CBX family C-terminal motif; This motif is found at the C-terminus of CBX family proteins. It is bound by the RAWUL domain of the RING1B protein.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1001579533 538 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 569
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1001579533  39 FAAECIQKKRIRKGRV-EYYVKWRGWSHKYNTWEPEENILDG-RLLEAFESS 88
Cdd:pfam00385   1 YEVERILDHRKDKGGKeEYLVKWKGYPYDENTWEPEENLSKCpELIEEFKDR 52

CBX family C-terminal motif; This motif is found at the C-terminus of CBX family proteins. It is bound by the RAWUL domain of the RING1B protein.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1001579533 538 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 569
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

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 1001579533  87 SSQRDSGSGKRGQKSKKERSHSTSEPQQDLRHDSNKAKSEDDTSNDAPATPHGNSSSTE------TNPAVSPPHSPPPVL 160
Cdd:pfam03154 112 SPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESDSDSSAQQQILQTQppvlqaQSGAASPPSPPPPGT 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 161 SPGATEEKDSSSATAASRLSASTLQSATPPQQQPPTPQPAAVTPKPQPAEAKEPSSKAKPAVAVASPPKT-LQSAKSPKE 239
Cdd:pfam03154 192 TQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVsPQPLPQPSL 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 240 EEEKAKQVTAAPSQPPSEKICEPAMPVSKPNQAEACLSSPPVLEASKKPDTAtkrkldvkpTSSSPQIQVAAVSQQPPSK 319
Cdd:pfam03154 272 HGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQ---------RIHTPPSQSQLQSQQPPRE 342

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 320 MPRLSRPMEVPTINTASKPP------PVSTTAASLVNGSSPVRAP--VRPPVAFKPitprlgMTHVHHTHPPASHlavPP 391
Cdd:pfam03154 343 QPLPPAPLSMPHIKPPPTTPipqlpnPQSHKHPPHLSGPSPFQMNsnLPPPPALKP------LSSLSTHHPPSAH---PP 413

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 392 VAARLGTGQLGPATVArisRPPHLALPTSAPSLHQAAPN-----SANSVGPVPHPTAVPISSPvPATGVVAPQQPVPSAT 466
Cdd:pfam03154 414 PLQLMPQSQQLPPPPA---QPPVLTQSQSLPPPAASHPPtsglhQVPSQSPFPQHPFVPGGPP-PITPPSGPPTSTSSAM 489

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1001579533 467 PVLNGRDSAPPQPGSDRENVCKPAVSAVSQGKPMHSHNGQAASPPMllPPKEASAEPAV 525
Cdd:pfam03154 490 PGIQPPSSASVSSSGPVPAAVSCPLPPVQIKEEALDEAEEPESPPP--PPRSPSPEPTV 546

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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFESSQ 89
Cdd:cd18644     1 DLVYAAEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIFERTN 54

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 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFESSQR 90
Cdd:cd18645     1 EHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRER 55

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 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFE 86
Cdd:cd18647     1 EQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQ 51

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 1001579533  39 FAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGR-LLEAFES 87
Cdd:cd00024     1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPeLIKEYEK 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKyntwepeenildgrlleafESSQRDSGSGKRGQKSKKE 104
Cdd:cd18963     1 ERVFAAECIIKRRVRKGRIEYLVKWKGWASK-------------------ERERELYGPKKRGPKPKKF 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 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENI-LDGRLLEAF 85
Cdd:cd18968     5 EVILAARVVKDAESRKKGWKYLVKWAGYPDEENTWEPEESFdGCDDLLERF 55

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1001579533  39 FAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFE 86
Cdd:cd18631     2 YVVEKVLDRRVVKGKVEYLLKWKGYPDEDNTWEPEENLDCPDLIAEFE 49

CBX family C-terminal motif; This motif is found at the C-terminus of CBX family proteins. It is bound by the RAWUL domain of the RING1B protein.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1001579533 538 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 569
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1001579533  39 FAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAF 85
Cdd:cd18651     2 YVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEF 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
                  ....*....|....*....|....*....|....*...
gi 1001579533  39 FAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENI 76
Cdd:cd18650     2 YVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL 39

