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Conserved domains on  [gi|1998284959|gb|QSO47721|]
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nucleoid occlusion protein [Alicyclobacillus mengziensis]

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 ...
 20-274 5.80e-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: 439.64  E-value: 5.80e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  20 NVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 100 AQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 180 LLALPSEEIQVKVLNECIDRGWNVKQTEERVKSLLTKLQQGPRPKPRRKGLSKDVRLAVNTIRQSLSMISKSGLTVDYKE 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEKPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTKE 240

                         250
                  ....*....|....*
gi 1998284959 260 QDDADFYEFIIRVPK 274
Cdd:TIGR04285 241 EDLDDYYEITIRIPK 255
 
Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 20-274 5.80e-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: 439.64  E-value: 5.80e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  20 NVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 100 AQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 180 LLALPSEEIQVKVLNECIDRGWNVKQTEERVKSLLTKLQQGPRPKPRRKGLSKDVRLAVNTIRQSLSMISKSGLTVDYKE 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEKPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTKE 240

                         250
                  ....*....|....*
gi 1998284959 260 QDDADFYEFIIRVPK 274
Cdd:TIGR04285 241 EDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 17-219 5.28e-84

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: 251.45  E-value: 5.28e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  17 EDTNVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAIVK 95
Cdd:COG1475     3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGLETVPAIVR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  96 VMNDAQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITER 175
Cdd:COG1475    83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1998284959 176 HARALLALPSEEIQVKVLNECIDRGWNVKQTEERVKSLLTKLQQ 219
Cdd:COG1475   163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKDLAR 206
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 21-116 1.62e-45

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: 148.40  E-value: 1.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  21 VVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNN-GRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:cd16393     1 VQEIPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGdGRYEIIAGERRWRAAKLAGLTEIPAIVRDLDD 80

                          90
                  ....*....|....*..
gi 1998284959 100 AQTASAALIENLQREGL 116
Cdd:cd16393    81 EEALELALIENIQREDL 97
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 22-111 1.24e-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: 102.00  E-value: 1.24e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959   22 VQIGVDEIVSNPFQPRTVFDESgISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQ 101
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTSEES-LEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79

                           90
                   ....*....|
gi 1998284959  102 TASAALIENL 111
Cdd:smart00470  80 AIALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 22-111 4.56e-25

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: 95.42  E-value: 4.56e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  22 VQIGVDEIVSNPFQPRTVFDESgISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDA 100
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEES-LEELAASIKKRGLLQPIIVRKTpDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDE 79

                          90
                  ....*....|.
gi 1998284959 101 QTASAALIENL 111
Cdd:pfam02195  80 EAIALSLIENI 90
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 32-157 2.18e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 66.65  E-value: 2.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  32 NPFQPR-TVFDESGISELAATIRTHGVIQPIIVR----RNNGrYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQTASAA 106
Cdd:PRK13832   14 NPDNTRrSKSSPQSDALLLATIKAVGIVQPPVVSpeedGGNG-YIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRS 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998284959 107 LIENLQREGLTPIEEAVAYQQLLEIhGLTQESLAQRLGKGQSTIaNKLRLL 157
Cdd:PRK13832   93 MVENIAREPLNPVDQWRAIERLVAL-GWTEEAIAVALALPVRQI-RKLRLL 141
 
Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 20-274 5.80e-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: 439.64  E-value: 5.80e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  20 NVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 100 AQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 180 LLALPSEEIQVKVLNECIDRGWNVKQTEERVKSLLTKLQQGPRPKPRRKGLSKDVRLAVNTIRQSLSMISKSGLTVDYKE 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEKPEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKTKE 240

                         250
                  ....*....|....*
gi 1998284959 260 QDDADFYEFIIRVPK 274
Cdd:TIGR04285 241 EDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 17-219 5.28e-84

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: 251.45  E-value: 5.28e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  17 EDTNVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAIVK 95
Cdd:COG1475     3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLgDGRYEIIAGERRLRAAKLLGLETVPAIVR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  96 VMNDAQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITER 175
Cdd:COG1475    83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1998284959 176 HARALLALPSEEIQVKVLNECIDRGWNVKQTEERVKSLLTKLQQ 219
Cdd:COG1475   163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKDLAR 206
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 20-197 7.45e-63

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: 195.68  E-value: 7.45e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  20 NVVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNN---GRYELIAGERRWRAVRSLGWSTIPAIVKV 96
Cdd:TIGR00180   4 GLIEIDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKHPdqpGRYEIIAGERRWRAAKLAGLKTIPAIVRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  97 MNDAQTASAALIENLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQR--KITE 174
Cdd:TIGR00180  84 LDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEAsgLLSS 163

