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Conserved domains on  [gi|1232718798|gb|OYZ47108.1|]
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replication protein B [Novosphingobium sp. 16-62-11]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
parB_part super family cl36599
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 64-239 3.35e-24

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: 97.45  E-value: 3.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  64 RMWAGHNRDYALLNEERCADLIESIKAQGRQEiPAIVRRLSGEDGyDFEVICGARRHWSISWLRTHNYPDFkflvdVREI 143
Cdd:TIGR00180  12 LLQPNPYQPRKDFSEESLAELIESIKEQGQLQ-PILVRKHPDQPG-RYEIIAGERRWRAAKLAGLKTIPAI-----VREL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 144 GDEEAFRLADLENRARDDLTDFERAKDYLRaLTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELGIR 223
Cdd:TIGR00180  85 DDEQMLADALIENIQREDLSPIEEAQAYKR-LLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSS 163

                         170
                  ....*....|....*..
gi 1232718798 224 N-AIALKALMKPEDRKE 239
Cdd:TIGR00180 164 GhARLLLALKKKPKLQE 180
 
Name Accession Description Interval E-value
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 64-239 3.35e-24

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: 97.45  E-value: 3.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  64 RMWAGHNRDYALLNEERCADLIESIKAQGRQEiPAIVRRLSGEDGyDFEVICGARRHWSISWLRTHNYPDFkflvdVREI 143
Cdd:TIGR00180  12 LLQPNPYQPRKDFSEESLAELIESIKEQGQLQ-PILVRKHPDQPG-RYEIIAGERRWRAAKLAGLKTIPAI-----VREL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 144 GDEEAFRLADLENRARDDLTDFERAKDYLRaLTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELGIR 223
Cdd:TIGR00180  85 DDEQMLADALIENIQREDLSPIEEAQAYKR-LLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSS 163

                         170
                  ....*....|....*..
gi 1232718798 224 N-AIALKALMKPEDRKE 239
Cdd:TIGR00180 164 GhARLLLALKKKPKLQE 180
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 52-241 2.97e-23

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: 96.21  E-value: 2.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  52 SRTHELVDPARCRMWAGHNRDYalLNEERCADLIESIKAQGrQEIPAIVRRLsgEDGyDFEVICGARRHWSISWLRTHNY 131
Cdd:COG1475     4 GEEIREIPIDKIVPSPYNPRRT--FDEEALEELAASIREHG-LLQPILVRPL--GDG-RYEIIAGERRLRAAKLLGLETV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 132 PdfkflVDVREIGDEEAFRLADLENRARDDLTDFERAKDYlRALTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELT 211
Cdd:COG1475    78 P-----AIVRDLDDEEALELALIENLQREDLNPLEEARAY-QRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQ 151

                         170       180       190
                  ....*....|....*....|....*....|
gi 1232718798 212 RAFANPqELGIRNAIALKALMKPEDRKERA 241
Cdd:COG1475   152 EALREG-KLSLGHARALAALSDPERQEELA 180
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
62-268 1.38e-14

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 73.35  E-value: 1.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  62 RCRMWAGHNRDYALLNEERCADLIESIKAQGrQEIPAIVRRLSGedgyDFEVICGARRHWSISWLRThnypDFKFLVDvr 141
Cdd:PRK13698   70 TSRVWSGNERDQELLTEDSLDDLIPSFLLTG-QQTPAFGRRVSG----VIEIADGSRRRKAAILTES----DYRVLVG-- 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 142 EIGDEEAFRLADLENRARDdLTDFERAKDYLRALTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELG 221
Cdd:PRK13698  139 ELDDEQMAALSRLGNDYRP-TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELS 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1232718798 222 IRNAialKALMKPEDRKERAFREAARLAAERERANHSPSVLEVIKAL 268
Cdd:PRK13698  218 ARSG---EALQKAFTDKEELLKQQTSNLHEQKKAGVIFETEEVITLL 261
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 58-156 2.94e-13

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: 64.49  E-value: 2.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  58 VDPARCRMWAGHNRDYALLNEERCADLIESIKAQGrQEIPAIVRRLSGEDGyDFEVICGARRHWSISWLrthnypDFKFL 137
Cdd:cd16405     1 LDPDLIDPSFIADRLEDDFDDDEFEELKESIRESG-QQVPILVRPHPEEGG-RYEIVYGHRRLRACREL------GLPVR 72

                          90
                  ....*....|....*....
gi 1232718798 138 VDVREIGDEEAFRLADLEN 156
Cdd:cd16405    73 AIVRELSDEELVVAQGQEN 91
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 56-157 5.09e-10