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  176 ASRLSASTLQSATPPQQQPPTPQPAAVTPKPQPAEAKEPSSKAKPAVAVASPpkTLQSAKSPKEE------------EEK 243
Cdd:PHA03247  2466 LSLLLGELFPGAPVYRRPAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAP--AILPDEPVGEPvhprmltwirglEEL 2543

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  244 AKQVTAAPSQPpsekiCEPAMPVSKPNQaeaclSSPPVLEASKKPD---TATKRKLDVKPTSSSPQIQVAavsqqPPSKM 320
Cdd:PHA03247  2544 ASDDAGDPPPP-----LPPAAPPAAPDR-----SVPPPRPAPRPSEpavTSRARRPDAPPQSARPRAPVD-----DRGDP 2608

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  321 PRLSRPMEVPTINTASKPPPVS-TTAASLVNGSSPVRAPVRPPVAFKPITPRLGMTHVHHTHPPASHLAVPPVAARLGTG 399
Cdd:PHA03247  2609 RGPAPPSPLPPDTHAPDPPPPSpSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAA 2688

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  400 QLGPATVARISRPPH-----LALPTSAPSLHQAAPNSANSVGPVPHPTAVPISSPVPAtGVVAPQQPVPSATPVLNgrdS 474
Cdd:PHA03247  2689 RPTVGSLTSLADPPPppptpEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPA-GPATPGGPARPARPPTT---A 2764

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1001579533  475 APPQPGSDRENVCKPAVSA-VSQGKPMHSHNGQAASPPMLLPPKEASAEPAVAEPEYSQLA 534
Cdd:PHA03247  2765 GPPAPAPPAAPAAGPPRRLtRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA 2825

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 1001579533  36 ERVFAAEciqKKRIRKGRVEYYVKWRGWSHKynTWEPEENILDGRLLEAFE 86
Cdd:cd18971     4 EEILAAR---RRRIRGKGREVLVKWVGYAEP--TWEPLDNLADTAALDRFE 49

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 1001579533  42 ECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDG-RLLEAFE 86
Cdd:cd18974     4 EEIVDEKMIDDELHYLVKWKGWPAEYNQWEPEDDMENApKAIQSYE 49

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1001579533  38 VFAAECIQKKRI-RKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFE 86
Cdd:cd18960     1 VFVVERILDKRLgRNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFE 50

repeat 1 of paired tandem chromodomains; 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 to CHD9, 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. 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 1001579533  55 EYYVKWRGWSHKYNTWEPEENILDGR 80
Cdd:cd18660    35 EFLVKWKGKSYLHCTWVTEETLEQLR 60

DNA polymerase III subunit gamma/tau;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 330 PTINTASKPPPVSTTAASLVNGSSPVRAPVRPPVAFKPITPRLGMTHVHHTHPPAshlAVPPVAARLGTGQLGPATVARI 409
Cdd:PRK12323  375 ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPA---PEALAAARQASARGPGGAPAPA 451

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 410 SRPPHLALPTSAPSLHQAAPNSAnsVGPVPHPTAVPISSPVPATGVVAPQQPVPSATPVLNGRDSAPPQPGSDRENVCKP 489
Cdd:PRK12323  452 PAPAAAPAAAARPAAAGPRPVAA--AAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDP 529

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1001579533 490 AVSAVSQGKPMHShngqAASPPMLLPPKEASAEPAVA 526
Cdd:PRK12323  530 ATADPDDAFETLA----PAPAAAPAPRAAAATEPVVA 562

DNA polymerase III subunits gamma and tau; Validated

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 170 SSSATAASRLSASTLQSATPPQQQPPTPQPAAVTPKPQPAEAKEPSSKAKPAVAVASPPKTLQSAKSPKEEEEKAKQVTA 249
Cdd:PRK07764  399 PSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTA 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 250 APSQPPSEKIcEPAMPVSKPNQAEACLSS----------PPVLEASKKPDTATKRKLDVKPTSSSPQIQVAAVSQQPPSK 319
Cdd:PRK07764  479 APAPAPPAAP-APAAAPAAPAAPAAPAGAddaatlrerwPEILAAVPKRSRKTWAILLPEATVLGVRGDTLVLGFSTGGL 557

