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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18627    1 FAAECILKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 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 998465370  512 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 543
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18627    1 FAAECILKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 49

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370   89 RHDSSKAKSEDDTSNDAPATPHGNSSSTETNPAVSPPHSPPPALSPSATEGKDSSSATAASRLSASMLQSVTA------T 162
Cdd:PHA03247 2588 RPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRvsrprrA 2667

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  163 QQQPQTHQATATTPKPQPAEAK---------------EPSVKPKPPAALASPPKPLQSARSQKEEEEKAKPVTTTPSQPP 227
Cdd:PHA03247 2668 RRLGRAAQASSPPQRPRRRAARptvgsltsladppppPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAG 2747

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  228 PEKICEPVTSVSKPNEAESGLSSPPVLEASKKPDTATK---------RKLDTKPMHASSSPQIQVAAIAQQPPSKMPKLS 298
Cdd:PHA03247 2748 PATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRpavaslsesRESLPSPWDPADPPAAVLAPAAALPPAASPAGP 2827

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  299 RPMDVPAIGTAAKPPPVTTSATSFMNGSS------SVRAPVRPPVAlKPITPrlgvthihhPHPPASHLAVPPVAARLGT 372
Cdd:PHA03247 2828 LPPPTSAQPTAPPPPPGPPPPSLPLGGSVapggdvRRRPPSRSPAA-KPAAP---------ARPPVRRLARPAVSRSTES 2897

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  373 GQLGPATVARISRPPHLAPPTSMPSPHQVAASSansvgPVPHPTSVPVSSPAPATGVVAPQQPVPSATPIVNGRdSAPPQ 452
Cdd:PHA03247 2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ-----PPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGA-LVPGR 2971

                         410       420       430
                  ....*....|....*....|....*....|.
gi 998465370  453 PGNDRENICKPAVSAVSQGKPMHSHNGQAAS 483
Cdd:PHA03247 2972 VAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002

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 998465370  512 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 543
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

Cell division protein ZipA, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  72 KSRKERShstgepqQDFRHDSSKAKSEDDTSNDAPATPHgnssstetnpAVSPPHSPPPALSPSATEGKDSSSATAASRL 151
Cdd:COG3115   25 RSRKERR-------SSFRDKPSKRDVLLDDDGIGEVRVV----------AAEAPERVEPEASFDAEDEVREPDQEEVDPL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 152 sASMLQSVTATQQQPQTHQATATTPKPQPAEAKEPSVKPKPPAALASPPKPLQSARSQKEEEEKAKPVtttpsQPPPEKI 231
Cdd:COG3115   88 -LDDEADIEAAPAEPVRWAGTAAAVEPAPEQEAYEEAGPAGESAEQEDAPAEEPEAEAPAEEALAAEL-----CAEPEEV 161

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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18627    1 FAAECILKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 49

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 998465370   8 ERVFAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFESSQRD 63
Cdd:cd18648    1 ERVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKERE 56

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 998465370   7 GERVFAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18649    1 GERVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEE 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 998465370   7 GERVFAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFESSQR 62
Cdd:cd18646    1 GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 56

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 998465370   11 FAAECIQRKRIRKGRV-EYYVKWRGWSHKYNTWEPEENILD-RRLLEAFESS 60
Cdd:pfam00385   1 YEVERILDHRKDKGGKeEYLVKWKGYPYDENTWEPEENLSKcPELIEEFKDR 52

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370   89 RHDSSKAKSEDDTSNDAPATPHGNSSSTETNPAVSPPHSPPPALSPSATEGKDSSSATAASRLSASMLQSVTA------T 162
Cdd:PHA03247 2588 RPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRvsrprrA 2667

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  163 QQQPQTHQATATTPKPQPAEAK---------------EPSVKPKPPAALASPPKPLQSARSQKEEEEKAKPVTTTPSQPP 227
Cdd:PHA03247 2668 RRLGRAAQASSPPQRPRRRAARptvgsltsladppppPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAG 2747

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  228 PEKICEPVTSVSKPNEAESGLSSPPVLEASKKPDTATK---------RKLDTKPMHASSSPQIQVAAIAQQPPSKMPKLS 298
Cdd:PHA03247 2748 PATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRpavaslsesRESLPSPWDPADPPAAVLAPAAALPPAASPAGP 2827

