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 2099874784   1 LQILRDELLSGHYQPLPARRVYIPKSNGKLRPLGIPALRDRI 42
Cdd:TIGR04416  36 LYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRV 77

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
                  ....*....|....*....|....*....|....*....|..
gi 2099874784   1 LQILRDELLSGHYQPLPARRVYIPKSNGKLRPLGIPALRDRI 42
Cdd:TIGR04416  36 LYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRV 77

IS5 family transposase;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099874784  20 RVYIPKSNGKLRPLGIPAL---RDRISIRAKVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLF 86
Cdd:NF033581  215 KPHIPRKKSRNRPLTEAQKrrnRLKSKIRARVEHVFGVLKRFFGLSKVRYRGLKRVGARFNLIAALYNLE 284

Transposase DDE domain; Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. This family contains transposases for IS4, IS421, IS5377, IS427, IS402, IS1355, IS5, which was original isolated in bacteriophage lambda.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2099874784  43 SIRAKVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLAN 84
Cdd:pfam01609 155 RRRWQIERVFKWLKRVFGLDRLRYRGLNAVEAELLLLALAYN 196

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
                  ....*....|....*....|....*....|....*....|..
gi 2099874784   1 LQILRDELLSGHYQPLPARRVYIPKSNGKLRPLGIPALRDRI 42
Cdd:TIGR04416  36 LYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRV 77

IS5 family transposase;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099874784  20 RVYIPKSNGKLRPLGIPAL---RDRISIRAKVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLF 86
Cdd:NF033581  215 KPHIPRKKSRNRPLTEAQKrrnRLKSKIRARVEHVFGVLKRFFGLSKVRYRGLKRVGARFNLIAALYNLE 284

Transposase DDE domain; Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. This family contains transposases for IS4, IS421, IS5377, IS427, IS402, IS1355, IS5, which was original isolated in bacteriophage lambda.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2099874784  43 SIRAKVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLAN 84
Cdd:pfam01609 155 RRRWQIERVFKWLKRVFGLDRLRYRGLNAVEAELLLLALAYN 196