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 1207117108 311 LACDASPYGVGAVLSHVMASVEERPIAFASKTLNSAESNYAQIEREA----*GVKNFHQYLFGRKFTLLTDHRPLTSIFG 386
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELlaivWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1207117108 387 AQTGIPslaahRMQRWALLLSAHQYDIKYRRSEHHCNADGLSRLP 431
Cdd:cd09274    82 QKDLNG-----RLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

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 1207117108 311 LACDASPYGVGAVLSHVMASVEERPIAFASKTLNSAESNYAQIEREA----*GVKNFHQYLFGRKFTLLTDHRPLTSIFG 386
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELlaivWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1207117108 387 AQTGIPslaahRMQRWALLLSAHQYDIKYRRSEHHCNADGLSRLP 431
Cdd:cd09274    82 QKDLNG-----RLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 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 1207117108  60 VLKKD-GTVRICGDI--------KVTVNPVLTVEQ--YPLPLIEDLFAGLSGGQKFSKIDLCQAYLQMQVDPVSQELLTI 128
Cdd:pfam00078   1 IPKKGkGKYRPISLLsidykalnKIIVKRLKPENLdsPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207117108 129 VTH-----------KGLYRYQRLPFGITSAPALFQRAMDQILSGLNG-----VQCYFDDLLITGKDDEEHLRNLNETLQR 192
Cdd:pfam00078  81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKragltLVRYADDILIFSKSEEEHQEALEEVLEW 160

                         170       180
                  ....*....|....*....|....*....
gi 1207117108 193 LKEYGLRVKKDKCEFF--QPTIEYLGHVI 219
Cdd:pfam00078 161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189

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 1207117108 311 LACDASPYGVGAVLSHVMASVEERPIAFASKTLNSAESNYAQIEREA----*GVKNFHQYLFGRKFTLLTDHRPLTSIFG 386
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELlaivWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1207117108 387 AQTGIPslaahRMQRWALLLSAHQYDIKYRRSEHHCNADGLSRLP 431
Cdd:cd09274    82 QKDLNG-----RLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

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 1207117108 304 NPSLPIQLACDASPYGVGAVLSHVMASVEERPIAFASKTLNSAESNYAQIEREA----*GVKNFHQYLFGRKFTLLTDHR 379
Cdd:pfam17917   1 DPSKPFILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELlaivWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....*....
gi 1207117108 380 PLTSIFGAQTGIPslaahRMQRWALLLSA 408
Cdd:pfam17917  81 PLKYLFTPKELNG-----RLARWALFLQE 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 1207117108  36 FACLEETGVLKTvSVSEWATPIVPVLKKDG-TVRICGDIKvTVNPVLTVEQYPLPLIEDLFAGLS-GGQKFSKIDLCQAY 113
Cdd:cd03715    21 IQELLEAGILVP-CQSPWNTPILPVKKPGGnDYRMVQDLR-LVNQAVLPIHPAVPNPYTLLSLLPpKHQWYTVLDLANAF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207117108 114 LQMQVDPVSQELLTIVTHKGLYRYQRLPFGITSAPALFQRAMDQIL-------SGLNGVQcYFDDLLITGKDDEEHLRNL 186
Cdd:cd03715    99 FSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLapfplehEGTILLQ-YVDDLLLAADSEEDCLKGT 177

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1207117108 187 NETLQRLKEYGLRVKKDKCEFFQPTIEYLGHVI 219
Cdd:cd03715   178 DALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 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 1207117108  49 SVSEWATPIVPVLKKDGTVRICGDIKvTVN----PVLTVEQ-YPLPliedlfAGLSGGQKFSKIDLCQAYLQMQVDPVSQ 123
Cdd:cd01645    33 STSPWNTPVFVIKKKSGKWRLLHDLR-AVNaqtqDMGALQPgLPHP------AALPKGWPLIVLDLKDCFFSIPLHPDDR 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207117108 124 EL--LTI--VTHKGLY-RYQ--RLPFGITSAPALFQRAMDQILSGLNGvQC-------YFDDLLITGKDDEEHLRNLNET 189
Cdd:cd01645   106 ERfaFTVpsINNKGPAkRYQwkVLPQGMKNSPTICQSFVAQALEPFRK-QYpdiviyhYMDDILIASDLEGQLREIYEEL 184

                         170       180       190
                  ....*....|....*....|....*....|
gi 1207117108 190 LQRLKEYGLRVKKDKCEfFQPTIEYLGHVI 219
Cdd:cd01645   185 RQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207117108 139 RLPFGITSAPALFQRAMDQILSGLNGVQ------CYFDDLLI--TGKDDEEHLRNLNETLQRlkeYGLRVKKDKCEFFQP 210
Cdd:cd00304    11 PLPQGSPLSPALANLYMEKLEAPILKQLlditliRYVDDLVViaKSEQQAVKKRELEEFLAR---LGLNLSDEKTQFTEK 87

                          90
                  ....*....|.
gi 1207117108 211 T--IEYLGHVI 219
Cdd:cd00304    88 EkkFKFLGILV 98

RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207117108 119 DPVSQELLTIVTHKGlyryqRLPFGITSAPA---LFQRAMDQILSGL---NGV--QCYFDDLLITGKD-DEEHLRNLNET 189
Cdd:cd03487    88 PDVATILAKLCTYNG-----HLPQGAPTSPAlsnLVFRKLDERLSKLaksNGLtyTRYADDITFSSNKkLKEALDKLLEI 162

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1207117108 190 LQR-LKEYGLRVKKDKCEFFQPT--IEYLGHVIDSTGLHTAPSKVKAI 234
Cdd:cd03487   163 IRSiLSEEGFKINKSKTRISSKGsrQIVTGLVVNNGKPSLPRKEKRKI 210