conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1583996286   1 YIDDILVFSKNEKDHLRHLEIMFSLVEKHGLVLSPTKMKIGVHSIGFLG 49
Cdd:cd01647   126 YLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLG 174

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1583996286   1 YIDDILVFSKNEKDHLRHLEIMFSLVEKHGLVLSPTKMKIGVHSIGFLG 49
Cdd:cd01647   126 YLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLG 174

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1583996286   1 YIDDILVFSKNEKDHLRHLEIMFSLVEKHGLVLSPTKMKI--GVHSIGFLG 49
Cdd:pfam00078 136 YADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFflKSKEVKYLG 186

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1583996286   1 YIDDILVFSKNEKDHLRHLEIMFSLVEKHGLVLSPTKMKIGVHSIGFLG 49
Cdd:cd01647   126 YLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLG 174

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1583996286   1 YIDDILVFSKNEKDHLRHLEIMFSLVEKHGLVLSPTKMKI--GVHSIGFLG 49
Cdd:pfam00078 136 YADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFflKSKEVKYLG 186

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 1583996286 149 ILETDGCMTGWGAICKwkekefdpqkseriCAYASGVFS---TVKSTIDAEINAVLHALESFKiFYLDQKGIIIRTDCQA 225
Cdd:cd09275     1 VLFTDASLSGWGAYLL--------------NSRAHGPWSadeRNKHINLLELKAVLLALQHFA-AELKNRKILIRTDNTT 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1583996286 226 IITFFNK----SFNHKPSRVR--WIRFIDFitgiGISYKFEHIKGEANQLADHLSRHT 277
Cdd:cd09275    66 AVAYINKqggtSSPPLLALARqiLLWCEQR----NIWLRASHIPGVLNTEADRLSRLG 119

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 1583996286 152 TDGCM----TGWGAICKWKEKEFdpQKSERICAYASgVFstvkstiDAEINAVLHALESFKIFYLDQKGIIIRTDCQAII 227
Cdd:cd09276     4 TDGSKlegsVGAGFVIYRGGEVI--SRSYRLGTHAS-VF-------DAELEAILEALELALATARRARKVTIFTDSQSAL 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1583996286 228 TFFNKSFNHKPS--RVRWIRFIDFITGIGISYKFEHIKG----EANQLADHLSR 275
Cdd:cd09276    74 QALRNPRRSSGQviLIRILRLLRLLKAKGVKVRLRWVPGhvgiEGNEAADRLAK 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 1583996286 195 AEINAVLHALESfkIFYLDQKGIIIRTDCQ-AIITFFNKSFNHKPSRVR------------WIRFIDFITGIGISYKFEH 261
Cdd:cd09280    46 AELLAVIHALEQ--APEEGIRKLEIRTDSKyAINCITKWIPKWKKNGWKtskgkpvknqdlIKELDKLLRKRGIKVKFEH 123

                          90
                  ....*....|....*...
gi 1583996286 262 IKG----EANQLADHLSR 275
Cdd:cd09280   124 VKGhsgdPGNEEADRLAR 141

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1583996286 177 RICAYASGVFSTVKSTIDAEINAVLHALEsfKIFYLDQKGIIIRTDCQAIITFFNKSFNHKPSRVRWIRFIDFITGIGIS 256
Cdd:pfam13456  25 NVLLAGQKKLGPGASVLEAEAQALIIGLQ--LAWKLGIRHLIVEGDSATVVQLINGRSPKQSKLANLLDEIRKLLKRFES 102

                          90       100
                  ....*....|....*....|
gi 1583996286 257 YKFEHIKGEANQLADHLSRH 276
Cdd:pfam13456 103 VSFEHIPREQNRVADTLAKM 122