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Conserved domains on  [gi|81785273|sp|Q9K5M9|]
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RecName: Full=Nucleoid occlusion protein; Short=Noc

Protein Classification

nucleoid occlusion protein( domain architecture ID 11500023)

nucleoid occlusion protein affects nucleoid occlusion by binding relatively nonspecifically to DNA and preventing the assembly of the division machinery in the vicinity of the nucleoid, especially under conditions that disturb the cell cycle

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 26-281 8.14e-158

nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete.


:

Pssm-ID: 275105 [Multi-domain]  Cd Length: 255  Bit Score: 439.26  E-value: 8.14e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    26 EVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   106 SQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISERHARA 185
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   186 LLSLKDDALETKLLEEIVEQHLNVKQTEERVKELLEdAPASKPKKKPTRKAYSKDMRIAMNTIRQSVDMVMKSGLKVDTA 265
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLE-KPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTK 239

                         250
                  ....*....|....*.
gi 81785273   266 EEEHEDFYQFTIRIPK 281
Cdd:TIGR04285 240 EEDLDDYYEITIRIPK 255
 
Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 26-281 8.14e-158

nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete.


Pssm-ID: 275105 [Multi-domain]  Cd Length: 255  Bit Score: 439.26  E-value: 8.14e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    26 EVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   106 SQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISERHARA 185
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   186 LLSLKDDALETKLLEEIVEQHLNVKQTEERVKELLEdAPASKPKKKPTRKAYSKDMRIAMNTIRQSVDMVMKSGLKVDTA 265
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLE-KPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTK 239

                         250
                  ....*....|....*.
gi 81785273   266 EEEHEDFYQFTIRIPK 281
Cdd:TIGR04285 240 EEDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 23-222 1.83e-82

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: 247.98  E-value: 1.83e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  23 KQEEVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQR-EGKYEIIAGERRFRAVTLLGWETIPAIIK 101
Cdd:COG1475   3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGLETVPAIVR 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273 102 EFNDSQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISER 181
Cdd:COG1475  83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 81785273 182 HARALLSLKDDALETKLLEEIVEQHLNVKQTEERVKELLED 222
Cdd:COG1475 163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKD 203
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 30-122 1.29e-44

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: 146.47  E-value: 1.29e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  30 LPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQRE-GKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQT 108
Cdd:cd16393   4 IPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGdGRYEIIAGERRWRAAKLAGLTEIPAIVRDLDDEEA 83

                        90
                ....*....|....
gi 81785273 109 ASVALIENLQREGL 122
Cdd:cd16393  84 LELALIENIQREDL 97
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 30-117 3.76e-27

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: 100.84  E-value: 3.76e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273     30 LPIKEIVPNRFQPRTIfDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTA 109
Cdd:smart00470   3 VPIEKLRPNPDQPRLT-SEESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEEAI 81


                   ....*...
gi 81785273    110 SVALIENL 117
Cdd:smart00470  82 ALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 28-117 1.44e-26

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: 99.66  E-value: 1.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    28 HQLPIKEIVPNRFQPRTIfDDERIEELAQTIRTHGIIQPIVVRQ-REGKYEIIAGERRFRAVTLLGWETIPAIIKEFNDS 106
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKD-SEESLEELAASIKKRGLLQPIIVRKtPDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDE 79

                          90
                  ....*....|.
gi 81785273   107 QTASVALIENL 117
Cdd:pfam02195  80 EAIALSLIENI 90
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 54-163 1.06e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 67.81  E-value: 1.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   54 LAQTIRTHGIIQPIVVRQREGK---YEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTASVALIENLQREGLTAVEEAVA 130
Cdd:PRK13832  31 LLATIKAVGIVQPPVVSPEEDGgngYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRSMVENIAREPLNPVDQWRA 110

                         90       100       110
                 ....*....|....*....|....*....|...
gi 81785273  131 YQKLIELhGLTQESLAQRLGKGQSTIaNKLRLL 163
Cdd:PRK13832 111 IERLVAL-GWTEEAIAVALALPVRQI-RKLRLL 141
 
Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 26-281 8.14e-158

nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete.