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: 55.75  E-value: 5.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  56 ELVDPARCRMWAGHNRdyaLLNEERCADLIESIKAQGRQEiPAIVRRLsgEDGYdFEVICGARRHWSISWLRThnypdFK 135
Cdd:pfam02195   1 EEVPISKLRPNPDQPR---KDSEESLEELAASIKKRGLLQ-PIIVRKT--PDGR-YEIIAGERRLRAAKLLGL-----KE 68

                          90       100
                  ....*....|....*....|..
gi 1232718798 136 FLVDVREIGDEEAFRLADLENR 157
Cdd:pfam02195  69 VPVIVREIDDEEAIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 56-157 2.11e-08

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: 51.15  E-value: 2.11e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798   56 ELVDPARCRMWAGHNRdyaLLNEERCADLIESIKAQGRQEiPAIVRRLSGEdgydFEVICGARRHWSISWLRthnypDFK 135
Cdd:smart00470   1 VEVPIEKLRPNPDQPR---LTSEESLEELAESIKENGLLQ-PIIVRPNDGR----YEIIDGERRLRAAKLLG-----LKE 67

                           90       100
                   ....*....|....*....|..
gi 1232718798  136 FLVDVREIGDEEAFRLADLENR 157
Cdd:smart00470  68 VPVIVRDLDDEEAIALSLEENI 89
 
Name Accession Description Interval E-value
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 64-239 3.35e-24

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: 97.45  E-value: 3.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  64 RMWAGHNRDYALLNEERCADLIESIKAQGRQEiPAIVRRLSGEDGyDFEVICGARRHWSISWLRTHNYPDFkflvdVREI 143
Cdd:TIGR00180  12 LLQPNPYQPRKDFSEESLAELIESIKEQGQLQ-PILVRKHPDQPG-RYEIIAGERRWRAAKLAGLKTIPAI-----VREL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 144 GDEEAFRLADLENRARDDLTDFERAKDYLRaLTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELGIR 223
Cdd:TIGR00180  85 DDEQMLADALIENIQREDLSPIEEAQAYKR-LLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSS 163

                         170
                  ....*....|....*..
gi 1232718798 224 N-AIALKALMKPEDRKE 239
Cdd:TIGR00180 164 GhARLLLALKKKPKLQE 180
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 52-241 2.97e-23

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: 96.21  E-value: 2.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  52 SRTHELVDPARCRMWAGHNRDYalLNEERCADLIESIKAQGrQEIPAIVRRLsgEDGyDFEVICGARRHWSISWLRTHNY 131
Cdd:COG1475     4 GEEIREIPIDKIVPSPYNPRRT--FDEEALEELAASIREHG-LLQPILVRPL--GDG-RYEIIAGERRLRAAKLLGLETV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 132 PdfkflVDVREIGDEEAFRLADLENRARDDLTDFERAKDYlRALTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELT 211
Cdd:COG1475    78 P-----AIVRDLDDEEALELALIENLQREDLNPLEEARAY-QRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQ 151

                         170       180       190
                  ....*....|....*....|....*....|
gi 1232718798 212 RAFANPqELGIRNAIALKALMKPEDRKERA 241
Cdd:COG1475   152 EALREG-KLSLGHARALAALSDPERQEELA 180
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
62-268 1.38e-14

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 73.35  E-value: 1.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  62 RCRMWAGHNRDYALLNEERCADLIESIKAQGrQEIPAIVRRLSGedgyDFEVICGARRHWSISWLRThnypDFKFLVDvr 141
Cdd:PRK13698   70 TSRVWSGNERDQELLTEDSLDDLIPSFLLTG-QQTPAFGRRVSG----VIEIADGSRRRKAAILTES----DYRVLVG-- 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798 142 EIGDEEAFRLADLENRARDdLTDFERAKDYLRALTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELG 221
Cdd:PRK13698  139 ELDDEQMAALSRLGNDYRP-TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELS 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1232718798 222 IRNAialKALMKPEDRKERAFREAARLAAERERANHSPSVLEVIKAL 268
Cdd:PRK13698  218 ARSG---EALQKAFTDKEELLKQQTSNLHEQKKAGVIFETEEVITLL 261
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 58-156 2.94e-13

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: 64.49  E-value: 2.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  58 VDPARCRMWAGHNRDYALLNEERCADLIESIKAQGrQEIPAIVRRLSGEDGyDFEVICGARRHWSISWLrthnypDFKFL 137
Cdd:cd16405     1 LDPDLIDPSFIADRLEDDFDDDEFEELKESIRESG-QQVPILVRPHPEEGG-RYEIVYGHRRLRACREL------GLPVR 72

