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 374532018 173 GPKVKQWPLTEEKIKALTEICT*MEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 253 AGLKKKKSVTVLDVGDAYFSVPLHESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRJKNPE 332
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374532018 333 IVIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLSWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 374532018  396 VQPI*LPDKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGAKALT 445
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLT 52

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 173 GPKVKQWPLTEEKIKALTEICT*MEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 253 AGLKKKKSVTVLDVGDAYFSVPLHESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRJKNPE 332
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374532018 333 IVIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLSWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

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 374532018   61 LWQRPLVTVKVGGQLKEALLDTGADDTVLEDIBLPGKW----KP*MIGGIGGFIKVRQYDQI*IEICGKKAIGTV--LVG 134
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 374532018  135 PT-PVNIIGRNMLTQLGCTLN 154
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 374532018  396 VQPI*LPDKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGAKALT 445
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLT 52

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 173 GPKVKQWPLTEEKIKALTEICT*MEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 253 AGLKKKKSVTVLDVGDAYFSVPLHESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRJKNPE 332
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374532018 333 IVIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLSWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

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 374532018 174 PKVKQWPLTEEKIKALTEICT*MEKEGKIskIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 253
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 254 GL-----KKKKSVTVLDVGDAYFSVPLHESFRKYTAFTIpsinnetPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRJ 328
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEW-------EGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 374532018 329 KNPEIVIYQYMDDLYVGSDLEIGQHRTKIEELRaHLLSWGFTTPDKKHQ 377
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197

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 374532018 210 PYNTPVFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLHESFRKYTA 284
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374532018 285 FTipsinneTPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRJKNPEIviyqYMDDLYVGSDleigqhrtKIEELRAHL 364
Cdd:cd01647   84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEV----YLDDILVYSK--------TEEEHLEHL 144

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 374532018  67 VTVKVGGQLKEALLDTGADDTVLEDIBLPGKWKP*MIGGIGG----FIKVRQYDQI*IEICGKKAIGTVLVGP--TPVNI 140
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTgiggAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80

                 ....*..
gi 374532018 141 IGRNMLT 147
Cdd:cd05482   81 WGRDILS 87

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 374532018 264 LDVGDAYFSVPLHESFRKYTAFtIPSinnetpGIRYQYNVLPQGWKGSPAIFqcsmTKILEP--FRJKNPEIVIYQYMDD 341
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEAllAPLRLLGVRIFSYLDD 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 374532018 342 LyvgsdLEIGQHRTKIEELRAHLLSW-----GFTTPDKKHQKEP 380
Cdd:cd03714   70 L-----LIIASSIKTSEAVLRHLRATllanlGFTLNLEKSKLGP 108