Ty1/Copia 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 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 Ty1/Copia family is 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 1129212379 1510 EAYVDSNWAPERNnDRRSLSGCVILVDGFPIKAFTRTQTSVAMSSAEAELVAITEGAKEAVGVVALVRHIWGTFrtcEDP 1589
Cdd:cd09272      1 EGYSDADWAGDPD-DRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPL---DGP 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1129212379 1590 PAVYSDSQAAINIGSMHGLLRRVRHIDLRVCWTQAAIQDKLITLSWVPGAKNPADIFTKALGKP 1653
Cdd:cd09272     77 TTIYCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140

Ty1/Copia 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 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 Ty1/Copia family is 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 1129212379 1510 EAYVDSNWAPERNnDRRSLSGCVILVDGFPIKAFTRTQTSVAMSSAEAELVAITEGAKEAVGVVALVRHIWGTFrtcEDP 1589
Cdd:cd09272      1 EGYSDADWAGDPD-DRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPL---DGP 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1129212379 1590 PAVYSDSQAAINIGSMHGLLRRVRHIDLRVCWTQAAIQDKLITLSWVPGAKNPADIFTKALGKP 1653
Cdd:cd09272     77 TTIYCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140

zinc finger;

                            10
                    ....*....|....*..
gi 1129212379   231 KCFNCGEKGHFARDCPK 247
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                           10        20        30
                   ....*....|....*....|....*....|.
gi 1129212379  222 SQSASPSKGKCFNCGEKGHFARDC-PKPRKS 251
Cdd:COG5082     90 RSNHCPKPKKCYNCGETGHLSRDCnPSKDQQ 120

Ty1/Copia 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 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 Ty1/Copia family is 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 1129212379 1510 EAYVDSNWAPERNnDRRSLSGCVILVDGFPIKAFTRTQTSVAMSSAEAELVAITEGAKEAVGVVALVRHIWGTFrtcEDP 1589
Cdd:cd09272      1 EGYSDADWAGDPD-DRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPL---DGP 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1129212379 1590 PAVYSDSQAAINIGSMHGLLRRVRHIDLRVCWTQAAIQDKLITLSWVPGAKNPADIFTKALGKP 1653
Cdd:cd09272     77 TTIYCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140

zinc finger;

                            10
                    ....*....|....*..
gi 1129212379   231 KCFNCGEKGHFARDCPK 247
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17

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 1129212379 1530 GCVILVDGFPIKAFTRTQTSvaMSSAEAELVAITEGAKEAVGVVALVRHIWgtfrtcedppaVYSDSQAA---INIGSMH 1606
Cdd:cd09276     16 GFVIYRGGEVISRSYRLGTH--ASVFDAELEAILEALELALATARRARKVT-----------IFTDSQSAlqaLRNPRRS 82

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1129212379 1607 GLLRRVRHIDLRVCwtQAAIQDKLITLSWVPG 1638
Cdd:cd09276     83 SGQVILIRILRLLR--LLKAKGVKVRLRWVPG 112

universal minicircle sequence binding protein (UMSBP); Provisional

                           10        20
                   ....*....|....*....|
gi 1129212379  231 KCFNCGEKGHFARDCPKPRK 250
Cdd:PTZ00368    79 SCYNCGQTGHISRECPNRAK 98

universal minicircle sequence binding protein (UMSBP); Provisional

                           10
                   ....*....|....*.
gi 1129212379  231 KCFNCGEKGHFARDCP 246
Cdd:PTZ00368   131 TCYNCGQTGHLSRDCP 146

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                           10        20
                   ....*....|....*....|....*.
gi 1129212379  221 RSQSASPSKgKCFNCGEKGHFARDCP 246
Cdd:COG5082     53 VSAIREENP-VCFNCGQNGHLRRDCP 77