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 1697167483  935 ELMCDASDYALGAVLGQRKE-KRPHVIYYASRTLNDAQLNYSTTEKELLAVVFALDKFRSYLLGTKVIIYTDHAALKYLF 1013
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1697167483 1014 TKKEAKPRLIRWMLLLQEFDIEIRDKKGSENVVADHLSRMV 1054
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

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 1697167483  325 IPCVIGNTKFeQCMLDLGASINVMPYSIYASMNLG-ELKNDGVIIQLADRSNAYPKGVLEDVLVQVGNLIFPADFYVLDM 403
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDL 79

                           90
                   ....*....|....*....
gi 1697167483  404 EDsphstpLPILLGRPFMK 422
Cdd:cd00303     80 LS------YDVILGRPWLE 92

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 1697167483  935 ELMCDASDYALGAVLGQRKE-KRPHVIYYASRTLNDAQLNYSTTEKELLAVVFALDKFRSYLLGTKVIIYTDHAALKYLF 1013
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1697167483 1014 TKKEAKPRLIRWMLLLQEFDIEIRDKKGSENVVADHLSRMV 1054
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

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 1697167483  686 TGWRVC----IDCRKLNATIRK-------DHFPLPFIDQMLERLAGHSFYCFLDGYSGYNQIVIAPDDQEKTTFTCP--- 751
Cdd:pfam00078    7 GKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPpin 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483  752 --------FGTFAYRRMPFGLCNAPATFQRCMVSIFSDF---VEKIIEVFMDDFSVFGDSFDGCLENLTKILKRCVETNL 820
Cdd:pfam00078   87 inwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGL 166

                          170       180
                   ....*....|....*....|...
gi 1697167483  821 VLNWEKCHFTVRQGIV--LGHIV 841
Cdd:pfam00078  167 KINPEKTQFFLKSKEVkyLGVTL 189

IS481 family transposase; null

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483 1210 DVWGIDFM--GPFPPSfGFTYILLAVDYVSKWVEAKATRTNDSKVVADFVKtNIFARFGMP--RVLiSDGGSHFCNRTI- 1284
Cdd:NF033577   129 ELWHIDIKklGRIPDV-GRLYLHTAIDDHSRFAYAELYPDETAETAADFLR-RAFAEHGIPirRVL-TDNGSEFRSRAHg 205

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1697167483 1285 -EALLKKYKVTHKVSTPYHPQTNGQAEVSNREIKQI-LEKTVGPSRRDwslrLDDALWAYRMAY 1346
Cdd:NF033577   206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEfAYARPYESLAE----LQAALDEWLHHY 265

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1697167483 1132 VHDSEFNAILTFCHTYacGGHFGTQKTaLKVIKCGFYWPTLFKNARTFCLTCDRCQRM 1189
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKT-LARLRRRYWWPGMRKDVKKYVKSCETCQRR 55

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 1697167483  935 ELMCDASDYALGAVLGQRKE-KRPHVIYYASRTLNDAQLNYSTTEKELLAVVFALDKFRSYLLGTKVIIYTDHAALKYLF 1013
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1697167483 1014 TKKEAKPRLIRWMLLLQEFDIEIRDKKGSENVVADHLSRMV 1054
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

RNase H-like domain found in reverse transcriptase;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483  904 FNKECEKAFNHLKEMLTSAPIIVPPDWSFPFELMCDASDYALGAVLGQRKE-KRPHVIYYASRTLNDAQLNYSTTEKELL 982
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1697167483  983 AVVFALDKFRSYLLGTKVII 1002
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100

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 1697167483 1210 DVWGIDF-MGPFPPSFGFTYILLAVDYVSKWVEA-KATRTNDSKVVADFVKTNIFARFGMPRVLISDGGSHFCNRTIEAL 1287
Cdd:pfam00665    3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAwALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1697167483 1288 LKKYKVTHKVSTPYHP 1303
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98

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 1697167483  619 PTREAQRRLNPPMMEVVKKEIIKLLDCGVIYPiSDSRWVSPVQCVPKKSGvivvknaenelvptriqTGWRVCIDCRKLN 698
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVP-CQSPWNTPILPVKKPGG-----------------NDYRMVQDLRLVN 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483  699 ATIRKDHFPLPFIDQMLERL-AGHSFYCFLDGYSGYNQIVIAPDDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMVS 777
Cdd:cd03715     63 QAVLPIHPAVPNPYTLLSLLpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALAR 142

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1697167483  778 IFSDF---VEKIIEV-FMDDFSVFGDSFDGCLENLTKILKRCVETNLVLNWEK---CHFTVRQ-GIVL 837
Cdd:cd03715    143 DLAPFpleHEGTILLqYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKaqiCRAEVKFlGVVW 210

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 1697167483  935 ELMCDASDYALGAVLGQRKekrphviyyASRTLNDAQLNYSTTEKELLAVVFALDKFRSYLLGTKVIIYTDHA-ALKYL- 1012
Cdd:cd09275      1 VLFTDASLSGWGAYLLNSR---------AHGPWSADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTtAVAYIn 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1697167483 1013 ---FTKKEAKPRLIRWMLLL-QEFDIEIRDK--KGSENVVADHLSRMVH 1055
Cdd:cd09275     72 kqgGTSSPPLLALARQILLWcEQRNIWLRAShiPGVLNTEADRLSRLGL 120

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1697167483 1132 VHDSEFNAILTFCHTYacGGHFGTQKTaLKVIKCGFYWPTLFKNARTFCLTCDRCQRM 1189
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKT-LARLRRRYWWPGMRKDVKKYVKSCETCQRR 55

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; 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. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483  974 YSTTEKELLAVVFALDKFRSyLLGTKVIIYTDHAALKYLFTKKEAKPR-----LIRWMLLLQEF-DIEIRDKKGSENVVA 1047
Cdd:cd06222     38 PTALEAELLALLLALELALD-LGYLKVIIESDSKYVVDLINSGSFKWSpnillIEDILLLLSRFwSVKISHVPREGNQVA 116

                   ....*
gi 1697167483 1048 DHLSR 1052
Cdd:cd06222    117 DALAK 121

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. 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 proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697167483  321 GSFTIPCVIGNTKFeQCMLDLGASINVMPYSIYASMNLGELKNDGVIIQLAD-RSNAYPKGVLEdvlVQVGNLIFP-ADF 398
Cdd:cd05483      1 GHFVVPVTINGQPV-RFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANgRVRAARVRLDS---LQIGGITLRnVPA 76

                           90       100
                   ....*....|....*....|....
gi 1697167483  399 YVLDMEdsphSTPLPILLGRPFMK 422
Cdd:cd05483     77 VVLPGD----ALGVDGLLGMDFLR 96