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 1731009143 198 KRAPFSLKGK---FQRCMMATFSDFLERSVEIFMDDFSGLGDSFKVCLRSLEDFLEKCEETRLVLNWEKRHFMVREGIVL 274
Cdd:cd01647    94 TRMPFGLKNApatFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFL 173

                  ....
gi 1731009143 275 GHKI 278
Cdd:cd01647   174 GHIV 177

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731009143 357 DVWGIDF-MGPFPQSGGHIYILLAINYVSKMFEAISCMKN-DAIIVNKFLKRNIFMRFRTPRALISDEGSHFINRIIAKL 434
Cdd:pfam00665   3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 1731009143 435 LAKYNINHKVATTYYP 450
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98

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 1731009143 198 KRAPFSLKGK---FQRCMMATFSDFLERSVEIFMDDFSGLGDSFKVCLRSLEDFLEKCEETRLVLNWEKRHFMVREGIVL 274
Cdd:cd01647    94 TRMPFGLKNApatFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFL 173

                  ....
gi 1731009143 275 GHKI 278
Cdd:cd01647   174 GHIV 177

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731009143 357 DVWGIDF-MGPFPQSGGHIYILLAINYVSKMFEAISCMKN-DAIIVNKFLKRNIFMRFRTPRALISDEGSHFINRIIAKL 434
Cdd:pfam00665   3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 1731009143 435 LAKYNINHKVATTYYP 450
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98

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        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731009143 208 FQRCMMATFSDFLER---SVEIFMDDFSGLGDSFKVCLRSLEDFLEKCEETRLVLNWEKRHFM--VREGIVLGHKI 278
Cdd:pfam00078 114 FQLFMNELLRPLRKRaglTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189

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 1731009143 198 KRAPFSLKGK---FQRCMMATFSDFLERSVEIFMDDFSGLGDSFKVCLRSLEDFLEKCEETRLVLNWEKRHFMVREGIVL 274
Cdd:cd01647    94 TRMPFGLKNApatFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFL 173

                  ....
gi 1731009143 275 GHKI 278
Cdd:cd01647   174 GHIV 177

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731009143 357 DVWGIDF-MGPFPQSGGHIYILLAINYVSKMFEAISCMKN-DAIIVNKFLKRNIFMRFRTPRALISDEGSHFINRIIAKL 434
Cdd:pfam00665   3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 1731009143 435 LAKYNINHKVATTYYP 450
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98

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        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731009143 208 FQRCMMATFSDFLER---SVEIFMDDFSGLGDSFKVCLRSLEDFLEKCEETRLVLNWEKRHFM--VREGIVLGHKI 278
Cdd:pfam00078 114 FQLFMNELLRPLRKRaglTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189