataaagaKH 274
Cdd:PHA03247  2733 PALPAAPAPPAVPAGPA------------TPGGP---------------ARPARPPTTA-------------------GP 2766

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  275 ALATKPAGQTGTPARSGTPTSQIGAGSGAPKVhPPSSVSSKLPIAWVPSTASSKLVVSASIGVKPPAASMPVETPRSTTP 354
Cdd:PHA03247  2767 PAPAPPAAPAAGPPRRLTRPAVASLSESRESL-PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGP 2845

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  355 snthSSTPLTRSGSHDAISSKPPLPPSTSSSDAATPLTRPSTSTPATATVTASTRRAFLPPTKLKHPPTIEvilPPEPWR 434
Cdd:PHA03247  2846 ----PPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQ---APPPPQ 2918

                   ....*....
gi 1001610236  435 RPSSLPAHP 443
Cdd:PHA03247  2919 PQPQPPPPP 2927

chromodomain of Hypsizygus marmoreus TY3B-I_0 protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Hypsizygus marmoreus TY3B-I_0 protein, a putative TY3/gypsy retrotransposon polyprotein, and similar proteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1001610236  58 WEVEAIVDKRVRKGKTEYLVKWLGWSPAENTWEPVDHLSHATAL 101
Cdd:cd18970     1 FFVERILDERRRGRGWQYLVRWLGYGPSDDSWLPRRELEECEAL 44

DNA polymerase III subunit gamma/tau;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 108 RADALRQVGAGLSSAPPKPPTLRRSTQPGPAAPLVNPPRPPSQPAVTPAPTISTTQLSAPQPDTSRKRKPSPKPRSPTSF 187
Cdd:PRK12323  359 RMLAFRPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ 438

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 188 SSHRGSNPRLSPNPQPQlkrAKPSSRHTHANILPFDVPSSDEDELVAAEAQPQFSSSRRPVPP-EHAKELLAARVLGTPA 266
Cdd:PRK12323  439 ASARGPGGAPAPAPAPA---AAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPwEELPPEFASPAPAQPD 515

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 267 TAAAGAKHALATKPAGQTGTPARSGTPTSQIGAGSGAPKVHPPSSVSSKLPIAWVPSTAS 326
Cdd:PRK12323  516 AAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPD 575

envelope glycoprotein C; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236 112 LRQVGAGLSSAPPKPPTLRRSTQPGPAAPLVNPPRPPSQPAVTPAPTISTTQLSAPQPDTSRKRKPSPKPrSPTSFSshr 191
Cdd:PHA03269   31 LHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAV-APQLAA--- 106

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1001610236 192 gsnprlSPNPQPQLKRAKPSSRHTHANILPFDVPSSDEDELVAAEAQPQ 240
Cdd:PHA03269  107 ------APKPDAAEAFTSAAQAHEAPADAGTSAASKKPDPAAHTQHSPP 149

chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Rhizoctonia solani AG-3 Rhs1AP, a putative Ty3/Gypsy polyprotein/retrotransposon which includes a protease, a reverse transcriptase, a ribonuclease H, and an integrase domain, in that order, with a chromodomain at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001610236  57 EWEVEAIVDKRVRKGK----TEYLVKWLGWSPAENTWEPVDHLSHATALL 102
Cdd:cd18977     3 EYEVEKIVGEKWKKRKnrrvKLYKVRFKGYGPEEDEWLTKEELKNAPEIL 52

repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 1 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        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1001610236  60 VEAIVDKRVR-----------KGKTEYLVKWLGWSPAENTWEPVDHLS 96
Cdd:cd18665     5 IDIVLDHRLKegleegelddpKENYEFLIKWTDESHLHNTWETYESLK 52

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  111 ALRQVGAGLSSAPPKPPTLRRSTQPGPAAPLVNPPRPPSQPAVTPAPTISTTQLSAPQPDTSrkrkPSPKPRSPTSFSSH 190
Cdd:PHA03247  2783 LTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG----PPPPSLPLGGSVAP 2858

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  191 RGSNPRLSPNPQPQLKRAKPssRHTHANILPFDVPSSDEDELvaaeAQPQFSSSRRPVPPehakellaarvlgTPATAAA 270
Cdd:PHA03247  2859 GGDVRRRPPSRSPAAKPAAP--ARPPVRRLARPAVSRSTESF----ALPPDQPERPPQPQ-------------APPPPQP 2919

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  271 GAKHALATKPAGQTGTPARSGTPTSQIGAGSGAPKVHPPssvsskLPIAWVPSTASSKLVVSASigvKPPAASMPVETPR 350
Cdd:PHA03247  2920 QPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGA------VPQPWLGALVPGRVAVPRF---RVPQPAPSREAPA 2990

                          250
                   ....*....|....*.
gi 1001610236  351 STTPSNTHSSTPLTRS 366
Cdd:PHA03247  2991 SSTPPLTGHSLSRVSS 3006

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  111 ALRQVGAGLSSAPPKPPTlRRSTQP--GPAAPLVNPPRPPSQPAVTPAPTISTTQLSaPQPDTSRKRKPSP--------- 179
Cdd:PHA03247  2667 ARRLGRAAQASSPPQRPR-RRAARPtvGSLTSLADPPPPPPTPEPAPHALVSATPLP-PGPAAARQASPALpaapappav 2744

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  180 ------------KPRSPTSFSSHRGSNPRLSPN-PQPQLKRAKPSSRHTHANILPFDVPSSDEDELV--AAEAQPQFSSS 244
Cdd:PHA03247  2745 pagpatpggparPARPPTTAGPPAPAPPAAPAAgPPRRLTRPAVASLSESRESLPSPWDPADPPAAVlaPAAALPPAASP 2824

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  245 RRPVPPEhakellAARVLGTPATAAAGAKHALATKPAGQTGTPARSGTPTSQIGAGSGAPKvHPPSSVSSKLPIAwvPST 324
Cdd:PHA03247  2825 AGPLPPP------TSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPA-RPPVRRLARPAVS--RST 2895

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001610236  325 ASSKLvvsasigvkPPAASMPVETPRSTTPSNTHSSTPLTRSGSHDAISSKPPLPPSTSSSDAAtPLTRPSTSTPATATV 404
Cdd:PHA03247  2896 ESFAL---------PPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA-GAGEPSGAVPQPWLG 2965

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 1001610236  405 TASTRRAFLPPTKLKHP-PTIEVILPPEPWRRPSSLPA 441
Cdd:PHA03247  2966 ALVPGRVAVPRFRVPQPaPSREAPASSTPPLTGHSLSR 3003