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 2037036700  846 RLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAVVACLTQWRHMLAGLPnqLVILTDHEALKY 924
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRP--FTVYTDHKALKY 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2037036700  925 FKSQRRITGRQARWAILLADFDFILQYRPGDKGGEPDALTRR 966
Cdd:cd09274     79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:cd00024      1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLtNAPELIKEYE 49

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700 1135 DFIEGlpPSKKYDSKTYdsILVIVDRLTKFAILAPTHKTVTAKQT-AVLLYghMVRLFGY-PDHMVSDRGRQFISGAWKA 1212
Cdd:pfam00665    8 DFTYI--RIPGGGGKLY--LLVIVDDFSREILAWALSSEMDAELVlDALER--AIAFRGGvPLIIHSDNGSEYTSKAFRE 81

                           90
                   ....*....|....*..
gi 2037036700 1213 FAEQMGVKHSLSTAYHP 1229
Cdd:pfam00665   82 FLKDLGIKPSFSRPGNP 98

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 2037036700  846 RLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAVVACLTQWRHMLAGLPnqLVILTDHEALKY 924
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRP--FTVYTDHKALKY 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2037036700  925 FKSQRRITGRQARWAILLADFDFILQYRPGDKGGEPDALTRR 966
Cdd:cd09274     79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  840 DYHLPTRLETDASDFAIAGVLKQ-EHEGRWHPVAFYSRKMSSAEKNYEIHDKELLAVVACLTQWRHMLAGlpNQLVILTD 918
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLG--RKFTVYTD 78

                           90       100
                   ....*....|....*....|....*.
gi 2037036700  919 HEALKYFKSQRRITGRQARWAILLAD 944
Cdd:pfam17917   79 HKPLKYLFTPKELNGRLARWALFLQE 104

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:cd00024      1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLtNAPELIKEYE 49

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 2037036700  314 LSGMVQDHPARILADTGAGLSIVSDSFISKYQIPTKPIKT-RSIHGVTGHQLSINSSASmQVSIGTHNL-GVVEASVADT 391
Cdd:cd00303      1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTpLKVKGANGSSVKTLGVIL-PVTIGIGGKtFTVDFYVLDL 79

                           90
                   ....*....|...
gi 2037036700  392 ADYDLILGFTELR 404
Cdd:cd00303     80 LSYDVILGRPWLE 92

Chromatin organization modifier domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 2037036700  1430 DFEVEALIDKRSH-NGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:smart00298    1 EYEVEKILDHRWKkKGELEYLVKWKGYSYSEDTWEPEENLlNCSKKLDNYK 51

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 2037036700  314 LSGMVQDHPARILADTGAGLSIVSDSFISKYQIPTKP-IKTRSIHG----VTGHQLSINSsasmqVSIGTHNLGVVEASV 388
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVISEALAERLGLDRLVdAYPVTVRTangtVRAARVRLDS-----VKIGGIELRNVPAVV 75

                           90
                   ....*....|....*..
gi 2037036700  389 ADTADYDLILGFTELRR 405
Cdd:pfam13975   76 LPGDLDDVLLGMDFLKR 92

IS30 family transposase;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700 1149 KTYDSILVIVDRLTKFAILA--PTHKTVTAKQTAVLLyghmvrLFGYPDHMV----SDRGRQFisGAWKAFAEQMGVKHS 1222
Cdd:NF033563   145 KHKSALLTLVERKSRFVILVklPDKTAESVNKALIKL------LKPLPKHLRksitADNGKEF--ARHSEIEEALGIDVY 216

                           90       100
                   ....*....|....*....|....
gi 2037036700 1223 LSTAYHPQTDGQTERVNQVIEQYL 1246
Cdd:NF033563   217 FADPYSPWQRGTNENTNGLLRQYL 240

