plasmid partitioning protein RepB [Rhizobium ruizarguesonis]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| partition_RepB super family | cl37271 | plasmid partitioning protein RepB; Members of this family are the RepB protein involved in ... |
11-338 | 1.67e-100 | ||||||
plasmid partitioning protein RepB; Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions] The actual alignment was detected with superfamily member TIGR03454: Pssm-ID: 274586 [Multi-domain] Cd Length: 325 Bit Score: 299.24 E-value: 1.67e-100
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| Name | Accession | Description | Interval | E-value | ||||||
| partition_RepB | TIGR03454 | plasmid partitioning protein RepB; Members of this family are the RepB protein involved in ... |
11-338 | 1.67e-100 | ||||||
plasmid partitioning protein RepB; Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions] Pssm-ID: 274586 [Multi-domain] Cd Length: 325 Bit Score: 299.24 E-value: 1.67e-100
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| PRK13866 | PRK13866 | plasmid partitioning protein RepB; Provisional |
11-341 | 6.71e-65 | ||||||
plasmid partitioning protein RepB; Provisional Pssm-ID: 172387 [Multi-domain] Cd Length: 336 Bit Score: 208.66 E-value: 6.71e-65
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| RepB_like_N | cd16405 | plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ... |
74-163 | 6.87e-43 | ||||||
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: 143.45 E-value: 6.87e-43
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| Spo0J | COG1475 | Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ... |
68-256 | 3.52e-36 | ||||||
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 441084 [Multi-domain] Cd Length: 241 Bit Score: 130.88 E-value: 3.52e-36
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| ParBc | pfam02195 | ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ... |
72-163 | 4.62e-15 | ||||||
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: 69.62 E-value: 4.62e-15
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| ParB | smart00470 | ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ... |
72-163 | 1.33e-14 | ||||||
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: 68.49 E-value: 1.33e-14
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| Name | Accession | Description | Interval | E-value | ||||||
| partition_RepB | TIGR03454 | plasmid partitioning protein RepB; Members of this family are the RepB protein involved in ... |
11-338 | 1.67e-100 | ||||||
plasmid partitioning protein RepB; Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions] Pssm-ID: 274586 [Multi-domain] Cd Length: 325 Bit Score: 299.24 E-value: 1.67e-100
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| PRK13866 | PRK13866 | plasmid partitioning protein RepB; Provisional |
11-341 | 6.71e-65 | ||||||
plasmid partitioning protein RepB; Provisional Pssm-ID: 172387 [Multi-domain] Cd Length: 336 Bit Score: 208.66 E-value: 6.71e-65
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| RepB_like_N | cd16405 | plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ... |
74-163 | 6.87e-43 | ||||||
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: 143.45 E-value: 6.87e-43
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| Spo0J | COG1475 | Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ... |
68-256 | 3.52e-36 | ||||||
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 441084 [Multi-domain] Cd Length: 241 Bit Score: 130.88 E-value: 3.52e-36
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| parB_part | TIGR00180 | ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ... |
69-254 | 3.50e-26 | ||||||
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: 102.84 E-value: 3.50e-26
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| ParB_N_like | cd16407 | ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ... |
84-158 | 1.71e-15 | ||||||
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319264 [Multi-domain] Cd Length: 86 Bit Score: 70.62 E-value: 1.71e-15
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| ParBc | pfam02195 | ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ... |
72-163 | 4.62e-15 | ||||||
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: 69.62 E-value: 4.62e-15
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| ParB | smart00470 | ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ... |
72-163 | 1.33e-14 | ||||||
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: 68.49 E-value: 1.33e-14
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| KorB_N_like | cd16398 | ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ... |
100-169 | 1.45e-14 | ||||||
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related domains; KorB, a member of the ParB like family, is present on the low copy number, broad host range plasmid RK2. KorB encodes a gene product involved in segregation of RK2 and acts as a transcriptional regulator, down-regulating at least 6 RK2 operons. KorB binds RNA polymerase and acts cooperatively with several co-repressors in modulating transcription. KorB is comprised of 3 domains, including a beta-strand C-terminal domain similar to SH3 domains and an alpha helical central domain that interacts with operator DNA. In ParB of P1 and SopB of F, the N-terminal region is responsible for interaction with the parA component. However, korB interaction with the RK2 parA-equivalent IncC has been mapped to the central HTH motif. This family is related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319256 [Multi-domain] Cd Length: 91 Bit Score: 68.45 E-value: 1.45e-14
