AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and ...
22-344
9.24e-111
AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41.
:
Pssm-ID: 240130 Cd Length: 232 Bit Score: 324.95 E-value: 9.24e-111
AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and ...
22-344
9.24e-111
AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41.
Pssm-ID: 240130 Cd Length: 232 Bit Score: 324.95 E-value: 9.24e-111
DNA primase small subunit; DNA primase synthesizes the RNA primers for the Okazaki fragments ...
108-334
8.21e-37
DNA primase small subunit; DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. The family also contains many bacterial DNA primases.
Pssm-ID: 460377 [Multi-domain] Cd Length: 158 Bit Score: 131.96 E-value: 8.21e-37
DNA primase, eukaryotic-type, small subunit, putative; Archaeal members differ substantially ...
12-335
2.85e-28
DNA primase, eukaryotic-type, small subunit, putative; Archaeal members differ substantially from eukaryotic members and should be considered putative pending experimental evidence. The protein is universal and single copy among completed archaeal and eukarotic genomes to date. DNA primase creates RNA primers needed for DNA replication.This model is named putative because the assignment is putative for archaeal proteins. Eukaryotic proteins scoring above the trusted cutoff can be considered authentic. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273020 Cd Length: 297 Bit Score: 113.07 E-value: 2.85e-28
AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and ...
22-344
9.24e-111
AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41.
Pssm-ID: 240130 Cd Length: 232 Bit Score: 324.95 E-value: 9.24e-111
DNA primase small subunit; DNA primase synthesizes the RNA primers for the Okazaki fragments ...
108-334
8.21e-37
DNA primase small subunit; DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. The family also contains many bacterial DNA primases.
Pssm-ID: 460377 [Multi-domain] Cd Length: 158 Bit Score: 131.96 E-value: 8.21e-37
DNA primase, eukaryotic-type, small subunit, putative; Archaeal members differ substantially ...
12-335
2.85e-28
DNA primase, eukaryotic-type, small subunit, putative; Archaeal members differ substantially from eukaryotic members and should be considered putative pending experimental evidence. The protein is universal and single copy among completed archaeal and eukarotic genomes to date. DNA primase creates RNA primers needed for DNA replication.This model is named putative because the assignment is putative for archaeal proteins. Eukaryotic proteins scoring above the trusted cutoff can be considered authentic. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273020 Cd Length: 297 Bit Score: 113.07 E-value: 2.85e-28
AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and ...
43-171
2.63e-16
AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro.
Pssm-ID: 238291 [Multi-domain] Cd Length: 136 Bit Score: 75.09 E-value: 2.63e-16
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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