nucleoid occlusion protein [Halalkalibacter krulwichiae]
Protein Classification
nucleoid occlusion protein( domain architecture ID 11500023)
nucleoid occlusion protein affects nucleoid occlusion by binding relatively nonspecifically to DNA and preventing the assembly of the division machinery in the vicinity of the nucleoid, especially under conditions that disturb the cell cycle
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| nucleoid_noc | TIGR04285 | nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ... |
35-288 | 3.48e-157 | |||||
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete. : Pssm-ID: 275105 [Multi-domain] Cd Length: 255 Bit Score: 438.10 E-value: 3.48e-157
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| Name | Accession | Description | Interval | E-value | |||||
| nucleoid_noc | TIGR04285 | nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ... |
35-288 | 3.48e-157 | |||||
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete. Pssm-ID: 275105 [Multi-domain] Cd Length: 255 Bit Score: 438.10 E-value: 3.48e-157
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| Spo0J | COG1475 | Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ... |
31-228 | 4.32e-84 | |||||
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: 252.22 E-value: 4.32e-84
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| SPO0J_N | cd16393 | Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ... |
36-131 | 2.69e-44 | |||||
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: 145.70 E-value: 2.69e-44
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| ParB | smart00470 | ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ... |
37-126 | 2.14e-27 | |||||
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: 101.61 E-value: 2.14e-27
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| ParBc | pfam02195 | ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ... |
37-126 | 7.77e-27 | |||||
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: 100.43 E-value: 7.77e-27
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| PRK13832 | PRK13832 | plasmid partitioning protein; Provisional |
52-200 | 3.48e-13 | |||||
plasmid partitioning protein; Provisional Pssm-ID: 184353 [Multi-domain] Cd Length: 520 Bit Score: 69.35 E-value: 3.48e-13
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| Name | Accession | Description | Interval | E-value | |||||
| nucleoid_noc | TIGR04285 | nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ... |
35-288 | 3.48e-157 | |||||
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete. Pssm-ID: 275105 [Multi-domain] Cd Length: 255 Bit Score: 438.10 E-value: 3.48e-157
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| Spo0J | COG1475 | Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ... |
31-228 | 4.32e-84 | |||||
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: 252.22 E-value: 4.32e-84
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| parB_part | TIGR00180 | ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ... |
34-212 | 1.37e-63 | |||||
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: 198.37 E-value: 1.37e-63
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| SPO0J_N | cd16393 | Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ... |
36-131 | 2.69e-44 | |||||
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: 145.70 E-value: 2.69e-44
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| Noc_N | cd16396 | nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ... |
34-127 | 2.26e-42 | |||||
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: 140.82 E-value: 2.26e-42
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| PRTRC_parB | TIGR03734 | PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ... |
44-233 | 4.57e-39 | |||||
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: 143.70 E-value: 4.57e-39
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| ParB | smart00470 | ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ... |
37-126 | 2.14e-27 | |||||
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: 101.61 E-value: 2.14e-27
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| ParBc | pfam02195 | ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ... |
37-126 | 7.77e-27 | |||||
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: 100.43 E-value: 7.77e-27
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| KorB_N_like | cd16398 | ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ... |
41-131 | 3.28e-21 | |||||
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: 85.40 E-value: 3.28e-21
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| ParB_N_like | cd16407 | ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ... |
41-124 | 6.77e-20 | |||||
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: 81.80 E-value: 6.77e-20
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| ParB_N_like | cd16406 | ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ... |
55-129 | 3.68e-19 | |||||
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: 319263 [Multi-domain] Cd Length: 82 Bit Score: 79.87 E-value: 3.68e-19
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| ParB_N_Srx | cd16387 | ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ... |
56-108 | 9.44e-19 | |||||
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: 78.01 E-value: 9.44e-19
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| ParB_N_like | cd16408 | ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ... |
44-124 | 1.95e-17 | |||||