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 2037036700  846 RLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAVVACLTQWRHMLAGLPnqLVILTDHEALKY 924
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRP--FTVYTDHKALKY 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2037036700  925 FKSQRRITGRQARWAILLADFDFILQYRPGDKGGEPDALTRR 966
Cdd:cd09274     79 LLTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  840 DYHLPTRLETDASDFAIAGVLKQ-EHEGRWHPVAFYSRKMSSAEKNYEIHDKELLAVVACLTQWRHMLAGlpNQLVILTD 918
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLG--RKFTVYTD 78

                           90       100
                   ....*....|....*....|....*.
gi 2037036700  919 HEALKYFKSQRRITGRQARWAILLAD 944
Cdd:pfam17917   79 HKPLKYLFTPKELNGRLARWALFLQE 104

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 2037036700  566 LDENLEKGFIRPSKSPARSPVLFVPKKDGG-LRLCVDYRGLNEITVKNRAPLPLIEEQLFLL-RKARIYTKLDLRAAYNL 643
Cdd:cd03715     21 IQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLpPKHQWYTVLDLANAFFS 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  644 IRIAKGDEWKTAF---GTQlglYEYLVMPFGLANAPAHFQsfiNDIFRDI-------IGIYVVVYLDDFLIFSDTEEAHV 713
Cdd:cd03715    101 LPLAPDSQPLFAFeweGQQ---YTFTRLPQGFKNSPTLFH---EALARDLapfplehEGTILLQYVDDLLLAADSEEDCL 174

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 2037036700  714 KHVTEVLTRLRSNRLFAKLSKCEFHTKTVEFLGYII 749
Cdd:cd03715    175 KGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  547 PQGPLylkgPKEMSE-LRRYLDENLEKGFIRPSKSPARSPVLFVPKKDGGLRLCVDYRGLNEITVknraplPLIEEQLFL 625
Cdd:cd01645      5 KQWPL----TEEKLEaLTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQ------DMGALQPGL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  626 -----LRKARIYTKLDLRAAYNLIRIAKGDEWKTAF----------GTQlglYEYLVMPFGLANAPAHFQSFINDIFRDI 690
Cdd:cd01645     75 phpaaLPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnkgpAKR---YQWKVLPQGMKNSPTICQSFVAQALEPF 151

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 2037036700  691 IG----IYVVVYLDDFLIFSDTEEAHVKHVTEVLTRL 723
Cdd:cd01645    152 RKqypdIVIYHYMDDILIASDLEGQLREIYEELRQTL 188

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        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2037036700 1430 DFEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYEV 1479
Cdd:cd18653      1 EYAVEKICDRRVRKGKVEYYLKWKGYPETENTWEPEENLDCQDLIQQYEA 50

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2037036700 1430 DFEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEY 1477
Cdd:cd18650      1 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEF 48

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 2037036700  314 LSGMVQDHPARILADTGAGLSIVSDSFISKYQIPTKPIKT-RSIHGVTGHQLSINSSASmQVSIGTHNL-GVVEASVADT 391
Cdd:cd00303      1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTpLKVKGANGSSVKTLGVIL-PVTIGIGGKtFTVDFYVLDL 79

                           90
                   ....*....|...
gi 2037036700  392 ADYDLILGFTELR 404
Cdd:cd00303     80 LSYDVILGRPWLE 92

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700 1135 DFIEGlpPSKKYDSKTYdsILVIVDRLTKFAILAPTHKTVTAKQT-AVLLYghMVRLFGY-PDHMVSDRGRQFISGAWKA 1212
Cdd:pfam00665    8 DFTYI--RIPGGGGKLY--LLVIVDDFSREILAWALSSEMDAELVlDALER--AIAFRGGvPLIIHSDNGSEYTSKAFRE 81

                           90
                   ....*....|....*..
gi 2037036700 1213 FAEQMGVKHSLSTAYHP 1229
Cdd:pfam00665   82 FLKDLGIKPSFSRPGNP 98

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKR-SHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYE 1478
Cdd:cd18960      2 FVVERILDKRlGRNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFE 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 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYE 1478
Cdd:cd18966      1 YEVERILAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKEWE 48

Chromatin organization modifier domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 2037036700  1430 DFEVEALIDKRSH-NGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:smart00298    1 EYEVEKILDHRWKkKGELEYLVKWKGYSYSEDTWEPEENLlNCSKKLDNYK 51

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
                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKR-SHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEY 1477
Cdd:cd18634      2 YEVERIVDKRkNKKGKTEYLVRWKGYDSEDDTWEPEQHLlNCEEFIHDF 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.