                         170       180
                  ....*....|....*....|....
gi 1998284959 175 RHARALLALP-SEEIQVKVLNECI 197
Cdd:TIGR00180 164 GHARLLLALKkKPKLQELLASIII 187
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 21-116 1.62e-45

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: 148.40  E-value: 1.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  21 VVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNN-GRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:cd16393     1 VQEIPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGdGRYEIIAGERRWRAAKLAGLTEIPAIVRDLDD 80

                          90
                  ....*....|....*..
gi 1998284959 100 AQTASAALIENLQREGL 116
Cdd:cd16393    81 EEALELALIENIQREDL 97
PRTRC_parB TIGR03734
PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ...
 34-217 5.40e-42

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: 151.02  E-value: 5.40e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  34 FQPRTVFDESGISELAATIRTHGVIQPIIVRRNNG--RYELIAGERRWRAVRSLGWS--TIPAIVKVMNDAQTASAALIE 109
Cdd:TIGR03734   6 NNPRRYFDPAEMAELVESIRAKGVLQPILVRPVPGsdLYEVVAGERRYRAALEVFGEdyDIPALIKVLTDEEAEAAALIE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959 110 NLQREGLTPIEEAVAYQQLLEIHGLTQESLAQRLGKGQSTIANKLRLLHLPESVREALLQRKITERHARALLALPsEEIQ 189
Cdd:TIGR03734  86 NVQRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLALMNCTDEVRQALIDRKILLGHAELLAGLP-KDKQ 164

                         170       180
                  ....*....|....*....|....*...
gi 1998284959 190 VKVLNECIDRGWNVKQTEERVKSLLTKL 217
Cdd:TIGR03734 165 DNVLTAILAEKPTVAELKKMIESAALSL 192
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 21-112 5.65e-39

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: 131.58  E-value: 5.65e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  21 VVQIGVDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNN-GRYELIAGERRWRAVRSLGWSTIPAIVKVMND 99
Cdd:cd16396     3 VLEIPVADIIPNPYQPRKEFDEEEIEELAESIKEHGLLQPIVVRKTKdGGYEIVAGERRWRAAKLLGWEKIPAIIRDLSD 82

                          90
                  ....*....|...
gi 1998284959 100 AQTASAALIENLQ 112
Cdd:cd16396    83 KEALEIALIENLQ 95
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 22-111 1.24e-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: 102.00  E-value: 1.24e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959   22 VQIGVDEIVSNPFQPRTVFDESgISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQ 101
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTSEES-LEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79

                           90
                   ....*....|
gi 1998284959  102 TASAALIENL 111
Cdd:smart00470  80 AIALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 22-111 4.56e-25

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: 95.42  E-value: 4.56e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  22 VQIGVDEIVSNPFQPRTVFDESgISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDA 100
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEES-LEELAASIKKRGLLQPIIVRKTpDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDE 79

                          90
                  ....*....|.
gi 1998284959 101 QTASAALIENL 111
Cdd:pfam02195  80 EAIALSLIENI 90
KorB_N_like cd16398
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ...
 26-116 7.86e-21

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: 84.24  E-value: 7.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  26 VDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNN---GRYELIAGERRWRAVRSLGWSTIPAIVKvmNDAQT 102
Cdd:cd16398     1 LDKIDEDPDNPRTEFDEEKIEELAASIKERGVKSPISVRPHPekpGKYIINHGARRYRASKWAGLKTIPAFID--NDHDD 78

                          90
                  ....*....|....
gi 1998284959 103 ASAAlIENLQREGL 116
Cdd:cd16398    79 FDQV-IENIQREDL 91
ParB_N_like cd16406
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 40-114 1.70e-19

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: 80.25  E-value: 1.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  40 FDESGISELAATIRTHGVIQPIIVRR--NNGRYELIAGERRWRAVRSL-GWSTIPA----IVKVMNDAQTASAALIENLQ 112
Cdd:cd16406     1 FDPAGIEELAASIAAHGLLQNLVVRPakKKGRYEVVAGGRRLRALQLLaERGRLPAdypvPVKVVPDADALEASLAENVQ 80


                  ..
gi 1998284959 113 RE 114
Cdd:cd16406    81 RE 82
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 26-101 3.70e-19

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: 79.48  E-value: 3.70e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1998284959  26 VDEIVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVR-RNNGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQ 101
Cdd:cd16407     1 LSELHPFPNHPFKVRDDEEMEELVESIKENGVLTPIIVRpREDGGYEIISGHRRKRACELAGLETIPVIVREMDDDE 77
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 41-93 1.36e-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: 77.24  E-value: 1.36e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1998284959  41 DESGISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAI 93
Cdd:cd16387     1 DEEELEELAESIREHGVLQPIIVRPLpDGRYEIIAGERRWRAAKLAGLTTIPVV 54
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 41-111 2.03e-16