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  299 RPMDVPAIGTAAKPPPVTTSATSFMNGSS------SVRAPVRPPVAlKPITPrlgvthihhPHPPASHLAVPPVAARLGT 372
Cdd:PHA03247 2828 LPPPTSAQPTAPPPPPGPPPPSLPLGGSVapggdvRRRPPSRSPAA-KPAAP---------ARPPVRRLARPAVSRSTES 2897

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  373 GQLGPATVARISRPPHLAPPTSMPSPHQVAASSansvgPVPHPTSVPVSSPAPATGVVAPQQPVPSATPIVNGRdSAPPQ 452
Cdd:PHA03247 2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ-----PPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGA-LVPGR 2971

                         410       420       430
                  ....*....|....*....|....*....|.
gi 998465370  453 PGNDRENICKPAVSAVSQGKPMHSHNGQAAS 483
Cdd:PHA03247 2972 VAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002

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        40
                 ....*....|....*....|....*....|....*....|....*....
gi 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18653    2 YAVEKICDRRVRKGKVEYYLKWKGYPETENTWEPEENLDCQDLIQQYEA 50

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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFE 58
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 998465370  512 DFWQKQSPVVDQVLITDVTANLVTVTVRECRT 543
Cdd:pfam17218   1 EYWRPSPAPPDKVVVTDVTANSLTVTFRECST 32

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAF 57
Cdd:cd18975    1 YEVESILNSRLHRGKLQYLIQWKGYPLEEASWELEDNIKNPRLIEEF 47

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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAF 57
Cdd:cd18651    2 YVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEF 48

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 998465370   8 ERVFAAEciqRKRIRKGRVEYYVKWRGWSHKynTWEPEENILDRRLLEAFE 58
Cdd:cd18971    4 EEILAAR---RRRIRGKGREVLVKWVGYAEP--TWEPLDNLADTAALDRFE 49

DNA polymerase III subunits gamma and tau; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 105 APATPHGNSSSTETNPAVSPPHSPPPALSPSATEGKDSSSATAASRLSASMLQSVTATQQQPQTHQATATTPKPQPAEAk 184
Cdd:PRK07764 393 APAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPA- 471

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 185 epsvkPKPPAALASPPKPLQSARSQKEEEEKAKPVTTTPSQP---PPEKICEPVTSVSKPNEAESGLSSPPVLEASKKPD 261
Cdd:PRK07764 472 -----AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDaatLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGD 546

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 262 TAT---KRKLDTKPMHASSSPQIQVAAIAQQppskmpkLSRPMDVPA-IGTAAKPPPVTTSATSFMNGS-------SSVR 330
Cdd:PRK07764 547 TLVlgfSTGGLARRFASPGNAEVLVTALAEE-------LGGDWQVEAvVGPAPGAAGGEGPPAPASSGPpeeaarpAAPA 619

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 331 APVRPPVALKPITPRLGVTHIHHPHP-PASHLAVPPVAARLGTGQLGPATVARISRPPHLAPPTSMPSPHQVAASSANSV 409
Cdd:PRK07764 620 APAAPAAPAPAGAAAAPAEASAAPAPgVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPA 699

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 410 GPVPHPTSVPVSSPAPATGVVAPQQPVPSATPIVNGRDSAPPQPGNDRENICKPAVSAVSQgkPMHSHNGQAASPPMLLP 489
Cdd:PRK07764 700 QPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPP--PPAPAPAAAPAAAPPPS 777

                        410
                 ....*....|....*.
gi 998465370 490 PKEAsAEPAVAEPEYS 505
Cdd:PRK07764 778 PPSE-EEEMAEDDAPS 792

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 998465370   59 SSQRDSGSGKRGQKSRKERSHSTGEPQQDFRHDSSKAKSEDDTSNDAPATPHGNSSSTE------TNPAVSPPHSPPPAL 132
Cdd:pfam03154 112 SPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESDSDSSAQQQILQTQppvlqaQSGAASPPSPPPPGT 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  133 SPSATEGKDSSSATAASRLSASMLQSVTATQQQPQTHQATATTPKPQPAEAKEPSvKPKPPAALASPPKPLQSARSQKEE 212
Cdd:pfam03154 192 TQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPH-PPLQPMTQPPPPSQVSPQPLPQPS 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  213 EEKAKPVTTTPSQPPPEKICEPVTSVSKPNEAESGLSSPPVLEASKKPDTATKRkldtkpmhaSSSPQIQVAAIAQQPPS 292
Cdd:pfam03154 271 LHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQR---------IHTPPSQSQLQSQQPPR 341