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: 75.36 E-value: 1.95e-17
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| ParB_N_like | cd16409 | ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ... |
56-126 | 1.20e-16 | |||||
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: 72.72 E-value: 1.20e-16
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| HTH_ParB | pfam17762 | HTH domain found in ParB protein; |
176-225 | 2.44e-16 | |||||
HTH domain found in ParB protein; Pssm-ID: 465489 Cd Length: 50 Bit Score: 71.26 E-value: 2.44e-16
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| RepB_like_N | cd16405 | plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ... |
42-125 | 6.33e-14 | |||||
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: 66.03 E-value: 6.33e-14
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| PRK13832 | PRK13832 | plasmid partitioning protein; Provisional |
52-200 | 3.48e-13 | |||||
plasmid partitioning protein; Provisional Pssm-ID: 184353 [Multi-domain] Cd Length: 520 Bit Score: 69.35 E-value: 3.48e-13
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| ParB_N_like | cd16410 | ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ... |
60-114 | 4.13e-12 | |||||
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: 319267 [Multi-domain] Cd Length: 80 Bit Score: 60.68 E-value: 4.13e-12
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| ParB_N_like_MT | cd16403 | ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ... |
41-111 | 7.71e-12 | |||||
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. 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: 319260 [Multi-domain] Cd Length: 88 Bit Score: 60.16 E-value: 7.71e-12
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| ParB_N_like_MT | cd16402 | ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ... |
41-110 | 1.62e-09 | |||||
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. 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: 319259 [Multi-domain] Cd Length: 87 Bit Score: 53.77 E-value: 1.62e-09
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| PRK13866 | PRK13866 | plasmid partitioning protein RepB; Provisional |
29-148 | 5.86e-08 | |||||
plasmid partitioning protein RepB; Provisional Pssm-ID: 172387 [Multi-domain] Cd Length: 336 Bit Score: 53.04 E-value: 5.86e-08
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| ParB_N_like | cd16411 | ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ... |
39-126 | 7.82e-08 | |||||
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: 49.14 E-value: 7.82e-08
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| ParB_N_like_MT | cd16401 | ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ... |
46-111 | 1.48e-07 | |||||
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. 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: 319258 [Multi-domain] Cd Length: 85 Bit Score: 48.37 E-value: 1.48e-07
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| pNOB8_ParB_N_like | cd16404 | pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ... |
49-115 | 5.30e-07 | |||||
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: 46.11 E-value: 5.30e-07
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| sopB_N | cd16394 | N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ... |
57-101 | 1.82e-05 | |||||
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: 41.81 E-value: 1.82e-05
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| ParB_N_like_MT | cd16844 | ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ... |
60-109 | 1.96e-05 | |||||
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. 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: 319272 [Multi-domain] Cd Length: 54 Bit Score: 41.48 E-value: 1.96e-05
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| ParB_Srx_like_nuclease | cd16400 | ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ... |
46-114 | 6.60e-05 | |||||
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB. Pssm-ID: 319257 [Multi-domain] Cd Length: 72 Bit Score: 40.22 E-value: 6.60e-05
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| IbrB_like | cd16397 | immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ... |
36-95 | 2.02e-04 | |||||
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx. Pssm-ID: 319255 [Multi-domain] Cd Length: 100 Bit Score: 39.86 E-value: 2.02e-04
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| Srx | cd16395 | Sulfiredoxin reactivates peroxiredoxins after oxidative inactivation; Sulfiredoxin reduces and ... |
36-107 | 2.42e-04 | |||||
Sulfiredoxin reactivates peroxiredoxins after oxidative inactivation; Sulfiredoxin reduces and thereby re-activates 2-cys peroxiredoxins. Peroxiredoxins act as molecular switches, inactivating in response to hyperoxidation from hydrogen peroxide and other free radicals. Sulfiredoxin reactivates Prx-SO(2)(-) via ATP-Mg(2+)-dependent reduction. Arabidopsis sulfiredoxin has been described as a dual function enzyme, having nuclease activity in addition to the sulfiredoxin activity. This protein is similar to ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems. Pssm-ID: 319253 [Multi-domain] Cd Length: 90 Bit Score: 39.13 E-value: 2.42e-04
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| SbnI_like_N | cd16388 | N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ... |
55-114 | 6.22e-03 | |||||
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression. Pssm-ID: 319247 [Multi-domain] Cd Length: 77 Bit Score: 34.79 E-value: 6.22e-03
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