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Conserved domains on  [gi|445986419|ref|WP_000064274|]
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MULTISPECIES: ParB family protein [Salmonella]

Protein Classification

transcriptional repressor gene korB( domain architecture ID 13507973)

transcriptional repressor gene korB plays a key role in regulation of the copy number of broad host range plasmid RK2

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ParB pfam08775
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 194-319 7.04e-53

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: 169.89  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  194 FPVQSELSFSDYKILLEVNEKLSEKGLTSEGLIQSVSDQHDAIlSDYERPDDEQKSSILKLISQASQALIAPPPKEKSVI 273
Cdd:pfam08775   1 FPVASELSFADYKLLLKVAEKLEEKGESLSELINDVSAEIKAI-ADDNLPEDEQKSEILKLIKSESQRLKDPPVKDKQVV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 445986419  274 SALWTFEEKDKFARKRVKGRTLTYEFSRMSKVVQDELDKAINEVLE 319
Cdd:pfam08775  80 EKLWEFDDKDQFARKKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
parB_part super family cl36599
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 46-217 8.74e-28

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: 106.69  E-value: 8.74e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419   46 VPASDVESKTFVNQETNGRDQLALTRESLKSIIQTIKFQQFF-PCIGIQ---QGERIEILDGSRRRASAIYI-RTGLDVM 120
Cdd:TIGR00180   1 VAEGLIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLqPILVRKhpdQPGRYEIIAGERRWRAAKLAgLKTIPAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  121 VTNELLSADEARHLAKDIQTAKEHNLREIGLRLMALKESGFNQKEIAELEGLSQAKVTRALQAAAVPQELISLFPVQSEL 200
Cdd:TIGR00180  81 VRELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGL 160

                         170
                  ....*....|....*..
gi 445986419  201 SFSDYKILLEVNEKLSE 217
Cdd:TIGR00180 161 LSSGHARLLLALKKKPK 177
 
Name Accession Description Interval E-value
ParB pfam08775
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 194-319 7.04e-53

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: 169.89  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  194 FPVQSELSFSDYKILLEVNEKLSEKGLTSEGLIQSVSDQHDAIlSDYERPDDEQKSSILKLISQASQALIAPPPKEKSVI 273
Cdd:pfam08775   1 FPVASELSFADYKLLLKVAEKLEEKGESLSELINDVSAEIKAI-ADDNLPEDEQKSEILKLIKSESQRLKDPPVKDKQVV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 445986419  274 SALWTFEEKDKFARKRVKGRTLTYEFSRMSKVVQDELDKAINEVLE 319
Cdd:pfam08775  80 EKLWEFDDKDQFARKKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 46-217 8.74e-28

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: 106.69  E-value: 8.74e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419   46 VPASDVESKTFVNQETNGRDQLALTRESLKSIIQTIKFQQFF-PCIGIQ---QGERIEILDGSRRRASAIYI-RTGLDVM 120
Cdd:TIGR00180   1 VAEGLIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLqPILVRKhpdQPGRYEIIAGERRWRAAKLAgLKTIPAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  121 VTNELLSADEARHLAKDIQTAKEHNLREIGLRLMALKESGFNQKEIAELEGLSQAKVTRALQAAAVPQELISLFPVQSEL 200
Cdd:TIGR00180  81 VRELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGL 160

                         170
                  ....*....|....*..
gi 445986419  201 SFSDYKILLEVNEKLSE 217
Cdd:TIGR00180 161 LSSGHARLLLALKKKPK 177
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 58-122 8.40e-14

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: 65.30  E-value: 8.40e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 445986419  58 NQETNGRDQLALTRESLKSIIQTIK-FQQFFPCIGIQQGERIEILDGSRRRASAIYIRTGLDVMVT 122
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKeNGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVS 66
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
36-201 6.73e-13

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 68.34  E-value: 6.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  36 GRKITFRFVRVPASDVESKTFVnQETNGRDQLALTRESLKSIIQTIKFQ-QFFPCIGIQQGERIEILDGSRRRASAIYIR 114
Cdd:PRK13698  52 GRDVKFTLEVIRGDSVEKTSRV-WSGNERDQELLTEDSLDDLIPSFLLTgQQTPAFGRRVSGVIEIADGSRRRKAAILTE 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419 115 TGLDVMVTNelLSADEARHLAKDIQTAKEHNLREIGLRLMALKESGF--NQKEIAELEGLSQAKVTRALQAAAVPQELIS 192
Cdd:PRK13698 131 SDYRVLVGE--LDDEQMAALSRLGNDYRPTSAYERGLRYASRLQNEFagNISALADAENISRKIITRCINTAKLPKSVVA 208


                 ....*....
gi 445986419 193 LFPVQSELS 201
Cdd:PRK13698 209 LFAHPGELS 217
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 72-242 1.65e-08

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: 54.22  E-value: 1.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  72 ESLKSIIQTIKFQ-QFFPCIGIQQGE-RIEILDGSRRRASAIYI-RTGLDVMVTNelLSADEARHLAKDIQTAKE-HNLR 147
Cdd:COG1475   29 EALEELAASIREHgLLQPILVRPLGDgRYEIIAGERRLRAAKLLgLETVPAIVRD--LDDEEALELALIENLQREdLNPL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419 148 EIGLRLMALKE-SGFNQKEIAELEGLSQAKVTRALQAAAVPQELISLFPvQSELSFSDYKILLEVN---------EKLSE 217
Cdd:COG1475  107 EEARAYQRLLEeFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALR-EGKLSLGHARALAALSdperqeelaEKIIE 185

