Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  475 YYDPSKDLIAEIQKQGEGQWTYQIYQEPFKNLKTGKYAKRRGTHTNDVKQLTEAVQKIATESIVIWGKTPKFRLPIQKET 554
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 2125447770  555 WETWWTEYWQATWIPEWEFVNT 576
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  594 AETFYVDGAANRETKLGKAGYVTDRGRQKIV-SLN-DTTNQKTELQAINLALQD--SGLEVNIVTDSQYALGII------ 663
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHENISaPLPgRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2125447770  664 ---QAQPDQSESELV--SQIIEQL---IKKEKVYLAWVPAHKGIGGNEQVDKLVSSGIR 714
Cdd:pfam00075   83 wkkNGWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141

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 2125447770  774 SPGIWQLDCTHLEGKI------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKTVHTDNGSNFTSNTVK 844
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 2125447770  845 AACWWAGIKQEFGIPYNP 862
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.

                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2125447770  727 DEHEKYHSNWRAMASDFNLPPVVAKEIVACCDKCQ 761
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35

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 2125447770  220 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 287
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  288 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIEQHRTKIEELR 363
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2125447770  364 AHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 391
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770   63 LWQRPLVTIKIGGQLKEALLDTGADDTVLEDMNLPGRW----KPKMIGGIGGFIKVRQYDQIQVEICGHKAIGTV--LIG 136
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 2125447770  137 PT-PVNIIGRNLLTQIGCTLN 156
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, 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 2125447770   69 VTIKIGGQLKEALLDTGADDTVLEDMNLPGRW----KPKMIGGIGGFIKVRQYDQIQVEICGHKAIGTVLIGP--TPVNI 142
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80

                   ....*..
gi 2125447770  143 IGRNLLT 149
Cdd:cd05482     81 WGRDILS 87

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 2125447770  774 SPGIWQLDCTHLEGKI------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKTVHTDNGSNFTSNTVK 844
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 2125447770  845 AACWWAGIKQEFGIPYNP 862
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98

Ribonuclease HI [Replication, recombination and repair];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  598 YVDGAANRETklGKAGY---VTDRGRQKIVS--LNDTTNQKTELQAINLALQ----DSGLEVNIVTDSQYALGIIQAQPD 668
Cdd:COG0328      6 YTDGACRGNP--GPGGWgavIRYGGEEKELSggLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIH 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2125447770  669 QSES---------ELVsQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSSGI 713
Cdd:COG0328     84 GWKKngwkpvknpDLW-QRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. 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 2125447770  596 TFYVDGAANrETKLGkAGYVTDRGRQKIVSLNDTTNQKT----ELQAINLALQ------DSGLEVNIVTDSQYALGIIQ- 664
Cdd:cd09276      1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSALQALRn 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2125447770  665 --AQPDQSESELVSQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKL 708
Cdd:cd09276     79 prRSSGQVILIRILRLLRLLKAKGvKVRLRWVPGHVGIEGNEAADRL 125

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  829 TVHTDNGSNFTSNTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 905
Cdd:COG2801    211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290

                   ....*..
gi 2125447770  906 GGIGGYS 912
Cdd:COG2801    291 SSLGYLT 297

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 2125447770  220 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 287
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  288 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIEQHRTKIEELR 363
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2125447770  364 AHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 391
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770   63 LWQRPLVTIKIGGQLKEALLDTGADDTVLEDMNLPGRW----KPKMIGGIGGFIKVRQYDQIQVEICGHKAIGTV--LIG 136
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 2125447770  137 PT-PVNIIGRNLLTQIGCTLN 156
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101

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 2125447770  176 PRVKQWPLTEEKIKALVEICTEMEKEGKIskIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 255
Cdd:cd03715      2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  256 GL-----KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPsinnetpGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRK 330
Cdd:cd03715     77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 2125447770  331 QNPDIVIYQYMDDLYVGSDLEIEQHRTKIEELRaHLLKWGFTTPDKKHQ 379
Cdd:cd03715    150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, 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 2125447770   69 VTIKIGGQLKEALLDTGADDTVLEDMNLPGRW----KPKMIGGIGGFIKVRQYDQIQVEICGHKAIGTVLIGP--TPVNI 142
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80

                   ....*..
gi 2125447770  143 IGRNLLT 149
Cdd:cd05482     81 WGRDILS 87

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 2125447770  306 LPQGWKGSPAIFQCSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLeiEQHRTKIEELRAHLLKWGFTTPDKKHQ---KEP 382
Cdd:cd00304     12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKS--EQQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89

                   ....*....
gi 2125447770  383 PFLWMGYEL 391
Cdd:cd00304     90 KFKFLGILV 98

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2125447770  942 VYYRDSRDPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 985
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.

                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2125447770  727 DEHEKYHSNWRAMASDFNLPPVVAKEIVACCDKCQ 761
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. 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 2125447770  596 TFYVDGAAnreTKLGKAGYVTDRGRQKIVSLNDTTNQKTELQAINLALQD-SGLEVNIVTDSQYALGIIQA--------- 665
Cdd:cd09273      1 TVFTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLletigierg 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 2125447770  666 -QPDQSESELVSQIIEQLIKKEKVYLAWVPAHKGIG-----GNEQVDKLV 709
Cdd:cd09273     78 fLKSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and 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 (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  598 YVDGAA-NRETKLGKAGYV------TDRGRQKIVSLNDTTNQKTELQAINLALQ----DSGLEVNIVTDSQYALGII--- 663
Cdd:cd09280      3 YTDGSClNNGKPGARAGIGvyfgpgDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCItkw 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2125447770  664 ----QAQPDQSES-------ELVSQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKL 708
Cdd:cd09280     83 ipkwKKNGWKTSKgkpvknqDLIKELDKLLRKRGiKVKFEHVKGHSGDPGNEEADRL 139

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and 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 (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  598 YVDGAANRETklGKAGY---VTDRGRQKIVS--LNDTTNQKTELQAINLALQ--DSGLEVNIVTDSQYAL-GIIQAQPD- 668
Cdd:cd09278      5 YTDGACLGNP--GPGGWaavIRYGDHEKELSggEPGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGITKWIKGw 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2125447770  669 ------QSESELVS-----QIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSSGIR 714
Cdd:cd09278     83 kkngwkTADGKPVKnrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125447770  266 LDVGDAYFSVPLDEDFRKYTAFtIPSinnetpGIRYQYNVLPQGWKGSPAIFqcsmTKILEP--FRKQNPDIVIYQYMDD 343
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEAllAPLRLLGVRIFSYLDD 69

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2125447770  344 -LYVGSDLEIEQHRtkIEELRAHLL-KWGFTTPDKKHQKEP 382
Cdd:cd03714     70 lLIIASSIKTSEAV--LRHLRATLLaNLGFTLNLEKSKLGP 108

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, 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 2125447770   69 VTIKIGGQLKEALLDTGADDTVL-EDMNLPGRWKPK--MIGGIGGFIK--VRQYDQiQVEICGHKAIGTVLIGPT-PVNI 142
Cdd:cd06095      1 VTITVEGVPIVFLVDTGATHSVLkSDLGPKQELSTTsvLIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDPL 79

                   ....*..
gi 2125447770  143 IGRNLLT 149
Cdd:cd06095     80 LGRDLLS 86