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Conserved domains on  [gi|640683605|ref|WP_025108068|]
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MULTISPECIES: ParB N-terminal domain-containing protein [Klebsiella]

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

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List of domain hits

 Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 15-184 1.14e-15

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: 74.25  E-value: 1.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  15 KRTDSGMFIRIDELHVKPNFNRREDDErtrQADDELFNYLMNGGTVPPLEVVVRDEGGVWIVEGHRRHRAylrCREAGKp 94
Cdd:COG1475    2 KEGEEIREIPIDKIVPSPYNPRRTFDE---EALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRA---AKLLGL- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  95 vERIQIISFTGNDVERIARIMTSNNQ-LPLTAVEQAAVVKDL-AAFNLTTAEIAKLVHKSIPTVEKLLTLSTADHAIQKS 172
Cdd:COG1475   75 -ETVPAIVRDLDDEEALELALIENLQrEDLNPLEEARAYQRLlEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEA 153

                        170
                 ....*....|..
gi 640683605 173 VKSGEVSASVAV 184
Cdd:COG1475  154 LREGKLSLGHAR 165
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 15-184 1.14e-15

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: 74.25  E-value: 1.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  15 KRTDSGMFIRIDELHVKPNFNRREDDErtrQADDELFNYLMNGGTVPPLEVVVRDEGGVWIVEGHRRHRAylrCREAGKp 94
Cdd:COG1475    2 KEGEEIREIPIDKIVPSPYNPRRTFDE---EALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRA---AKLLGL- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  95 vERIQIISFTGNDVERIARIMTSNNQ-LPLTAVEQAAVVKDL-AAFNLTTAEIAKLVHKSIPTVEKLLTLSTADHAIQKS 172
Cdd:COG1475   75 -ETVPAIVRDLDDEEALELALIENLQrEDLNPLEEARAYQRLlEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEA 153

                        170
                 ....*....|..
gi 640683605 173 VKSGEVSASVAV 184
Cdd:COG1475  154 LREGKLSLGHAR 165
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 22-200 7.34e-06

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: 45.45  E-value: 7.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605   22 FIRIDELHVKPNFNRREddeRTRQADDELFNYLMNGGTVPPleVVVR----DEGGVWIVEGHRRHRAylrCREAGKPVER 97
Cdd:TIGR00180   7 EIDIDLLQPNPYQPRKD---FSEESLAELIESIKEQGQLQP--ILVRkhpdQPGRYEIIAGERRWRA---AKLAGLKTIP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605   98 IQIISFTgnDVERIARIMTSNNQ-LPLTAVEQAAVVKD-LAAFNLTTAEIAKLVHKSIPTVEKLLTLSTADHAIQKSVKS 175
Cdd:TIGR00180  79 AIVRELD--DEQMLADALIENIQrEDLSPIEEAQAYKRlLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPE 156

                         170       180
                  ....*....|....*....|....*
gi 640683605  176 GEVSASVAVDRIKEHGEKAGEVLEQ 200
Cdd:TIGR00180 157 ASGLLSSGHARLLLALKKKPKLQEL 181
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 25-92 8.37e-04

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: 37.50  E-value: 8.37e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  25 IDELHVKPN--FNRREDDERtrqadDELFNYLMNGGTVPPLEVVVRDEGGVWIVEGHRRHRAylrCREAG 92
Cdd:cd16407    1 LSELHPFPNhpFKVRDDEEM-----EELVESIKENGVLTPIIVRPREDGGYEIISGHRRKRA---CELAG 62
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 21-119 2.67e-03

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: 36.13  E-value: 2.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605    21 MFIRIDELHVKPNFNRREDDERtrqaDDELFNYLMNGGTVPPLeVVVRDEGGVWIVEGHRRHRAylrCREAGkpVERIQI 100
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTSEES----LEELAESIKENGLLQPI-IVRPNDGRYEIIDGERRLRA---AKLLG--LKEVPV 70

                           90
                   ....*....|....*....
gi 640683605   101 ISFTGNDVERIARIMTSNN 119
Cdd:smart00470  71 IVRDLDDEEAIALSLEENI 89
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 15-184 1.14e-15

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: 74.25  E-value: 1.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  15 KRTDSGMFIRIDELHVKPNFNRREDDErtrQADDELFNYLMNGGTVPPLEVVVRDEGGVWIVEGHRRHRAylrCREAGKp 94
Cdd:COG1475    2 KEGEEIREIPIDKIVPSPYNPRRTFDE---EALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRA---AKLLGL- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  95 vERIQIISFTGNDVERIARIMTSNNQ-LPLTAVEQAAVVKDL-AAFNLTTAEIAKLVHKSIPTVEKLLTLSTADHAIQKS 172
Cdd:COG1475   75 -ETVPAIVRDLDDEEALELALIENLQrEDLNPLEEARAYQRLlEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEA 153

                        170
                 ....*....|..
gi 640683605 173 VKSGEVSASVAV 184
Cdd:COG1475  154 LREGKLSLGHAR 165
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 22-200 7.34e-06

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: 45.45  E-value: 7.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605   22 FIRIDELHVKPNFNRREddeRTRQADDELFNYLMNGGTVPPleVVVR----DEGGVWIVEGHRRHRAylrCREAGKPVER 97
Cdd:TIGR00180   7 EIDIDLLQPNPYQPRKD---FSEESLAELIESIKEQGQLQP--ILVRkhpdQPGRYEIIAGERRWRA---AKLAGLKTIP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605   98 IQIISFTgnDVERIARIMTSNNQ-LPLTAVEQAAVVKD-LAAFNLTTAEIAKLVHKSIPTVEKLLTLSTADHAIQKSVKS 175
Cdd:TIGR00180  79 AIVRELD--DEQMLADALIENIQrEDLSPIEEAQAYKRlLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPE 156

                         170       180
                  ....*....|....*....|....*
gi 640683605  176 GEVSASVAVDRIKEHGEKAGEVLEQ 200
Cdd:TIGR00180 157 ASGLLSSGHARLLLALKKKPKLQEL 181
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 25-92 8.37e-04

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: 37.50  E-value: 8.37e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605  25 IDELHVKPN--FNRREDDERtrqadDELFNYLMNGGTVPPLEVVVRDEGGVWIVEGHRRHRAylrCREAG 92
Cdd:cd16407    1 LSELHPFPNhpFKVRDDEEM-----EELVESIKENGVLTPIIVRPREDGGYEIISGHRRKRA---CELAG 62
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 21-119 2.67e-03

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: 36.13  E-value: 2.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640683605    21 MFIRIDELHVKPNFNRREDDERtrqaDDELFNYLMNGGTVPPLeVVVRDEGGVWIVEGHRRHRAylrCREAGkpVERIQI 100
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTSEES----LEELAESIKENGLLQPI-IVRPNDGRYEIIDGERRLRA---AKLLG--LKEVPV 70

                           90
                   ....*....|....*....
gi 640683605   101 ISFTGNDVERIARIMTSNN 119
Cdd:smart00470  71 IVRDLDDEEAIALSLEENI 89
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 56-98 6.03e-03

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: 35.21  E-value: 6.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 640683605  56 NGGTVPpleVVVR---DEGGVW-IVEGHRRHRAylrCREAGKPVERI 98
Cdd:cd16405   34 SGQQVP---ILVRphpEEGGRYeIVYGHRRLRA---CRELGLPVRAI 74
 
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.
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