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Conserved domains on  [gi|908266154|gb|AKT04112|]
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protein sopB (plasmid) [Yersinia pestis 1045]

Protein Classification

PRK13698 family protein( domain architecture ID 11486800)

PRK13698 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
2-320 0e+00

ParB/RepB/Spo0J family plasmid partition protein;


:

Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 524.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   2 MKRSPVLRNAPSinfdDAKPAISNAEPSVSAPAVSQLASRVSGM-KGNTIVLPVCGRNVAFTLKVIAAPDVESKTIVFSG 80
Cdd:PRK13698   1 MKRAPVIPKHTS----DTQPAEDTSEPSPAAPMVDSLIARVGGMaRGNAITLPVCGRDVKFTLEVIRGDSVEKTSRVWSG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  81 NERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTGSDYKVLVGNLNDEQMLWLSQIANEYR 160
Cdd:PRK13698  77 NERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVSGVIEIADGSRRRKAAILTESDYRVLVGELDDEQMAALSRLGNDYR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 161 PTSAYERGLRYAQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYENNVDTLK 240
Cdd:PRK13698 157 PTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDKEELLK 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 241 RVTHKIMKQKQEGRQFTTEELIVLLMPERKQPENIH-----KKSFGKNIEAKYSKDNVSFYLKS--VPESLVKQIEELLN 313
Cdd:PRK13698 237 QQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASRtslssRHQFAPGATALYKGDKVVFNLDRsrVPTECIEKIEAILK 316


                 ....*..
gi 908266154 314 TYAKEHS 320
Cdd:PRK13698 317 ELEKPAS 323
 
Name Accession Description Interval E-value
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
2-320 0e+00

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 524.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   2 MKRSPVLRNAPSinfdDAKPAISNAEPSVSAPAVSQLASRVSGM-KGNTIVLPVCGRNVAFTLKVIAAPDVESKTIVFSG 80
Cdd:PRK13698   1 MKRAPVIPKHTS----DTQPAEDTSEPSPAAPMVDSLIARVGGMaRGNAITLPVCGRDVKFTLEVIRGDSVEKTSRVWSG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  81 NERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTGSDYKVLVGNLNDEQMLWLSQIANEYR 160
Cdd:PRK13698  77 NERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVSGVIEIADGSRRRKAAILTESDYRVLVGELDDEQMAALSRLGNDYR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 161 PTSAYERGLRYAQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYENNVDTLK 240
Cdd:PRK13698 157 PTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDKEELLK 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 241 RVTHKIMKQKQEGRQFTTEELIVLLMPERKQPENIH-----KKSFGKNIEAKYSKDNVSFYLKS--VPESLVKQIEELLN 313
Cdd:PRK13698 237 QQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASRtslssRHQFAPGATALYKGDKVVFNLDRsrVPTECIEKIEAILK 316


                 ....*..
gi 908266154 314 TYAKEHS 320
Cdd:PRK13698 317 ELEKPAS 323
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 79-247 4.57e-36

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: 128.27  E-value: 4.57e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   79 SGNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHN---GNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQ 154
Cdd:TIGR00180  15 PNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKHPdqpGRYEIIAGERRWRAAKLAGlKTIPAIVRELDDEQMLADAL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  155 IANEYR-PTSAYERGLRYAqRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYE 233
Cdd:TIGR00180  95 IENIQReDLSPIEEAQAYK-RLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALK 173

                         170
                  ....*....|....
gi 908266154  234 NNVDTLKRVTHKIM 247
Cdd:TIGR00180 174 KKPKLQELLASIII 187
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 77-142 1.72e-22

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: 88.80  E-value: 1.72e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 908266154  77 VFSGNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTGSDYKVLVG 142
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVS 66
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 88-311 5.43e-18

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: 81.57  E-value: 5.43e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  88 LSETSLDDLIPSFLTSGQQIPAFAREH-NGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIANEYR-PTSA 164
Cdd:COG1475   26 FDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGlETVPAIVRDLDDEEALELALIENLQReDLNP 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 165 YERGLRYaQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPnELSARSGEALSKAyeNNVDTLKRVTH 244
Cdd:COG1475  106 LEEARAY-QRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREG-KLSLGHARALAAL--SDPERQEELAE 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 908266154 245 KIMKQKQEGRQftTEELIVLLMPERKQPENIHKKsFGKNIEAKYSKDNvsfylKSVPESLVKQIEEL 311
Cdd:COG1475  182 KIIEEGLSVRE--TEELVKALAKDLARLERRLSE-LGTKVKIELEKKG-----KISLEDLDRLLERL 240
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 80-157 2.34e-12

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: 61.94  E-value: 2.34e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 908266154    80 GNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIAN 157
Cdd:smart00470  10 PNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGlKEVPVIVRDLDDEEAIALSLEEN 88
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 81-158 1.22e-11

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: 59.99  E-value: 1.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   81 NERNQALLSETSLDDLIPSFLTSGQQIPAFAREH-NGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIANE 158
Cdd:pfam02195  11 NPDQPRKDSEESLEELAASIKKRGLLQPIIVRKTpDGRYEIIAGERRLRAAKLLGlKEVPVIVREIDDEEAIALSLIENI 90
 
Name Accession Description Interval E-value
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
2-320 0e+00