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                   ....*....|....*....|....*....|....*....|....*....|..
gi 2037036700 1430 DFEVEALIDKRSHNGTTE--YKVLWRGYSEEAASWEPVENLN-CPDLIQEYE 1478
Cdd:cd18632      1 EYEVEKIVDEKTDRNTAEplYLVRWKNYSKNHDTWEPAENLSgCQAVLEKWK 52

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 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEY 1477
Cdd:cd18639      1 YEVEYLCDYKKIREQEYYLVKWKGYPDSENTWEPRQNLKCSRLLKQF 47

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
                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:cd18973      1 YVVEAILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENLeHAQKLLKKYY 49

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 2037036700 1433 VEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL--NCPDLIQEYE 1478
Cdd:cd18976      3 VESLLDRRKVRGQVQYLVKWRGFPRSEATWEPREELmrRCAELVAAYD 50

chromodomain of Drosophila melanogaster Rhino, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of Drosophila melanogaster Rhino (also known as heterochromatin protein 1-like), and similar proteins. Rhino is a female-specific protein that affects chromosome structure and egg polarity that is required for germline PIWI-interacting RNA (piRNA) production. In Drosophila the RDC (rhino, deadlock, and cutoff) complex, composed of rhino, the protein deadlock (Del) and the Rai1-like transcription termination cofactor cutoff (Cuff) binds to chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is anchored to H3K9me3-marked chromatin in part via the H3K9me3-binding activity of Rhino, and is required for transcription of piRNA precursors. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2037036700 1433 VEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:cd18630      4 VEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENLgNCMKLVADYE 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.

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                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2037036700 1430 DFEVEALI------DKRSHNGTTEYKVLWRGYSEEAASWEPVENLN-CPDLIQEY 1477
Cdd:cd18968      1 EYEVEVILaarvvkDAESRKKGWKYLVKWAGYPDEENTWEPEESFDgCDDLLERF 55

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2037036700  635 LDLRAAYNLIRIAKgDEWK-TAFGTQLGLYEYLVMPFGLANAPAHFQSFINDIFRDI--IGIYVVVYLDDFLIFSDTEea 711
Cdd:cd03714      1 VDLKDAYFHIPILP-RSRDlLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLrlLGVRIFSYLDDLLIIASSI-- 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2037036700  712 hvKHVTEVLTRLRSNRLFA-----KLSKCE-FHTKTVEFLGYII 749
Cdd:cd03714     78 --KTSEAVLRHLRATLLANlgftlNLEKSKlGPTQRITFLGLEL 119

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.

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                   ....*....|....*....|....*....|....*....|....*....|.
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYEVSE 1481
Cdd:cd18645      4 FAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRE 54

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.

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                   ....*....|....*....|....*....|....*....|....*....|.
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYEVSE 1481
Cdd:cd18646      5 FAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKE 55

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.

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                   ....*....|....*....|....*....|....*....|....*....
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENL-NCPDLIQEYE 1478
Cdd:cd18974      1 WEVEEIVDEKMIDDELHYLVKWKGWPAEYNQWEPEDDMeNAPKAIQSYE 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.

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                   ....*....|....*....|....*....|....*....|....*....|....
gi 2037036700 1431 FEVEALIDKRSHNGTTEYKVLWRGYSEEAASWEPVENLNCPDLIQEYEVSEGGR 1484
Cdd:cd18648      4 FAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKERER 57