Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  525 EVETDASDFAIGGQLGQRDDQGRLHPVAFFSKKLHGPELNYQIHDKELMAIIEAFKEWRTYLSGarHEVKVYTDHKNLAH 604
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLG--RPFTVYTDHKALKY 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 329351122  605 FTTNKDLNKRQIRWAEFLSEFNFTIIYRKGSENGRADILSRR 646
Cdd:cd09274    79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   34 VRINVGGRWASALLDSGAQGNYMSPEYINKNKITWKYKEEPYQLSTVEGQAVSYGGGIVntetaPLQVFISRRQGHITFD 113
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIL-----PVTIGIGGKTFTVDFY 75

                          90
                  ....*....|....*..
gi 329351122  114 ITNMGGKQIILGIPWLR 130
Cdd:cd00303    76 VLDLLSYDVILGRPWLE 92

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 329351122   687 PPTEALELIRQVHEAkaHGHQGVAKTFARLKKHHNFKGTRQDVTTVIRNCDLCKKSKA 744
Cdd:pfam17921    2 PKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  525 EVETDASDFAIGGQLGQRDDQGRLHPVAFFSKKLHGPELNYQIHDKELMAIIEAFKEWRTYLSGarHEVKVYTDHKNLAH 604
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLG--RPFTVYTDHKALKY 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 329351122  605 FTTNKDLNKRQIRWAEFLSEFNFTIIYRKGSENGRADILSRR 646
Cdd:cd09274    79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   271 VPKKN-GKERLC----VDYRQLNDITIK-------NCYPLPLISELRDALAGANWFTALDLKGAYNLIRIKDGEEWKTAF 338
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   339 RTR-----------RGHYEYLVMPFGLTNAPATFQNMINDVLREFL---DVFVVVYLDDILIFSKTMEEHKGHVHQVLTR 404
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 329351122   405 LHQHELLVEPEKAKF--HTQEVDFLGYTI 431
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   34 VRINVGGRWASALLDSGAQGNYMSPEYINKNKITWKYKEEPYQLSTVEGQAVSYGGGIVntetaPLQVFISRRQGHITFD 113
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIL-----PVTIGIGGKTFTVDFY 75

                          90
                  ....*....|....*..
gi 329351122  114 ITNMGGKQIILGIPWLR 130
Cdd:cd00303    76 VLDLLSYDVILGRPWLE 92

Chromatin organization modifier domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 329351122   1058 EYEVERIIDYR-KTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQSQ 1109
Cdd:smart00298    1 EYEVEKILDHRwKKKGELEYLVKWKGYSYSEDTWEPEENLlNCSKKLDNYKKKE 54

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 329351122   687 PPTEALELIRQVHEAkaHGHQGVAKTFARLKKHHNFKGTRQDVTTVIRNCDLCKKSKA 744
Cdd:pfam17921    2 PKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122    34 VRINvgGRWASALLDSGAQGNYMSPEYINKNKITWKYKEEPYQLSTVEGQAVSYGGGIVNTETAPLQVfisrrqGHITFD 113
Cdd:pfam13975    3 VTIN--GRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRAARVRLDSVKIGGIEL------RNVPAV 74

                           90
                   ....*....|....*...
gi 329351122   114 ITNMGGKQIILGIPWLRQ 131
Cdd:pfam13975   75 VLPGDLDDVLLGMDFLKR 92

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  783 GTSYdnILVVVDRLTKYSY--FLPYKATGTAEDlayvFLRNIVGQhgLPKELV----SDRDKLFTSnfWKSLIAQLGAKH 856
Cdd:COG2826   185 GKSA--LLTLVERKSRFVIllKLPDKTAESVAD----ALIRLLRK--LPAFLRksitTDNGKEFAD--HKEIEAALGIKV 254

                          90       100
                  ....*....|....*....|....*
gi 329351122  857 KLSTAFHPQTDGQTERTNQTLEQYL 881
Cdd:COG2826   255 YFADPYSPWQRGTNENTNGLLRQYF 279

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  525 EVETDASDFAIGGQLGQRDDQGRLHPVAFFSKKLHGPELNYQIHDKELMAIIEAFKEWRTYLSGarHEVKVYTDHKNLAH 604
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLG--RPFTVYTDHKALKY 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 329351122  605 FTTNKDLNKRQIRWAEFLSEFNFTIIYRKGSENGRADILSRR 646
Cdd:cd09274    79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

RNase H-like domain found in reverse transcriptase;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   494 WNEPQEKAFRQIIDAVLSEPVLRMIDPEKPMEVETDASDFAIGGQLGQRDDQGRLHPVAFFSKKLHGPELNYQIHDKELM 573
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|..
gi 329351122   574 AIIEAFKEWRTYLSGarHEVKV 595
Cdd:pfam17919   81 AIVFALKKFRHYLLG--RKFTV 100

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  248 LKENLRKGYIRPSTSPAGYPILFVPKKNGKE-RLCVDYRQLNDITIKNCYPLPLISELRDALAGAN-WFTALDLKGAYNL 325
Cdd:cd03715    21 IQELLEAGILVPCQSPWNTPILPVKKPGGNDyRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPKHqWYTVLDLANAFFS 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  326 IRI-KDGEEWkTAFRTRRGHYEYLVMPFGLTNAPATFQNMINDVLREF----LDVFVVVYLDDILIFSKTMEEHKGHVHQ 400
Cdd:cd03715   101 LPLaPDSQPL-FAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFplehEGTILLQYVDDLLLAADSEEDCLKGTDA 179