Pssm-ID: 275105 [Multi-domain]  Cd Length: 255  Bit Score: 439.26  E-value: 8.14e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    26 EVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   106 SQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISERHARA 185
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   186 LLSLKDDALETKLLEEIVEQHLNVKQTEERVKELLEdAPASKPKKKPTRKAYSKDMRIAMNTIRQSVDMVMKSGLKVDTA 265
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLE-KPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTK 239

                         250
                  ....*....|....*.
gi 81785273   266 EEEHEDFYQFTIRIPK 281
Cdd:TIGR04285 240 EEDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 23-222 1.83e-82

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: 247.98  E-value: 1.83e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  23 KQEEVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQR-EGKYEIIAGERRFRAVTLLGWETIPAIIK 101
Cdd:COG1475   3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGLETVPAIVR 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273 102 EFNDSQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISER 181
Cdd:COG1475  83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 81785273 182 HARALLSLKDDALETKLLEEIVEQHLNVKQTEERVKELLED 222
Cdd:COG1475 163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKD 203
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 25-192 9.29e-62

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: 193.36  E-value: 9.29e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    25 EEVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQ---REGKYEIIAGERRFRAVTLLGWETIPAIIK 101
Cdd:TIGR00180   3 EGLIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKhpdQPGRYEIIAGERRWRAAKLAGLKTIPAIVR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   102 EFNDSQTASVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMER--KIS 179
Cdd:TIGR00180  83 ELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEAsgLLS 162

                         170
                  ....*....|...
gi 81785273   180 ERHARALLSLKDD 192
Cdd:TIGR00180 163 SGHARLLLALKKK 175
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 30-122 1.29e-44

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: 146.47  E-value: 1.29e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  30 LPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQRE-GKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQT 108
Cdd:cd16393   4 IPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGdGRYEIIAGERRWRAAKLAGLTEIPAIVRDLDDEEA 83

                        90
                ....*....|....
gi 81785273 109 ASVALIENLQREGL 122
Cdd:cd16393  84 LELALIENIQREDL 97
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 25-118 1.08e-43

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: 143.90  E-value: 1.08e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  25 EEVHQLPIKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQ-REGKYEIIAGERRFRAVTLLGWETIPAIIKEF 103
Cdd:cd16396   1 GEVLEIPVADIIPNPYQPRKEFDEEEIEELAESIKEHGLLQPIVVRKtKDGGYEIVAGERRWRAAKLLGWEKIPAIIRDL 80

                        90
                ....*....|....*
gi 81785273 104 NDSQTASVALIENLQ 118
Cdd:cd16396  81 SDKEALEIALIENLQ 95
PRTRC_parB TIGR03734
PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ...
 34-223 1.87e-38

PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.


Pssm-ID: 274755 [Multi-domain]  Cd Length: 554  Bit Score: 141.77  E-value: 1.87e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    34 EIVPNRfQPRTIFDDERIEELAQTIRTHGIIQPIVVRQREGK--YEIIAGERRFRAVTLLGWE--TIPAIIKEFNDSQTA 109
Cdd:TIGR03734   1 LIVPGN-NPRRYFDPAEMAELVESIRAKGVLQPILVRPVPGSdlYEVVAGERRYRAALEVFGEdyDIPALIKVLTDEEAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   110 SVALIENLQREGLTAVEEAVAYQKLIELHGLTQESLAQRLGKGQSTIANKLRLLHLSEPVQQAIMERKISERHARALLSL 189
Cdd:TIGR03734  80 AAALIENVQRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLALMNCTDEVRQALIDRKILLGHAELLAGL 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 81785273   190 ---KDDALETKLLEEI--VEQhlnVKQTEERVKELLEDA 223
Cdd:TIGR03734 160 pkdKQDNVLTAILAEKptVAE---LKKMIESAALSLSAA 195
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 30-117 3.76e-27

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: 100.84  E-value: 3.76e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273     30 LPIKEIVPNRFQPRTIfDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTA 109
Cdd:smart00470   3 VPIEKLRPNPDQPRLT-SEESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEEAI 81


                   ....*...
gi 81785273    110 SVALIENL 117
Cdd:smart00470  82 ALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 28-117 1.44e-26

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: 99.66  E-value: 1.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273    28 HQLPIKEIVPNRFQPRTIfDDERIEELAQTIRTHGIIQPIVVRQ-REGKYEIIAGERRFRAVTLLGWETIPAIIKEFNDS 106
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKD-SEESLEELAASIKKRGLLQPIIVRKtPDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDE 79

                          90
                  ....*....|.
gi 81785273   107 QTASVALIENL 117
Cdd:pfam02195  80 EAIALSLIENI 90
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 32-107 5.15e-23