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  293 KMPKLSRPMDVPAIgtaaKPPPVT------TSATSFMNGSSSVRAPVRPPVALKPITPRLGVTHIHHPHPPASHlavPPV 366
Cdd:pfam03154 342 EQPLPPAPLSMPHI----KPPPTTpipqlpNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAH---PPP 414

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370  367 AARLGTGQLGPATVArisRPPHLA-----PPTSMPSPHQVAASSANSVGPVPHPTSVPVSSPaPATGVVAPQQPVPSATP 441
Cdd:pfam03154 415 LQLMPQSQQLPPPPA---QPPVLTqsqslPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPP-PITPPSGPPTSTSSAMP 490

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 998465370  442 IVNGRDSAPPQPGNDRENICKPAVSAVSQGKPMHSHNGQAASPPMllPPKEASAEPAV 499
Cdd:pfam03154 491 GIQPPSSASVSSSGPVPAAVSCPLPPVQIKEEALDEAEEPESPPP--PPRSPSPEPTV 546

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 998465370  10 VFAAECIQRKRI-RKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFE 58
Cdd:cd18960    1 VFVVERILDKRLgRNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFE 50

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 998465370  14 ECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILD-RRLLEAFE 58
Cdd:cd18974    4 EEIVDEKMIDDELHYLVKWKGWPAEYNQWEPEDDMENaPKAIQSYE 49

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 998465370  14 ECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILD----RRLLEAFES 59
Cdd:cd18965    4 EALLKKRQFNRKLEYLVKWHGLPESENTWEREKDIKHvshwKQLLKDLRA 53

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 998465370  10 VFAAECIQRKRIRK-GRVEYYVKWRGWSHKYNTWEPEENI 48
Cdd:cd18636    1 VYEVEDILADRVNKnGINEYYIKWAGYDWYDNTWEPEQNL 40

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        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 998465370   8 ERVFAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAF 57
Cdd:cd18962    1 EGHYVVEAIVNDVLIDGKHMYEVKWEGYPSDHNNWVAEWDLNDKEILRKY 50

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 998465370  19 KRIRKgrVEYY-VKWRGWSHKYNTWEPEENILDRRLLEAFES 59
Cdd:cd18639   10 KKIRE--QEYYlVKWKGYPDSENTWEPRQNLKCSRLLKQFHK 49

DNA polymerase III subunits gamma and tau; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 101 TSNDAPATPHGNSSS--TETNPAVSPPHSPPPALSPSATEGKDSSSATAASRLSASMLQSVTATQQqPQTHQATATTPKP 178
Cdd:PRK07994 363 APLPEPEVPPQSAAPaaSAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQ-LQRAQGATKAKKS 441

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 179 QPAEAkepsVKPKPPAALASPPKPLQSARSQKEEEEKAKPVTTTPSQPPPEKICEPVTSVSKPneaesglssPPVLEASK 258
Cdd:PRK07994 442 EPAAA----SRARPVNSALERLASVRPAPSALEKAPAKKEAYRWKATNPVEVKKEPVATPKAL---------KKALEHEK 508

                 ....*..
gi 998465370 259 KPDTATK 265
Cdd:PRK07994 509 TPELAAK 515

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
                 ....*....|....*....|....*....|....
gi 998465370  16 IQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENIL 49
Cdd:cd18634    8 VDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLL 41

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 998465370  11 FAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILDRRLLEAFE 58
Cdd:cd18966    1 YEVERILAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKEWE 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 998465370  10 VFAAECIQRKRIRKGRVEYYVKWRGWSHKYNTWEPEENILD-RRLLEAFE 58
Cdd:cd18633    1 VFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEVHLEDcKEVLLEFR 50

DNA polymerase III subunit gamma/tau;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 331 APVRPPVALKPITPRLGVTHIHHPHPPASHLAVPPVAArlgtgqLGPATVARISRPPHLAPPTSMPSPHQVAASSANSVG 410
Cdd:PRK07003 372 VPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAA------LAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADG 445

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998465370 411 PVPHPTSVPVSSPAPATGVVAPQQPVPSATPIVNGRDSAPPQPGNDRENICKPAVSAVSQGKPMHSHNGQAASPPMLLPP 490
Cdd:PRK07003 446 DAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAA 525