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 2221560340   3 QHIDDPVLIGLIEQYLYYSIEDGGEIF-----TPQHGIcrgcaLSPLIGASLLHHVDSYFAAQEGTF-YARYMDDFVLLT 76
Cdd:TIGR04416 148 RRISDKRVLRLIRRWLKAGVMEDGEVQeteegTPQGGV-----ISPLLANIYLHYLDDEWEKRGYKVrFVRYADDFVILC 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340  77 RTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGRIEH-GFDWLGVWFTPTGT-------TIAPRAlENHRAQRLRLYEQ-A 147
Cdd:TIGR04416 223 RSKEAAERVLEALTKRLEELGLELNPEKTKIVHCKDgGFDFLGFTFRKRKSkngkgklLIKPSK-KAVKKFKEKIRELtK 301

                  ....*....
gi 2221560340 148 RRRGLPVAD 156
Cdd:TIGR04416 302 RRRGLSLEE 310

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340   3 QHIDDPVLIGLIEQYLYYSIEDGGEIF-----TPQHGIcrgcaLSPLIGASLLHHVDSYFAAQEGTF-YARYMDDFVLLT 76
Cdd:TIGR04416 148 RRISDKRVLRLIRRWLKAGVMEDGEVQeteegTPQGGV-----ISPLLANIYLHYLDDEWEKRGYKVrFVRYADDFVILC 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340  77 RTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGRIEH-GFDWLGVWFTPTGT-------TIAPRAlENHRAQRLRLYEQ-A 147
Cdd:TIGR04416 223 RSKEAAERVLEALTKRLEELGLELNPEKTKIVHCKDgGFDFLGFTFRKRKSkngkgklLIKPSK-KAVKKFKEKIRELtK 301

                  ....*....
gi 2221560340 148 RRRGLPVAD 156
Cdd:TIGR04416 302 RRRGLSLEE 310

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340   1 MQQHIDDPVLIGLIEQYLYYSIEDGGEIFTPQHGICRGCALSPL------------IGASLLHHVDSYFAAQEGTFYARY 68
Cdd:cd01651    93 LKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLlaniylheldkfVEEKLKEYYDTSDPKFRRLRYVRY 172

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2221560340  69 MDDFVLLTRTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGRI-EHGFDWLGVWF 121
Cdd:cd01651   173 ADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFkSEGFDFLGFTF 226

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340   3 QHIDDPVLIGLIEQYLYYSIEDGGEIF-----TPQHGIcrgcaLSPLIGASLLHHVDSYFAAQEGTF-YARYMDDFVLLT 76
Cdd:TIGR04416 148 RRISDKRVLRLIRRWLKAGVMEDGEVQeteegTPQGGV-----ISPLLANIYLHYLDDEWEKRGYKVrFVRYADDFVILC 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340  77 RTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGRIEH-GFDWLGVWFTPTGT-------TIAPRAlENHRAQRLRLYEQ-A 147
Cdd:TIGR04416 223 RSKEAAERVLEALTKRLEELGLELNPEKTKIVHCKDgGFDFLGFTFRKRKSkngkgklLIKPSK-KAVKKFKEKIRELtK 301

                  ....*....
gi 2221560340 148 RRRGLPVAD 156
Cdd:TIGR04416 302 RRRGLSLEE 310

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340   1 MQQHIDDPVLIGLIEQYLYYSIEDGGEIFTPQHGICRGCALSPL------------IGASLLHHVDSYFAAQEGTFYARY 68
Cdd:cd01651    93 LKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLlaniylheldkfVEEKLKEYYDTSDPKFRRLRYVRY 172

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2221560340  69 MDDFVLLTRTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGRI-EHGFDWLGVWF 121
Cdd:cd01651   173 ADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFkSEGFDFLGFTF 226

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2221560340  31 PQHGICRGCALSPLIGASLLHHVDSYFA-AQEGTFYARYMDDFVLLTRTRWQLRRCVKRLHEFFNLSGFETHPDKTHLGR 109
Cdd:cd01646    50 QTNGLPIGPLTSRFLANIYLNDVDHELKsKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILP 129

                          90
                  ....*....|....*...
gi 2221560340 110 IEHG---FDWLGVWFTPT 124
Cdd:cd01646   130 LPEGtasKDFLGYRFSPI 147

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2221560340  68 YMDDFVLLTRTRWQLRRCVKRLHEFFNLSGFETHPDKThlgRIEHGFDWLG 118
Cdd:cd01645   163 YMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKV---QKEPPFQYLG 210