                        170       180
                 ....*....|....*....|....*...
gi 445986419 218 KGLTS---EGLIQSVSDQHDAILSDYER 242
Cdd:COG1475  186 EGLSVretEELVKALAKDLARLERRLSE 213
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 63-138 2.52e-04

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: 39.21  E-value: 2.52e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 445986419    63 GRDQLALT-RESLKSIIQTIKFQ-QFFPCIGIQQGERIEILDGSRRRASAIYIR-TGLDVMVTNELLSADEARHLAKDI 138
Cdd:smart00470  11 NPDQPRLTsEESLEELAESIKENgLLQPIIVRPNDGRYEIIDGERRLRAAKLLGlKEVPVIVRDLDDEEAIALSLEENI 89
 
Name Accession Description Interval E-value
ParB pfam08775
ParB family; ParB is a component of the par system which mediates accurate DNA partition ...
 194-319 7.04e-53

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: 169.89  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  194 FPVQSELSFSDYKILLEVNEKLSEKGLTSEGLIQSVSDQHDAIlSDYERPDDEQKSSILKLISQASQALIAPPPKEKSVI 273
Cdd:pfam08775   1 FPVASELSFADYKLLLKVAEKLEEKGESLSELINDVSAEIKAI-ADDNLPEDEQKSEILKLIKSESQRLKDPPVKDKQVV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 445986419  274 SALWTFEEKDKFARKRVKGRTLTYEFSRMSKVVQDELDKAINEVLE 319
Cdd:pfam08775  80 EKLWEFDDKDQFARKKTKGRTFSYEFSRISKEVQDELDKAIRDVLK 125
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 46-217 8.74e-28

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: 106.69  E-value: 8.74e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419   46 VPASDVESKTFVNQETNGRDQLALTRESLKSIIQTIKFQQFF-PCIGIQ---QGERIEILDGSRRRASAIYI-RTGLDVM 120
Cdd:TIGR00180   1 VAEGLIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLqPILVRKhpdQPGRYEIIAGERRWRAAKLAgLKTIPAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  121 VTNELLSADEARHLAKDIQTAKEHNLREIGLRLMALKESGFNQKEIAELEGLSQAKVTRALQAAAVPQELISLFPVQSEL 200
Cdd:TIGR00180  81 VRELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGL 160

                         170
                  ....*....|....*..
gi 445986419  201 SFSDYKILLEVNEKLSE 217
Cdd:TIGR00180 161 LSSGHARLLLALKKKPK 177
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 58-122 8.40e-14

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: 65.30  E-value: 8.40e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 445986419  58 NQETNGRDQLALTRESLKSIIQTIK-FQQFFPCIGIQQGERIEILDGSRRRASAIYIRTGLDVMVT 122
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKeNGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVS 66
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
36-201 6.73e-13

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 68.34  E-value: 6.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  36 GRKITFRFVRVPASDVESKTFVnQETNGRDQLALTRESLKSIIQTIKFQ-QFFPCIGIQQGERIEILDGSRRRASAIYIR 114
Cdd:PRK13698  52 GRDVKFTLEVIRGDSVEKTSRV-WSGNERDQELLTEDSLDDLIPSFLLTgQQTPAFGRRVSGVIEIADGSRRRKAAILTE 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419 115 TGLDVMVTNelLSADEARHLAKDIQTAKEHNLREIGLRLMALKESGF--NQKEIAELEGLSQAKVTRALQAAAVPQELIS 192
Cdd:PRK13698 131 SDYRVLVGE--LDDEQMAALSRLGNDYRPTSAYERGLRYASRLQNEFagNISALADAENISRKIITRCINTAKLPKSVVA 208


                 ....*....
gi 445986419 193 LFPVQSELS 201
Cdd:PRK13698 209 LFAHPGELS 217
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 72-242 1.65e-08

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: 54.22  E-value: 1.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419  72 ESLKSIIQTIKFQ-QFFPCIGIQQGE-RIEILDGSRRRASAIYI-RTGLDVMVTNelLSADEARHLAKDIQTAKE-HNLR 147
Cdd:COG1475   29 EALEELAASIREHgLLQPILVRPLGDgRYEIIAGERRLRAAKLLgLETVPAIVRD--LDDEEALELALIENLQREdLNPL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445986419 148 EIGLRLMALKE-SGFNQKEIAELEGLSQAKVTRALQAAAVPQELISLFPvQSELSFSDYKILLEVN---------EKLSE 217
Cdd:COG1475  107 EEARAYQRLLEeFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALR-EGKLSLGHARALAALSdperqeelaEKIIE 185

                        170       180
                 ....*....|....*....|....*...
gi 445986419 218 KGLTS---EGLIQSVSDQHDAILSDYER 242
Cdd:COG1475  186 EGLSVretEELVKALAKDLARLERRLSE 213
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 63-138 2.52e-04

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: 39.21  E-value: 2.52e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 445986419    63 GRDQLALT-RESLKSIIQTIKFQ-QFFPCIGIQQGERIEILDGSRRRASAIYIR-TGLDVMVTNELLSADEARHLAKDI 138
Cdd:smart00470  11 NPDQPRLTsEESLEELAESIKENgLLQPIIVRPNDGRYEIIDGERRLRAAKLLGlKEVPVIVRDLDDEEAIALSLEENI 89
 
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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