TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
158-233
1.14e-05
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
:
Pssm-ID: 173779 [Multi-domain] Cd Length: 79 Bit Score: 43.80 E-value: 1.14e-05
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a ...
366-683
2.23e-47
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: 169.83 E-value: 2.23e-47
Family of unknown function (DUF5906); This is a family of proteins of unknown function found ...
455-570
4.63e-10
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: 57.38 E-value: 4.63e-10
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
158-233
1.14e-05
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Pssm-ID: 173779 [Multi-domain] Cd Length: 79 Bit Score: 43.80 E-value: 1.14e-05
phage/plasmid primase, P4 family, C-terminal domain; This model represents a clade within a ...
366-683
2.23e-47
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: 169.83 E-value: 2.23e-47
Family of unknown function (DUF5906); This is a family of proteins of unknown function found ...
455-570
4.63e-10
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: 57.38 E-value: 4.63e-10
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
158-233
1.14e-05
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Pssm-ID: 173779 [Multi-domain] Cd Length: 79 Bit Score: 43.80 E-value: 1.14e-05
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
159-231
2.01e-04
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 40.49 E-value: 2.01e-04
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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Functional characterization of the conserved domain architecture found on the query.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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