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Conserved domains on  [gi|447201582|ref|WP_001278838|]
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MULTISPECIES: ParB family protein [Enterobacterales]

Protein Classification

DNA sulfur modification protein DndB( domain architecture ID 13507920)

DNA sulfur modification protein DndB acts in the regulation of DNA modifications, including DNA phosphorothioation, by binding near the phosphorothioate modification site and regulating access of the Dnd modification machinery to DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 68-134 2.64e-23

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: 91.11  E-value: 2.64e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447201582  68 VHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVKRDGVYLLIEGSRRRFCCIKAEKDLPLWVLP 134
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVSK 67
parB_part super family cl36599
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 60-232 2.16e-08

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.


The actual alignment was detected with superfamily member TIGR00180:

Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 53.15  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582   60 QRVEKETLVHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVK---RDGVYLLIEGSRRRFCCIKAEKDlPLWVLPDE 136
Cdd:TIGR00180   5 LIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKhpdQPGRYEIIAGERRWRAAKLAGLK-TIPAIVRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  137 LTED--DINSIISAAQTSRKFSYREVgfQFIKKMEEKGFSTNEELAAYLGISHVSVAKRIQAARIDETLISLFPDYEGIP 214
Cdd:TIGR00180  84 LDDEqmLADALIENIQREDLSPIEEA--QAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLL 161

                         170
                  ....*....|....*...
gi 447201582  215 NSYYSRLSRLQKYVQKNL 232
Cdd:TIGR00180 162 SSGHARLLLALKKKPKLQ 179
ParB super family cl38291
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 207-331 8.53e-08

ParB family; ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognizes A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site.


The actual alignment was detected with superfamily member pfam08775:

Pssm-ID: 430210  Cd Length: 125  Bit Score: 50.09  E-value: 8.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  207 FPDYEgIPNSYYSRLSRLQKyvqknlfPLDEVIDNVKEETKDLDIGDLQVA--QKVVMEKITQSVESVCEKTYSTKWETS 284
Cdd:pfam08775   9 FADYK-LLLKVAEKLEEKGE-------SLSELINDVSAEIKAIADDNLPEDeqKSEILKLIKSESQRLKDPPVKDKQVVE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 447201582  285 DLITFDNKDKYARisKNNTGRKIRFEFNRINAGFIKELEEFIKEKLK 331
Cdd:pfam08775  81 KLWEFDDKDQFAR--KKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
 
Name Accession Description Interval E-value
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 68-134 2.64e-23

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: 91.11  E-value: 2.64e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447201582  68 VHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVKRDGVYLLIEGSRRRFCCIKAEKDLPLWVLP 134
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVSK 67
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 60-232 2.16e-08

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: 53.15  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582   60 QRVEKETLVHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVK---RDGVYLLIEGSRRRFCCIKAEKDlPLWVLPDE 136
Cdd:TIGR00180   5 LIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKhpdQPGRYEIIAGERRWRAAKLAGLK-TIPAIVRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  137 LTED--DINSIISAAQTSRKFSYREVgfQFIKKMEEKGFSTNEELAAYLGISHVSVAKRIQAARIDETLISLFPDYEGIP 214
Cdd:TIGR00180  84 LDDEqmLADALIENIQREDLSPIEEA--QAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLL 161

                         170
                  ....*....|....*...
gi 447201582  215 NSYYSRLSRLQKYVQKNL 232
Cdd:TIGR00180 162 SSGHARLLLALKKKPKLQ 179
ParB pfam08775
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 207-331 8.53e-08

ParB family; ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognizes A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site.


Pssm-ID: 430210  Cd Length: 125  Bit Score: 50.09  E-value: 8.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  207 FPDYEgIPNSYYSRLSRLQKyvqknlfPLDEVIDNVKEETKDLDIGDLQVA--QKVVMEKITQSVESVCEKTYSTKWETS 284
Cdd:pfam08775   9 FADYK-LLLKVAEKLEEKGE-------SLSELINDVSAEIKAIADDNLPEDeqKSEILKLIKSESQRLKDPPVKDKQVVE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 447201582  285 DLITFDNKDKYARisKNNTGRKIRFEFNRINAGFIKELEEFIKEKLK 331
Cdd:pfam08775  81 KLWEFDDKDQFAR--KKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
56-247 1.17e-06

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 49.46  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  56 IVPAQRVEKETLVHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVKRDGVYLLIEGSRRRFCCIKAEKDLPlwVLPD 135
Cdd:PRK13698  61 VIRGDSVEKTSRVWSGNERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVSGVIEIADGSRRRKAAILTESDYR--VLVG 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582 136 ELTEDDINSIISAAQTSRKFSYREVGFQFIKKMEEKgFSTN-EELAAYLGISHVSVAKRIQAARIDETLISLFPDyegiP 214
Cdd:PRK13698 139 ELDDEQMAALSRLGNDYRPTSAYERGLRYASRLQNE-FAGNiSALADAENISRKIITRCINTAKLPKSVVALFAH----P 213

                        170       180       190
                 ....*....|....*....|....*....|....
gi 447201582 215 NSYYSRLSR-LQKYVQKNLFPLDEVIDNVKEETK 247
Cdd:PRK13698 214 GELSARSGEaLQKAFTDKEELLKQQTSNLHEQKK 247
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 68-209 2.60e-06

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: 48.06  E-value: 2.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  68 VHPANPRNQeaLTDYSVRDILKQIEERGVdTEGIAVKR--DGVYLLIEGSRRRFCCIKAEKD-LPLWVLpdELTEDDINS 144
Cdd:COG1475   17 PSPYNPRRT--FDEEALEELAASIREHGL-LQPILVRPlgDGRYEIIAGERRLRAAKLLGLEtVPAIVR--DLDDEEALE 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447201582 145 IISAAQTSRK-FSYREVGFQFIKKMEEKGFsTNEELAAYLGISHVSVAKRIQAARIDETLISLFPD 209
Cdd:COG1475   92 LALIENLQREdLNPLEEARAYQRLLEEFGL-TQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALRE 156
 
Name Accession Description Interval E-value
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 68-134 2.64e-23

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: 91.11  E-value: 2.64e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447201582  68 VHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVKRDGVYLLIEGSRRRFCCIKAEKDLPLWVLP 134
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVSK 67
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 60-232 2.16e-08

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: 53.15  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582   60 QRVEKETLVHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVK---RDGVYLLIEGSRRRFCCIKAEKDlPLWVLPDE 136
Cdd:TIGR00180   5 LIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKhpdQPGRYEIIAGERRWRAAKLAGLK-TIPAIVRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  137 LTED--DINSIISAAQTSRKFSYREVgfQFIKKMEEKGFSTNEELAAYLGISHVSVAKRIQAARIDETLISLFPDYEGIP 214
Cdd:TIGR00180  84 LDDEqmLADALIENIQREDLSPIEEA--QAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLL 161

                         170
                  ....*....|....*...
gi 447201582  215 NSYYSRLSRLQKYVQKNL 232
Cdd:TIGR00180 162 SSGHARLLLALKKKPKLQ 179
ParB pfam08775
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 207-331 8.53e-08

ParB family; ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognizes A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site.


Pssm-ID: 430210  Cd Length: 125  Bit Score: 50.09  E-value: 8.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  207 FPDYEgIPNSYYSRLSRLQKyvqknlfPLDEVIDNVKEETKDLDIGDLQVA--QKVVMEKITQSVESVCEKTYSTKWETS 284
Cdd:pfam08775   9 FADYK-LLLKVAEKLEEKGE-------SLSELINDVSAEIKAIADDNLPEDeqKSEILKLIKSESQRLKDPPVKDKQVVE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 447201582  285 DLITFDNKDKYARisKNNTGRKIRFEFNRINAGFIKELEEFIKEKLK 331
Cdd:pfam08775  81 KLWEFDDKDQFAR--KKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
56-247 1.17e-06

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 49.46  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  56 IVPAQRVEKETLVHPANPRNQEALTDYSVRDILKQIEERGVDTEGIAVKRDGVYLLIEGSRRRFCCIKAEKDLPlwVLPD 135
Cdd:PRK13698  61 VIRGDSVEKTSRVWSGNERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVSGVIEIADGSRRRKAAILTESDYR--VLVG 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582 136 ELTEDDINSIISAAQTSRKFSYREVGFQFIKKMEEKgFSTN-EELAAYLGISHVSVAKRIQAARIDETLISLFPDyegiP 214
Cdd:PRK13698 139 ELDDEQMAALSRLGNDYRPTSAYERGLRYASRLQNE-FAGNiSALADAENISRKIITRCINTAKLPKSVVALFAH----P 213

                        170       180       190
                 ....*....|....*....|....*....|....
gi 447201582 215 NSYYSRLSR-LQKYVQKNLFPLDEVIDNVKEETK 247
Cdd:PRK13698 214 GELSARSGEaLQKAFTDKEELLKQQTSNLHEQKK 247
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 68-209 2.60e-06

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: 48.06  E-value: 2.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201582  68 VHPANPRNQeaLTDYSVRDILKQIEERGVdTEGIAVKR--DGVYLLIEGSRRRFCCIKAEKD-LPLWVLpdELTEDDINS 144
Cdd:COG1475   17 PSPYNPRRT--FDEEALEELAASIREHGL-LQPILVRPlgDGRYEIIAGERRLRAAKLLGLEtVPAIVR--DLDDEEALE 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447201582 145 IISAAQTSRK-FSYREVGFQFIKKMEEKGFsTNEELAAYLGISHVSVAKRIQAARIDETLISLFPD 209
Cdd:COG1475   92 LALIENLQREdLNPLEEARAYQRLLEEFGL-TQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALRE 156
 
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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