NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|712915986|ref|YP_009103767|]
View 

ParB-like partition protein [Shewanella sp. phage 1/44]

Protein Classification

ParB/RepB/Spo0J family partition protein( domain architecture ID 11445026)

ParB/RepB/Spo0J family partition protein may be involved in segregation and competition between plasmids and chromosomes, such as the ParB/SpoJ-type DNA-binding component of the prokaryotic parABS partitioning system

CATH:  1.10.10.2830
Gene Ontology:  GO:0003677
PubMed:  16677298|11522360|17161598
SCOP:  4002475

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 36-208 8.25e-20

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: 85.42  E-value: 8.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986  36 FNVR-DICPDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL-IERYECKDYIGTDADQIAMMVTSSQG 113
Cdd:COG1475   20 YNPRrTFDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLgLETVPAIVRDLDDEEALELALIENLQ 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986 114 RV-LSHTERAMAYLRLH-RHGYTYDEIATKCKRSRADVDNHMTLATADARVFQHVKDGTITMNEVNQVIR-KKGDKATEI 190
Cdd:COG1475  100 REdLNPLEEARAYQRLLeEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLGHARALAAlSDPERQEEL 179

                        170       180
                 ....*....|....*....|
gi 712915986 191 IETAVTNATS--KGEKKVKA 208
Cdd:COG1475  180 AEKIIEEGLSvrETEELVKA 199
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 36-208 8.25e-20

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: 85.42  E-value: 8.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986  36 FNVR-DICPDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL-IERYECKDYIGTDADQIAMMVTSSQG 113
Cdd:COG1475   20 YNPRrTFDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLgLETVPAIVRDLDDEEALELALIENLQ 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986 114 RV-LSHTERAMAYLRLH-RHGYTYDEIATKCKRSRADVDNHMTLATADARVFQHVKDGTITMNEVNQVIR-KKGDKATEI 190
Cdd:COG1475  100 REdLNPLEEARAYQRLLeEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLGHARALAAlSDPERQEEL 179

                        170       180
                 ....*....|....*....|
gi 712915986 191 IETAVTNATS--KGEKKVKA 208
Cdd:COG1475  180 AEKIIEEGLSvrETEELVKA 199
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 59-157 7.36e-07

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: 48.14  E-value: 7.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986   59 LPPIVVK--DMGDGNFKIIDGHHRYHA----GEGLIERYECKDYIGT-DADQIAmmvTSSQGRVLSHTERAMAYLRLHRH 131
Cdd:TIGR00180  42 LQPILVRkhPDQPGRYEIIAGERRWRAaklaGLKTIPAIVRELDDEQmLADALI---ENIQREDLSPIEEAQAYKRLLEK 118

                          90       100
                  ....*....|....*....|....*..
gi 712915986  132 GY-TYDEIATKCKRSRADVDNHMTLAT 157
Cdd:TIGR00180 119 FSmTQEDLAKKIGKSRAHITNLLRLLK 145
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 43-83 3.52e-05

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: 40.26  E-value: 3.52e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 712915986  43 PDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHA 83
Cdd:cd16387    2 EEELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERRWRA 42
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 37-106 5.20e-05

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: 41.14  E-value: 5.20e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 712915986    37 NVRDICPDHVAAIRQSYEAGEYLPPIVVkDMGDGNFKIIDGHHRYHAGEGL-IERYEC--KDYIGTDADQIAM 106
Cdd:smart00470  14 QPRLTSEESLEELAESIKENGLLQPIIV-RPNDGRYEIIDGERRLRAAKLLgLKEVPVivRDLDDEEAIALSL 85
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 36-106 5.17e-04

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: 38.03  E-value: 5.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 712915986   36 FNVRDICPDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL-IERYECkdYIGTDADQIAM 106
Cdd:pfam02195  13 DQPRKDSEESLEELAASIKKRGLLQPIIVRKTPDGRYEIIAGERRLRAAKLLgLKEVPV--IVREIDDEEAI 82
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 36-208 8.25e-20

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: 85.42  E-value: 8.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986  36 FNVR-DICPDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL-IERYECKDYIGTDADQIAMMVTSSQG 113
Cdd:COG1475   20 YNPRrTFDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLgLETVPAIVRDLDDEEALELALIENLQ 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986 114 RV-LSHTERAMAYLRLH-RHGYTYDEIATKCKRSRADVDNHMTLATADARVFQHVKDGTITMNEVNQVIR-KKGDKATEI 190
Cdd:COG1475  100 REdLNPLEEARAYQRLLeEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLGHARALAAlSDPERQEEL 179

                        170       180
                 ....*....|....*....|
gi 712915986 191 IETAVTNATS--KGEKKVKA 208
Cdd:COG1475  180 AEKIIEEGLSvrETEELVKA 199
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 59-157 7.36e-07

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: 48.14  E-value: 7.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 712915986   59 LPPIVVK--DMGDGNFKIIDGHHRYHA----GEGLIERYECKDYIGT-DADQIAmmvTSSQGRVLSHTERAMAYLRLHRH 131
Cdd:TIGR00180  42 LQPILVRkhPDQPGRYEIIAGERRWRAaklaGLKTIPAIVRELDDEQmLADALI---ENIQREDLSPIEEAQAYKRLLEK 118

                          90       100
                  ....*....|....*....|....*..
gi 712915986  132 GY-TYDEIATKCKRSRADVDNHMTLAT 157
Cdd:TIGR00180 119 FSmTQEDLAKKIGKSRAHITNLLRLLK 145
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 43-83 3.52e-05

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: 40.26  E-value: 3.52e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 712915986  43 PDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHA 83
Cdd:cd16387    2 EEELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERRWRA 42
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 37-106 5.20e-05

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: 41.14  E-value: 5.20e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 712915986    37 NVRDICPDHVAAIRQSYEAGEYLPPIVVkDMGDGNFKIIDGHHRYHAGEGL-IERYEC--KDYIGTDADQIAM 106
Cdd:smart00470  14 QPRLTSEESLEELAESIKENGLLQPIIV-RPNDGRYEIIDGERRLRAAKLLgLKEVPVivRDLDDEEAIALSL 85
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 43-87 6.42e-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: 40.36  E-value: 6.42e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 712915986  43 PDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL 87
Cdd:cd16409    3 PEHVEALAQSIAEHGLLTPITVRQDPGGRYTLIAGAHRLAAAKLL 47
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 36-106 5.17e-04

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: 38.03  E-value: 5.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 712915986   36 FNVRDICPDHVAAIRQSYEAGEYLPPIVVKDMGDGNFKIIDGHHRYHAGEGL-IERYECkdYIGTDADQIAM 106
Cdd:pfam02195  13 DQPRKDSEESLEELAASIKKRGLLQPIIVRKTPDGRYEIIAGERRLRAAKLLgLKEVPV--IVREIDDEEAI 82
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 59-83 1.78e-03

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: 36.82  E-value: 1.78e-03
                         10        20
                 ....*....|....*....|....*
gi 712915986  59 LPPIVVKDMGDGNFKIIDGHHRYHA 83
Cdd:cd16396   40 LQPIVVRKTKDGGYEIVAGERRWRA 64
SbnI_like_N cd16388
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ...
 40-83 2.23e-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: 35.94  E-value: 2.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 712915986  40 DICPDHVAAIRQSYEAGEYL--PPIVVKdMGDGNFKIIDGHHRYHA 83
Cdd:cd16388   14 EHEPNRLEKLVERIEAEGVLrnPPIVTP-LQDGRYLILDGAHRTTA 58
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH