ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
64-243
1.05e-44
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Pssm-ID: 272946 [Multi-domain] Cd Length: 187 Bit Score: 150.99 E-value: 1.05e-44
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
73-139
4.20e-24
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; Escherichia coli SopB acts in the equitable partitioning of the F plasmid in the SopABC system. SopA binds to the sopAB promoter, while SopB binds SopC and helps stimulate polymerization of SopA in the presence of ATP and Mg(II). Mutation of SopA inhibits proper plasmid segregation. This N-terminal domain is related to the ParB N-terminal domain of bacterial and plasmid parABS partitioning systems, which binds parA.
Pssm-ID: 319252 [Multi-domain] Cd Length: 67 Bit Score: 93.04 E-value: 4.20e-24
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity.
Pssm-ID: 214678 [Multi-domain] Cd Length: 89 Bit Score: 58.08 E-value: 5.56e-11
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
77-153
2.70e-09
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4.
Pssm-ID: 426651 [Multi-domain] Cd Length: 90 Bit Score: 53.44 E-value: 2.70e-09
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
64-243
1.05e-44
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Pssm-ID: 272946 [Multi-domain] Cd Length: 187 Bit Score: 150.99 E-value: 1.05e-44
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
73-139
4.20e-24
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; Escherichia coli SopB acts in the equitable partitioning of the F plasmid in the SopABC system. SopA binds to the sopAB promoter, while SopB binds SopC and helps stimulate polymerization of SopA in the presence of ATP and Mg(II). Mutation of SopA inhibits proper plasmid segregation. This N-terminal domain is related to the ParB N-terminal domain of bacterial and plasmid parABS partitioning systems, which binds parA.
Pssm-ID: 319252 [Multi-domain] Cd Length: 67 Bit Score: 93.04 E-value: 4.20e-24
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity.
Pssm-ID: 214678 [Multi-domain] Cd Length: 89 Bit Score: 58.08 E-value: 5.56e-11
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
77-153
2.70e-09
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4.
Pssm-ID: 426651 [Multi-domain] Cd Length: 90 Bit Score: 53.44 E-value: 2.70e-09
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
79-146
1.41e-06
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on plasmids and secondary chromosomes, works along with repA in directing plasmid segregation, and has been shown in Rhizobium etli to require the parS centromere-like sequence for full transcriptional repression of the repABC operon, inducing plasmid incompatibility. RepA is a Walker-type ATPase that complexes with RepB to form DNA-protein complexes in the presence of ATP/ADP. RepC is an initiator protein for the plasmid. repA and repB are homologous to the parA and ParB genes of the parABS partitioning system found on primary chromosomes.
Pssm-ID: 319262 [Multi-domain] Cd Length: 91 Bit Score: 45.61 E-value: 1.41e-06
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein ...
158-231
2.97e-05
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.
Pssm-ID: 375543 Cd Length: 75 Bit Score: 41.64 E-value: 2.97e-05
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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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
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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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(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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