                         170       180       190
                  ....*....|....*....|....*....|.
gi 329351122  401 VLTRLHQHELLVEPEKAKFHTQEVDFLGYTI 431
Cdd:cd03715   180 LLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122   34 VRINVGGRWASALLDSGAQGNYMSPEYINKNKITWKYKEEPYQLSTVEGQAVSYGGGIVntetaPLQVFISRRQGHITFD 113
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIL-----PVTIGIGGKTFTVDFY 75

                          90
                  ....*....|....*..
gi 329351122  114 ITNMGGKQIILGIPWLR 130
Cdd:cd00303    76 VLDLLSYDVILGRPWLE 92

Chromo (CHRromatin organization MOdifier) domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 329351122  1059 YEVERIIDYRKT-NKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQS 1108
Cdd:pfam00385    1 YEVERILDHRKDkGGKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKDR 52

Chromatin organization modifier domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 329351122   1058 EYEVERIIDYR-KTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQSQ 1109
Cdd:smart00298    1 EYEVEKILDHRwKKKGELEYLVKWKGYSYSEDTWEPEENLlNCSKKLDNYKKKE 54

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 329351122 1057 NEYEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18978     2 ESYEVEKIINHRGEKNRRKYLVKWKGYDDTDNSWVTQEDFNDKDMIDEYEN 52

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 329351122 1058 EYEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18650     1 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ 50

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 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18975     1 YEVESILNSRLHRGKLQYLIQWKGYPLEEASWELEDNIKNPRLIEEFHK 49

chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. 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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQ 1107
Cdd:cd18973     1 YVVEAILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENLeHAQKLLKKYYQ 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
                  ....*....|....*....|....*....|....*....|....*....
gi 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18966     1 YEVERILAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKEWEE 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 329351122 1058 EYEVERIIDYRKTNK-QDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYH 1106
Cdd:cd18634     1 LYEVERIVDKRKNKKgKTEYLVRWKGYDSEDDTWEPEQHLlNCEEFIHDFN 51

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
                  ....*....|....*....|....*....|....*....|....*....
gi 329351122 1058 EYEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQY 1105
Cdd:cd18630     1 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENLgNCMKLVADY 49

chromodomain of Drosophila melanogaster chromator chromodomain protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in chromodomain of Drosophila melanogaster chromator (also known as Chriz/Chro) chromodomain protein, and similar proteins. Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 329351122 1059 YEVERIIDYR--KTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQ 1107
Cdd:cd18640     1 EPVEKIVAKRfnPRKKTWEYLVKWENRSHHENTWEPMANLeRCKYLLQMFEK 52

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 329351122 1059 YEVERIIDYRKT-NKQDEYLIKWKNYGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18960     2 FVVERILDKRLGrNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFEK 51

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQYHQ 1107
Cdd:cd18974     1 WEVEEIVDEKMIDDELHYLVKWKGWPAEYNQWEPEDDMeNAPKAIQSYEK 50

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 329351122 1058 EYEVERIIDYRKTNKQDE--YLIKWKNYGHEENTWEPIKNLN-CPQLLKQYHQ 1107
Cdd:cd18632     1 EYEVEKIVDEKTDRNTAEplYLVRWKNYSKNHDTWEPAENLSgCQAVLEKWKR 53

repeat 2 of paired tandem chromodomains; Repeat 2 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 329351122 1060 EVERIIDYRKTNKQD-EYLIKWKNYGHEENTWEPIKNLN--CPQLLKQYHQ 1107
Cdd:cd18659     4 IVERIIAHREDDEGVtEYLVKWKGLPYDECTWESEEDISdiFQEAIDEYKK 54

chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Moniliophthora perniciosa FA553 putative retrotelement polyprotein, which includes domains in the following order: 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 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNL-NCPQLLKQY 1105
Cdd:cd18972     1 YEVEAIVGHKPKKKPRQFLVSWLGYDSSHNEWKQKEELeNARELLQDY 48

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 329351122 1059 YEVERIIDYRKTNKQDEYLIKWKNYGHEENTWEPIKNL--NCPQLLKQY 1105
Cdd:cd18976     1 YIVESLLDRRKVRGQVQYLVKWRGFPRSEATWEPREELmrRCAELVAAY 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 329351122 1059 YEVERIIDyRKTNKQD-----EYLIKWKNYGHEENTWEPIKNLN-CPQLLKQYHQ 1107
Cdd:cd18964     1 FFVERIIG-RRPSARDgpgkfLWLVKWDGYPIEDATWEPPENLGeHAKLIEDFEK 54

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329351122  525 EVETDASDFAIGGQLGQRDDQGrlhpvaFFSKKlhgpELNYQIHDKELMAIIEAFKEWRTYLSGARheVKVYTDHK-NLA 603
Cdd:cd09275     1 VLFTDASLSGWGAYLLNSRAHG------PWSAD----ERNKHINLLELKAVLLALQHFAAELKNRK--ILIRTDNTtAVA 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 329351122  604 HF-----TTNKDLNK--RQI-RWAEflsEFNFTI--IYRKGSENGRADILSRRSD 648
Cdd:cd09275    69 YInkqggTSSPPLLAlaRQIlLWCE---QRNIWLraSHIPGVLNTEADRLSRLGL 120

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 329351122 1059 YEVERIIDYR---KTNKQDEYLIKWKnyGHEENTWEPIKNLNCPQLLKQYHQ 1107
Cdd:cd18971     1 YEVEEILAARrrrIRGKGREVLVKWV--GYAEPTWEPLDNLADTAALDRFEA 50

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 329351122 1058 EYEVERIIDYRKTNKQD--EYLIKWKNYGH-EENTWEPIKNL-NCPQLLKQY 1105
Cdd:cd18637     1 EYVVEKILKHRMARKGGgyEYLLKWEGYDDpSDNTWSSEADCaGCKDLIEAY 52