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: 89.88  E-value: 5.15e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 81785273  32 IKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQRE-GKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQ 107
Cdd:cd16407   1 LSELHPFPNHPFKVRDDEEMEELVESIKENGVLTPIIVRPREdGGYEIISGHRRKRACELAGLETIPVIVREMDDDE 77
KorB_N_like cd16398
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ...
 32-122 5.81e-22

ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related domains; KorB, a member of the ParB like family, is present on the low copy number, broad host range plasmid RK2. KorB encodes a gene product involved in segregation of RK2 and acts as a transcriptional regulator, down-regulating at least 6 RK2 operons. KorB binds RNA polymerase and acts cooperatively with several co-repressors in modulating transcription. KorB is comprised of 3 domains, including a beta-strand C-terminal domain similar to SH3 domains and an alpha helical central domain that interacts with operator DNA. In ParB of P1 and SopB of F, the N-terminal region is responsible for interaction with the parA component. However, korB interaction with the RK2 parA-equivalent IncC has been mapped to the central HTH motif. This family is related to 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: 319256 [Multi-domain]  Cd Length: 91  Bit Score: 87.32  E-value: 5.81e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  32 IKEIVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVR---QREGKYEIIAGERRFRAVTLLGWETIPAIIKE-FNDSQ 107
Cdd:cd16398   1 LDKIDEDPDNPRTEFDEEKIEELAASIKERGVKSPISVRphpEKPGKYIINHGARRYRASKWAGLKTIPAFIDNdHDDFD 80

                        90
                ....*....|....*
gi 81785273 108 tasvALIENLQREGL 122
Cdd:cd16398  81 ----QVIENIQREDL 91
ParB_N_like cd16406
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 46-120 8.45e-20

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: 319263 [Multi-domain]  Cd Length: 82  Bit Score: 81.41  E-value: 8.45e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  46 FDDERIEELAQTIRTHGIIQPIVVRQ--REGKYEIIAGERRFRAVTLL-GWETIPA------IIKEFNDSQTASvaLIEN 116
Cdd:cd16406   1 FDPAGIEELAASIAAHGLLQNLVVRPakKKGRYEVVAGGRRLRALQLLaERGRLPAdypvpvKVVPDADALEAS--LAEN 78


                ....
gi 81785273 117 LQRE 120
Cdd:cd16406  79 VQRE 82
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 47-117 1.14e-18

ParB N-terminal-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: 319266 [Multi-domain]  Cd Length: 74  Bit Score: 78.11  E-value: 1.14e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 81785273  47 DDERIEELAQTIRTHGIIQPIVVRQR-EGKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTASVALIENL 117
Cdd:cd16409   2 DPEHVEALAQSIAEHGLLTPITVRQDpGGRYTLIAGAHRLAAAKLLGWDTIDAIIVKADDLEAELLEIDENL 73
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
 35-115 1.18e-18

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: 319265 [Multi-domain]  Cd Length: 84  Bit Score: 78.44  E-value: 1.18e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  35 IVPNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQRE-GKYEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTASVAL 113
Cdd:cd16408   1 LVPFSDHPFKLYTGERLEDMVESIKENGVLQPIIVRPIEdGKYEILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKLIV 80


                ..
gi 81785273 114 IE 115
Cdd:cd16408  81 VE 82
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 47-99 1.25e-18

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: 77.63  E-value: 1.25e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 81785273  47 DDERIEELAQTIRTHGIIQPIVVRQRE-GKYEIIAGERRFRAVTLLGWETIPAI 99
Cdd:cd16387   1 DEEELEELAESIREHGVLQPIIVRPLPdGRYEIIAGERRWRAAKLAGLTTIPVV 54
HTH_ParB pfam17762
HTH domain found in ParB protein;
167-216 2.54e-15

HTH domain found in ParB protein;


Pssm-ID: 465489  Cd Length: 50  Bit Score: 68.56  E-value: 2.54e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 81785273   167 EPVQQAIMERKISERHARALLSLKDDALETKLLEEIVEQHLNVKQTEERV 216
Cdd:pfam17762   1 PEVQELLREGKLSEGHARALLSLKDEEKQLELAKKIIEEGLSVRETEKLV 50
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 30-116 1.35e-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: 64.87  E-value: 1.35e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  30 LPIKEIVPNRFQPR--TIFDDERIEELAQTIRTHGIIQPIVVRQRE---GKYEIIAGERRFRAVTLLGWeTIPAIIKEFN 104
Cdd:cd16405   1 LDPDLIDPSFIADRleDDFDDDEFEELKESIRESGQQVPILVRPHPeegGRYEIVYGHRRLRACRELGL-PVRAIVRELS 79

