zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1219107116  11 LFQRGMNIDPICPMCGSENETILHMLALCPEAKRI 45
Cdd:pfam13966  50 LKKRGIPIDSRCPLCGQEEETIDHLFFSCPFARQL 84

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 1219107116 151 INSDAAIFDNSA-VGLGGVMRDALGEVVVATClCLRSKYEVDVAEALALRHSLRIALESEFRKVCLETDCMKVFSHLTKG 229
Cdd:cd06222     1 INVDGSCRGNPGpAGIGGVLRDHEGGWLGGFA-LKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1219107116 230 CAPATILGMVINDIMQLARGCQSCSFSFVKRSGNGAAHALAK 271
Cdd:cd06222    80 SFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121

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 1219107116 151 INSDAAIFDNSA-VGLGGVMRDALGEVVVATClCLRSKYEVDVAEALALRHSLRIALESEFRKVCLETDCMKVFSHLTKG 229
Cdd:cd06222     1 INVDGSCRGNPGpAGIGGVLRDHEGGWLGGFA-LKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1219107116 230 CAPATILGMVINDIMQLARGCQSCSFSFVKRSGNGAAHALAK 271
Cdd:cd06222    80 SFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; 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. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219107116 192 VAEALALRHSLRIALESEFRKVCLETDCMKVFSHLTKGCaPATILGMVI--NDIMQLARGCQSCSFSFVKRSGNGAAHAL 269
Cdd:cd09279    44 EAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEY-KVKNERLKPllEKVLELLAKFELVELKWIPREQNKEADAL 122

                  ...
gi 1219107116 270 AKL 272
Cdd:cd09279   123 ANQ 125