AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and ...
11-146
7.16e-03
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.
The actual alignment was detected with superfamily member smart00943:
Pssm-ID: 470148 Cd Length: 154 Bit Score: 37.71 E-value: 7.16e-03
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a ...
361-635
2.64e-08
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions]
Pssm-ID: 273716 [Multi-domain] Cd Length: 304 Bit Score: 55.81 E-value: 2.64e-08
Family of unknown function (DUF5906); This is a family of proteins of unknown function found ...
435-547
1.08e-05
Family of unknown function (DUF5906); This is a family of proteins of unknown function found in viruses. This family is a P-loop member whose proteins are thought to be SF3 helicases, which are involved in replication initiation.
Pssm-ID: 466016 [Multi-domain] Cd Length: 114 Bit Score: 45.05 E-value: 1.08e-05
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
11-146
7.16e-03
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.
Pssm-ID: 214927 Cd Length: 154 Bit Score: 37.71 E-value: 7.16e-03
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a ...
361-635
2.64e-08
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions]
Pssm-ID: 273716 [Multi-domain] Cd Length: 304 Bit Score: 55.81 E-value: 2.64e-08
Family of unknown function (DUF5906); This is a family of proteins of unknown function found ...
435-547
1.08e-05
Family of unknown function (DUF5906); This is a family of proteins of unknown function found in viruses. This family is a P-loop member whose proteins are thought to be SF3 helicases, which are involved in replication initiation.
Pssm-ID: 466016 [Multi-domain] Cd Length: 114 Bit Score: 45.05 E-value: 1.08e-05
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
11-146
7.16e-03
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.
Pssm-ID: 214927 Cd Length: 154 Bit Score: 37.71 E-value: 7.16e-03
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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