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 524.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   2 MKRSPVLRNAPSinfdDAKPAISNAEPSVSAPAVSQLASRVSGM-KGNTIVLPVCGRNVAFTLKVIAAPDVESKTIVFSG 80
Cdd:PRK13698   1 MKRAPVIPKHTS----DTQPAEDTSEPSPAAPMVDSLIARVGGMaRGNAITLPVCGRDVKFTLEVIRGDSVEKTSRVWSG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  81 NERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTGSDYKVLVGNLNDEQMLWLSQIANEYR 160
Cdd:PRK13698  77 NERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVSGVIEIADGSRRRKAAILTESDYRVLVGELDDEQMAALSRLGNDYR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 161 PTSAYERGLRYAQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYENNVDTLK 240
Cdd:PRK13698 157 PTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDKEELLK 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 241 RVTHKIMKQKQEGRQFTTEELIVLLMPERKQPENIH-----KKSFGKNIEAKYSKDNVSFYLKS--VPESLVKQIEELLN 313
Cdd:PRK13698 237 QQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASRtslssRHQFAPGATALYKGDKVVFNLDRsrVPTECIEKIEAILK 316


                 ....*..
gi 908266154 314 TYAKEHS 320
Cdd:PRK13698 317 ELEKPAS 323
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 79-247 4.57e-36

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: 128.27  E-value: 4.57e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   79 SGNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHN---GNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQ 154
Cdd:TIGR00180  15 PNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKHPdqpGRYEIIAGERRWRAAKLAGlKTIPAIVRELDDEQMLADAL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  155 IANEYR-PTSAYERGLRYAqRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYE 233
Cdd:TIGR00180  95 IENIQReDLSPIEEAQAYK-RLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALK 173

                         170
                  ....*....|....
gi 908266154  234 NNVDTLKRVTHKIM 247
Cdd:TIGR00180 174 KKPKLQELLASIII 187
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 77-142 1.72e-22

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: 88.80  E-value: 1.72e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 908266154  77 VFSGNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTGSDYKVLVG 142
Cdd:cd16394    1 VSSLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAGLDLRVLVS 66
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 88-311 5.43e-18

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: 81.57  E-value: 5.43e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  88 LSETSLDDLIPSFLTSGQQIPAFAREH-NGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIANEYR-PTSA 164
Cdd:COG1475   26 FDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGlETVPAIVRDLDDEEALELALIENLQReDLNP 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154 165 YERGLRYaQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPnELSARSGEALSKAyeNNVDTLKRVTH 244
Cdd:COG1475  106 LEEARAY-QRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREG-KLSLGHARALAAL--SDPERQEELAE 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 908266154 245 KIMKQKQEGRQftTEELIVLLMPERKQPENIHKKsFGKNIEAKYSKDNvsfylKSVPESLVKQIEEL 311
Cdd:COG1475  182 KIIEEGLSVRE--TEELVKALAKDLARLERRLSE-LGTKVKIELEKKG-----KISLEDLDRLLERL 240
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 80-157 2.34e-12

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: 61.94  E-value: 2.34e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 908266154    80 GNERNQALLSETSLDDLIPSFLTSGQQIPAFAREHNGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIAN 157
Cdd:smart00470  10 PNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGlKEVPVIVRDLDDEEAIALSLEEN 88
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 81-158 1.22e-11

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: 59.99  E-value: 1.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154   81 NERNQALLSETSLDDLIPSFLTSGQQIPAFAREH-NGNIEVADGSRRRKAAILTG-SDYKVLVGNLNDEQMLWLSQIANE 158
Cdd:pfam02195  11 NPDQPRKDSEESLEELAASIKKRGLLQPIIVRKTpDGRYEIIAGERRLRAAKLLGlKEVPVIVREIDDEEAIALSLIENI 90
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 83-150 5.00e-08

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: 49.85  E-value: 5.00e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 908266154  83 RNQALLSETSLDDLIPSFLTSGQQIPAFAREHN---GNIEVADGSRRRKAAILTGSDYKVLVGNLNDEQML 150
Cdd:cd16405   14 RLEDDFDDDEFEELKESIRESGQQVPILVRPHPeegGRYEIVYGHRRLRACRELGLPVRAIVRELSDEELV 84
SoPB_HTH pfam18090
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein ...
 163-234 6.87e-04

Centromere-binding protein HTH domain; This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.


Pssm-ID: 375543  Cd Length: 75  Bit Score: 37.79  E-value: 6.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 908266154  163 SAYERGLRYAQRLISEFEGNISKLAEAEHLSRKIIQRCIKTAGLPLKTIQLFANPNELSARSGEALSKAYEN 234
Cdd:pfam18090   2 SAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTD 73
PRK13866 PRK13866
plasmid partitioning protein RepB; Provisional
 93-149 2.89e-03

plasmid partitioning protein RepB; Provisional


Pssm-ID: 172387 [Multi-domain]  Cd Length: 336  Bit Score: 38.78  E-value: 2.89e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 908266154  93 LDDLIPSFLTSGQQIPAFAREH---NGNIEVADGSRRRKAAILTGSDYKVLVGNLNDEQM 149
Cdd:PRK13866  90 FEQLEASISQEGQQVPILVRPHpeaAGRYQIVYGRRRLRAAVNLRREVSAIVRNLTDREL 149
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 89-134 3.31e-03

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: 35.26  E-value: 3.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 908266154  89 SETSLDDLIPSFLTSGQQIPAFAREH-NGNIEVADGSRRRKAAILTG 134
Cdd:cd16387    1 DEEELEELAESIREHGVLQPIIVRPLpDGRYEIIAGERRWRAAKLAG 47
 
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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