                        90
                ....*....|..
gi 81785273 105 DSQTASVALIEN 116
Cdd:cd16405  80 DEELVVAQGQEN 91
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 51-105 5.31e-13

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: 319267 [Multi-domain]  Cd Length: 80  Bit Score: 62.99  E-value: 5.31e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 81785273  51 IEELAQTIRTHGIIQPIVVrqrEGKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:cd16410  17 IEALAESIKRHGLLNPIVV---TPDNELIAGERRLEAAKLLGWETIEVRVMDIED 68
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 54-163 1.06e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 67.81  E-value: 1.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   54 LAQTIRTHGIIQPIVVRQREGK---YEIIAGERRFRAVTLLGWETIPAIIKEFNDSQTASVALIENLQREGLTAVEEAVA 130
Cdd:PRK13832  31 LLATIKAVGIVQPPVVSPEEDGgngYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRSMVENIAREPLNPVDQWRA 110

                         90       100       110
                 ....*....|....*....|....*....|...
gi 81785273  131 YQKLIELhGLTQESLAQRLGKGQSTIaNKLRLL 163
Cdd:PRK13832 111 IERLVAL-GWTEEAIAVALALPVRQI-RKLRLL 141
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 31-102 1.60e-11

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. 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: 319260 [Multi-domain]  Cd Length: 88  Bit Score: 59.39  E-value: 1.60e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 81785273  31 PIKEIVPNRFQPRTiFDDERIEELAQTIRTHGIIQPIVVRQregKYEIIAGERRFRAVTLLGWETIPAIIKE 102
Cdd:cd16403   1 PIDDLKPYPRNART-HSEKQIEQLAASIREFGFTNPILVDE---DGVIIAGHGRLLAAKLLGLKEVPVIRLD 68
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 31-101 2.15e-10

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. 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: 319259 [Multi-domain]  Cd Length: 87  Bit Score: 56.09  E-value: 2.15e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 81785273  31 PIKEIVPNRFQPRTifDDERIEELAQTIRTHGIIQPIVVrqrEGKYEIIAGERRFRAVTLLGWETIPAIIK 101
Cdd:cd16402   1 KISELKPYENNPRN--NDKAVEKVAESIKEFGFLVPIVV---DKNNVIVAGHTRYKAAKRLGLEEVPCIVA 66
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 37-102 1.16e-08

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. 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: 319258 [Multi-domain]  Cd Length: 85  Bit Score: 51.07  E-value: 1.16e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 81785273  37 PNRFQPRTI--FDDERIEELAQTIRTHGIIQPIVVRQREGkyEIIAGERRFRAVTLLGWETIPAIIKE 102
Cdd:cd16401   1 PAPYNPRKDlkPGDKEYEKLKESIEEFGLVDPLIVNKRTN--VLIGGHQRLKVLKELGYTEVPVVVVD 66
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
 30-117 3.57e-08

ParB N-terminal, parA -binding, 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: 319268 [Multi-domain]  Cd Length: 90  Bit Score: 49.91  E-value: 3.57e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  30 LPIKEI-VPN-RFQPRTIFDderieELAQTIRTHGIIQPIVVRQREG-----KYEIIAGERRFRAVTLLGWETIPAIIKE 102
Cdd:cd16411   1 IPIDDIrVLNpRSRNRKIFR-----EIVESIATVGLKRPITVRRRSSddggyKYDLVCGQGRLEAFKALGETEIPAIVVD 75

                        90
                ....*....|....*
gi 81785273 103 FNDSQTASVALIENL 117
Cdd:cd16411  76 VDEEDALLMSLVENI 90
PRK13866 PRK13866
plasmid partitioning protein RepB; Provisional
 48-128 1.98e-07

plasmid partitioning protein RepB; Provisional


Pssm-ID: 172387 [Multi-domain]  Cd Length: 336  Bit Score: 51.49  E-value: 1.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273   48 DERIEELAQTIRTHGIIQPIVVR---QREGKYEIIAGERRFRAVTLLGWEtIPAIIKEFNDSQTASVALIENLQREGLTA 124
Cdd:PRK13866  87 DPKFEQLEASISQEGQQVPILVRphpEAAGRYQIVYGRRRLRAAVNLRRE-VSAIVRNLTDRELVVAQGRENLDRADLSF 165


                 ....
gi 81785273  125 VEEA 128
Cdd:PRK13866 166 IEKA 169
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 40-106 2.46e-07

pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins.