                          90
                  ....*....|....*....
gi 1232718798 138 VDVREIGDEEAFRLADLEN 156
Cdd:cd16405    73 AIVRELSDEELVVAQGQEN 91
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 56-157 5.09e-10

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: 55.75  E-value: 5.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  56 ELVDPARCRMWAGHNRdyaLLNEERCADLIESIKAQGRQEiPAIVRRLsgEDGYdFEVICGARRHWSISWLRThnypdFK 135
Cdd:pfam02195   1 EEVPISKLRPNPDQPR---KDSEESLEELAASIKKRGLLQ-PIIVRKT--PDGR-YEIIAGERRLRAAKLLGL-----KE 68

                          90       100
                  ....*....|....*....|..
gi 1232718798 136 FLVDVREIGDEEAFRLADLENR 157
Cdd:pfam02195  69 VPVIVREIDDEEAIALSLIENI 90
SoPB_HTH pfam18090
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein ...
 162-228 3.81e-09

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: 52.81  E-value: 3.81e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1232718798 162 LTDFERAKDYLRALTAYYEGRQKTMAERLKVSESWLTRYLDLARLPEELTRAFANPQELGIRNAIAL 228
Cdd:pfam18090   1 TSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDAL 67
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 56-157 2.11e-08

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: 51.15  E-value: 2.11e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798   56 ELVDPARCRMWAGHNRdyaLLNEERCADLIESIKAQGRQEiPAIVRRLSGEdgydFEVICGARRHWSISWLRthnypDFK 135
Cdd:smart00470   1 VEVPIEKLRPNPDQPR---LTSEESLEELAESIKENGLLQ-PIIVRPNDGR----YEIIDGERRLRAAKLLG-----LKE 67

                           90       100
                   ....*....|....*....|..
gi 1232718798  136 FLVDVREIGDEEAFRLADLENR 157
Cdd:smart00470  68 VPVIVRDLDDEEAIALSLEENI 89
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 77-162 1.47e-05

Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; Spo0J (stage 0 sporulation protein J) is a ParB family member, a critical component of the ParABS-type bacterial chromosome segregation system. The Spo0J N-terminal region acts in protein-protein interaction and is adjacent to the DNA-binding domain that binds to parS sites. Two Spo0J bind per parS site, and Spo0J interacts with neighbors via the N-terminal domain to form oligomers via an Arginine-rich patch (RRXR). This superfamily 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: 319251 [Multi-domain]  Cd Length: 97  Bit Score: 43.24  E-value: 1.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  77 NEERCADLIESIKAQGRQEiPAIVRRlSGEDGYdfEVICGARRhwsiswLRTHNYPDFKFL-VDVREIGDEEAFRLADLE 155
Cdd:cd16393    21 DEEALKELAESIKEHGLLQ-PIVVRK-VGDGRY--EIIAGERR------WRAAKLAGLTEIpAIVRDLDDEEALELALIE 90


                  ....*..
gi 1232718798 156 NRARDDL 162
Cdd:cd16393    91 NIQREDL 97
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 77-156 1.52e-04

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: 40.28  E-value: 1.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718798  77 NEERCADLIESIKAQGRQEiPAIVRRLSGEDgydFEVICGARR---HWSISWlrthnypdFKFLVDVREIGDEEAFRLAD 153
Cdd:cd16396    23 DEEEIEELAESIKEHGLLQ-PIVVRKTKDGG---YEIVAGERRwraAKLLGW--------EKIPAIIRDLSDKEALEIAL 90


                  ...
gi 1232718798 154 LEN 156
Cdd:cd16396    91 IEN 93
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 73-148 4.47e-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: 38.65  E-value: 4.47e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1232718798  73 YALLNEERCADLIESIKAQGRQEiPAIVRRLsGEDGYdfEVICGARRHWSISWLRTHNYPdfkflVDVREIGDEEA 148
Cdd:cd16407    12 FKVRDDEEMEELVESIKENGVLT-PIIVRPR-EDGGY--EIISGHRRKRACELAGLETIP-----VIVREMDDDEA 78
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 66-142 1.39e-03

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: 36.80  E-value: 1.39e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1232718798  66 WAGHNRDYALLNEERCADLIESIKAQGrQEIPAIVRRLSGEdgydFEVICGARRhwsiswLRTHNYPDFKFLVDVRE 142
Cdd:cd16394     2 SSLNGRDQELLTEEAVSDIIPSIKENG-QFVPAIGYRVDGK----IELLDGSRR------RRAAILAGLDLRVLVSK 67
 
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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