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 320 MPRLSRPMEVPTINTA-------------------------SKPPPVSTTAASLVNGSSPVRAPVRPPVAFKPITPRLGM 374
Cdd:PRK07764  558 ARRFASPGNAEVLVTAlaeelggdwqveavvgpapgaaggeGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPA 637

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533 375 THVHHTHP-PASHLAVPPVAARLGTGQLGPATVARISRPPHLALPTSAPSLHQAAPNSANSVGPVPHPTAVPISSPVPAT 453
Cdd:PRK07764  638 EASAAPAPgVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDP 717

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1001579533 454 GVVAPQQPVPSATPVLNGRDSAPPQPGSDRENVCKPAVSAVSQgkPMHSHNGQAASPPMLLPPKEAsAEPAVAEPEYS 531
Cdd:PRK07764  718 AAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPP--PPAPAPAAAPAAAPPPSPPSE-EEEMAEDDAPS 792

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 1001579533  38 VFAAECIQKKRIRK-GRVEYYVKWRGWSHKYNTWEPEENI 76
Cdd:cd18636     1 VYEVEDILADRVNKnGINEYYIKWAGYDWYDNTWEPEQNL 40

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 1001579533  38 VFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENI 76
Cdd:cd18630     1 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENL 39

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 1001579533  46 KKRIRKgrVEYY-VKWRGWSHKYNTWEPEENILDGRLLEAFES 87
Cdd:cd18639     9 YKKIRE--QEYYlVKWKGYPDSENTWEPRQNLKCSRLLKQFHK 49

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 1001579533  51 KGRVEYYVKWRGWSHKYNTWEPEENILD 78
Cdd:cd18666    44 ETEIQYLIKWKGWSHIHNTWESEESLKD 71

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        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1001579533  36 ERVFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGRLLEAFE 86
Cdd:cd18978     1 DESYEVEKIINHRGEKNRRKYLVKWKGYDDTDNSWVTQEDFNDKDMIDEYE 51

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1001579533  38 VFAAECIQKKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDGR--LLE 83
Cdd:cd18633     1 VFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEVHLEDCKevLLE 48

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  133 APATPHGNSSSTETNPAVSPPHSPPPVLSPGAT----------------EEKDSSSATAASRLSASTLQSATPPQQQPPT 196
Cdd:PHA03247  2492 AGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPvgepvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPP 2571

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  197 PqpaavtPKPQPAEAKEPSSKAKPAVavasPPKTlQSAKSPKEEEEKAKQVTAAPSQPPSEKICEPAMPVSKPNQAEACL 276
Cdd:PHA03247  2572 R------PAPRPSEPAVTSRARRPDA----PPQS-ARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDP 2640

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  277 SSPPVLEASKKPDTATKRKLDVKPTSSSPQIQVAAVSQQPPSKMPRLSRPMEVPTINTASKPPPVST------------- 343
Cdd:PHA03247  2641 HPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTpepaphalvsatp 2720

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  344 ----TAASLVNGSSPVRAPVRPPVAFKPITP--------RLGMTHVHHTHPPASHLAVPPVAA-RLGTGQLGPATVARIS 410
Cdd:PHA03247  2721 lppgPAAARQASPALPAAPAPPAVPAGPATPggparparPPTTAGPPAPAPPAAPAAGPPRRLtRPAVASLSESRESLPS 2800

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1001579533  411 RPPHLALPTSAPSLHQAAPNSANSVGPVPHPTAV----------PISSPVPATGVVAPQQPVPSATPVlngrDSAPPQPG 480
Cdd:PHA03247  2801 PWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAqptapppppgPPPPSLPLGGSVAPGGDVRRRPPS----RSPAAKPA 2876

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1001579533  481 SDRenvcKPAVSAVSQGKPMHSHNGQAASPPMLLPPKEASAEPAVAEPEYSQLAIIP 537
Cdd:PHA03247  2877 APA----RPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQP 2929