Pssm-ID: 319261 [Multi-domain]  Cd Length: 69  Bit Score: 46.89  E-value: 2.46e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 81785273  40 FQPRTIFDDERIEELAQTIRTHGIIQPIVVRQregKYEIIAGERRFRAVTLLGWETIPAIIKEFNDS 106
Cdd:cd16404   6 EFRTPNPTNEEFEELKESIRKNGIIVPIIVDQ---DGVIIDGHHRYRIAKELGIKEVPVIVYDFDDE 69
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 30-86 7.27e-05

immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx.


Pssm-ID: 319255 [Multi-domain]  Cd Length: 100  Bit Score: 41.02  E-value: 7.27e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 81785273  30 LPIKEIVPNRFQPRTIFDDERiEELAQTIRTHGIIQPIVVRQ--REGKYEIIAGERRFR 86
Cdd:cd16397   8 VPIEKVQANDYNPNKVAPPEM-KLLKLSILEDGFTQPIVVYYdeEDDKYVIVDGFHRYT 65
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 47-100 2.39e-04

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. 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: 319272 [Multi-domain]  Cd Length: 54  Bit Score: 38.40  E-value: 2.39e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 81785273  47 DDERIEELAQTIRTHGIIQPIVVRQREgkyEIIAGERRFRAVTLLGWETIPAII 100
Cdd:cd16844   2 NDAQIERVAASIREFGFRVPVLIDKDG---EIVDGHLRLEAARRLGLETVPVIR 52
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 46-105 2.93e-04

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.


Pssm-ID: 319257 [Multi-domain]  Cd Length: 72  Bit Score: 38.30  E-value: 2.93e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 81785273  46 FDDERIEELAQTIRTHGI-IQPIVVRQRegKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:cd16400  13 VDPDRVEELIEKILEEGVwTKPIIVDKN--TGIILDGHHRLEAAKRLGLKRVPCVLLDYDD 71
Srx cd16395
Sulfiredoxin reactivates peroxiredoxins after oxidative inactivation; Sulfiredoxin reduces and ...
 27-101 4.17e-04

Sulfiredoxin reactivates peroxiredoxins after oxidative inactivation; Sulfiredoxin reduces and thereby re-activates 2-cys peroxiredoxins. Peroxiredoxins act as molecular switches, inactivating in response to hyperoxidation from hydrogen peroxide and other free radicals. Sulfiredoxin reactivates Prx-SO(2)(-) via ATP-Mg(2+)-dependent reduction. Arabidopsis sulfiredoxin has been described as a dual function enzyme, having nuclease activity in addition to the sulfiredoxin activity. This protein is similar to ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems.


Pssm-ID: 319253 [Multi-domain]  Cd Length: 90  Bit Score: 38.36  E-value: 4.17e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81785273  27 VHQLPIKEIvpNRFQPRTIfDDERIEELAQTIR--THGIIQPI----VVRQREGKYEIIAGERRFRAVTLLGWETIPA-I 99
Cdd:cd16395   1 VHEVPLSVI--RRPLPPVL-DENKVQSLMETIKgiAPGLLPPIdvlwVKGEGGGYYYSFGGCHRYEAHKRLGRETIRCkI 77


                ..
gi 81785273 100 IK 101
Cdd:cd16395  78 IK 79
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 37-92 1.02e-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: 1.02e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 81785273  37 PNRFQPRTIFDDERIEELAQTIRTHGIIQPIVVRQREGKYEIIAGERRFRAVTLLG 92
Cdd:cd16394   3 SLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAG 58
SbnI_like_N cd16388
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ...
 46-105 1.52e-03

N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression.


Pssm-ID: 319247 [Multi-domain]  Cd Length: 77  Bit Score: 36.71  E-value: 1.52e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 81785273  46 FDDERIEELAQTIRTHGIIQ--PIVVRQREGKYEIIAGERRFRAVTLLGWETIPAIIKEFND 105
Cdd:cd16388  15 HEPNRLEKLVERIEAEGVLRnpPIVTPLQDGRYLILDGAHRTTALKKLGCKRIPVQVVDEED 76
 
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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