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| SPO0J_N | cd16393 | Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ... |
101-169 | 1.69e-12 | ||||||
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; Spo0J (stage 0 sporulation protein J) is a ParB family member, a critical component of the ParABS-type bacterial chromosome segregation system. The Spo0J N-terminal region acts in protein-protein interaction and is adjacent to the DNA-binding domain that binds to parS sites. Two Spo0J bind per parS site, and Spo0J interacts with neighbors via the N-terminal domain to form oligomers via an Arginine-rich patch (RRXR). This superfamily represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319251 [Multi-domain] Cd Length: 97 Bit Score: 62.89 E-value: 1.69e-12
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| Noc_N | cd16396 | nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ... |
92-163 | 7.22e-12 | ||||||
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning protein family; Nucleoid occlusion protein has been shown in Bacillus subtilis to bind to specific DNA sequences on the chromosome (Noc-binding DNA sequences, NBS), inhibiting cell division near the nucleoid and thereby protecting the chromosome. This N-terminal domain is related to the N-terminal domain of ParB/repB partitioning system proteins. Pssm-ID: 319254 [Multi-domain] Cd Length: 95 Bit Score: 61.08 E-value: 7.22e-12
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| PRTRC_parB | TIGR03734 | PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ... |
93-196 | 1.37e-11 | ||||||
PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein. Pssm-ID: 274755 [Multi-domain] Cd Length: 554 Bit Score: 65.50 E-value: 1.37e-11
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| RepB | pfam07506 | RepB plasmid partitioning protein; This family includes proteins with sequence similarity to ... |
166-312 | 3.15e-09 | ||||||
RepB plasmid partitioning protein; This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens. Pssm-ID: 311449 Cd Length: 185 Bit Score: 55.94 E-value: 3.15e-09
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| ParB_N_Srx | cd16387 | ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ... |
93-146 | 5.07e-08 | ||||||
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain/Sulfiredoxin (Srx) superfamily contains proteins with diverse activities. Many of the families are involved in segregation and competition between plasmids and chromosomes. Several families share similar activities with the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system. Also within this superfamily is sulfiredoxin (Srx; reactivator of oxidatively inactivated 2-cys peroxiredoxins), RepB N-terminal domain (plasmid segregation replication protein B like protein), nucleoid occlusion protein, KorB N-terminal domain partition protein of low copy number plasmid RK2, irbB (immunoglobulin-binding regulator that activates eib genes), N-terminal domain of sopB protein (promotes proper partitioning of F1 plasmid), fertility inhibition factors OSA and FiwA,DNA sulfur modification protein DndB, and a ParB-like toxin domain. Other activities includes a StrR (regulator in the streptomycin biosynthetic gene cluster), and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators sbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ). Nuclease activity has also been reported in Arabidopsis Srx. Pssm-ID: 319246 [Multi-domain] Cd Length: 54 Bit Score: 48.74 E-value: 5.07e-08
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| ParB_N_like | cd16411 | ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ... |
72-163 | 1.83e-06 | ||||||
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319268 [Multi-domain] Cd Length: 90 Bit Score: 45.67 E-value: 1.83e-06
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| ParB_N_like | cd16408 | ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ... |
99-154 | 2.32e-05 | ||||||
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319265 [Multi-domain] Cd Length: 84 Bit Score: 42.23 E-value: 2.32e-05
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| ParB_N_like | cd16409 | ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ... |
101-163 | 2.49e-05 | ||||||
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci. Pssm-ID: 319266 [Multi-domain] Cd Length: 74 Bit Score: 41.90 E-value: 2.49e-05
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| pNOB8_ParB_N_like | cd16404 | pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ... |
95-153 | 4.02e-04 | ||||||
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins. Pssm-ID: 319261 [Multi-domain] Cd Length: 69 Bit Score: 38.41 E-value: 4.02e-04
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