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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 347 LEPSTIPISkAPYRMAPTKLKELKVQ--FQEL----PDKGFIRPNVSPW-----------------GYHQLRIKDSDIPK 403
Cdd:cd01647     3 IEPSSSPYA-SPVVVVKKKDGKLRLCvdYRKLnkvtIKDRYPLPTIDELleelagakvfskldlrsGYHQIPLAEESRPK 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1731035081 404 TVFRSRYGHYEFIVMSFGLTNASTMFMDLMNK 435
Cdd:cd01647    82 TAFRTPFGLYEYTRMPFGLKNAPATFQRLMNK 113

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 268 QGKVFATNKSEAERASTVVT---------------------------------RVELLDHVLSMSTPSREDMLSNEKIKA 314
Cdd:pfam08284   2 QGRVNHLSAEEAEASPDVIQgtflvnsipatvlfdsgathsfishafvgklklPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100
                  ....*....|....*....|....*.
gi 1731035081 315 CQIEIMSHVIDVTLLVLDMHNFDVIL 340
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVIL 107

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 347 LEPSTIPISkAPYRMAPTKLKELKVQ--FQEL----PDKGFIRPNVSPW-----------------GYHQLRIKDSDIPK 403
Cdd:cd01647     3 IEPSSSPYA-SPVVVVKKKDGKLRLCvdYRKLnkvtIKDRYPLPTIDELleelagakvfskldlrsGYHQIPLAEESRPK 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1731035081 404 TVFRSRYGHYEFIVMSFGLTNASTMFMDLMNK 435
Cdd:cd01647    82 TAFRTPFGLYEYTRMPFGLKNAPATFQRLMNK 113

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 268 QGKVFATNKSEAERASTVVT---------------------------------RVELLDHVLSMSTPSREDMLSNEKIKA 314
Cdd:pfam08284   2 QGRVNHLSAEEAEASPDVIQgtflvnsipatvlfdsgathsfishafvgklklPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100
                  ....*....|....*....|....*.
gi 1731035081 315 CQIEIMSHVIDVTLLVLDMHNFDVIL 340
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVIL 107

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 347 LEPSTIPISkAPYRMAPTKLKELKVQ--FQEL----PDKGFIRPNVSPW-----------------GYHQLRIKDSDIPK 403
Cdd:cd01647     3 IEPSSSPYA-SPVVVVKKKDGKLRLCvdYRKLnkvtIKDRYPLPTIDELleelagakvfskldlrsGYHQIPLAEESRPK 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1731035081 404 TVFRSRYGHYEFIVMSFGLTNASTMFMDLMNK 435
Cdd:cd01647    82 TAFRTPFGLYEYTRMPFGLKNAPATFQRLMNK 113

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731035081 268 QGKVFATNKSEAERASTVVT---------------------------------RVELLDHVLSMSTPSREDMLSNEKIKA 314
Cdd:pfam08284   2 QGRVNHLSAEEAEASPDVIQgtflvnsipatvlfdsgathsfishafvgklklPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100
                  ....*....|....*....|....*.
gi 1731035081 315 CQIEIMSHVIDVTLLVLDMHNFDVIL 340
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVIL 107