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: 71.95  E-value: 2.03e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1998284959  41 DESGISELAATIRTHGVIQPIIVRRN-NGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQTASAALIENL 111
Cdd:cd16409     2 DPEHVEALAQSIAEHGLLTPITVRQDpGGRYTLIAGAHRLAAAKLLGWDTIDAIIVKADDLEAELLEIDENL 73
HTH_ParB pfam17762
HTH domain found in ParB protein;
161-210 2.97e-16

HTH domain found in ParB protein;


Pssm-ID: 465489  Cd Length: 50  Bit Score: 70.87  E-value: 2.97e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1998284959 161 ESVREALLQRKITERHARALLALPSEEIQVKVLNECIDRGWNVKQTEERV 210
Cdd:pfam17762   1 PEVQELLREGKLSEGHARALLSLKDEEKQLELAKKIIEEGLSVRETEKLV 50
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 24-110 9.92e-16

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: 70.65  E-value: 9.92e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  24 IGVDEIVSNPFQPR--TVFDESGISELAATIRTHGVIQPIIVRRNN---GRYELIAGERRWRAVRSLGWsTIPAIVKVMN 98
Cdd:cd16405     1 LDPDLIDPSFIADRleDDFDDDEFEELKESIRESGQQVPILVRPHPeegGRYEIVYGHRRLRACRELGL-PVRAIVRELS 79

                          90
                  ....*....|..
gi 1998284959  99 DAQTASAALIEN 110
Cdd:cd16405    80 DEELVVAQGQEN 91
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
 29-109 1.91e-14

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: 66.88  E-value: 1.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  29 IVSNPFQPRTVFDESGISELAATIRTHGVIQPIIVRR-NNGRYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQTASAAL 107
Cdd:cd16408     1 LVPFSDHPFKLYTGERLEDMVESIKENGVLQPIIVRPiEDGKYEILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKLIV 80


                  ..
gi 1998284959 108 IE 109
Cdd:cd16408    81 VE 82
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 41-109 2.82e-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: 63.76  E-value: 2.82e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1998284959  41 DESGISELAATIRTHGVIQPIIVrrnNGRYELIAGERRWRAVRSLGWSTIPaiVKVMNDAQTASAALIE 109
Cdd:cd16410    13 DLGDIEALAESIKRHGLLNPIVV---TPDNELIAGERRLEAAKLLGWETIE--VRVMDIEDEKEKLELE 76
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 32-157 2.18e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 66.65  E-value: 2.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  32 NPFQPR-TVFDESGISELAATIRTHGVIQPIIVR----RNNGrYELIAGERRWRAVRSLGWSTIPAIVKVMNDAQTASAA 106
Cdd:PRK13832   14 NPDNTRrSKSSPQSDALLLATIKAVGIVQPPVVSpeedGGNG-YIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRS 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998284959 107 LIENLQREGLTPIEEAVAYQQLLEIhGLTQESLAQRLGKGQSTIaNKLRLL 157
Cdd:PRK13832   93 MVENIAREPLNPVDQWRAIERLVAL-GWTEEAIAVALALPVRQI-RKLRLL 141
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 26-101 1.98e-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: 59.01  E-value: 1.98e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1998284959  26 VDEIVSNPFQPRTvFDESGISELAATIRTHGVIQPIIVRRNNgryELIAGERRWRAVRSLGWSTIPAIVKV-MNDAQ 101
Cdd:cd16403     2 IDDLKPYPRNART-HSEKQIEQLAASIREFGFTNPILVDEDG---VIIAGHGRLLAAKLLGLKEVPVIRLDhLSEAQ 74
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 26-95 8.85e-09

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: 51.46  E-value: 8.85e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  26 VDEIVSNPFQPRTvfDESGISELAATIRTHGVIQPIIVRRNNgryELIAGERRWRAVRSLGWSTIPAIVK 95
Cdd:cd16402     2 ISELKPYENNPRN--NDKAVEKVAESIKEFGFLVPIVVDKNN---VIVAGHTRYKAAKRLGLEEVPCIVA 66
PRK13866 PRK13866
plasmid partitioning protein RepB; Provisional
 21-122 1.68e-07

plasmid partitioning protein RepB; Provisional


Pssm-ID: 172387 [Multi-domain]  Cd Length: 336  Bit Score: 51.49  E-value: 1.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  21 VVQIGVDEIVSNPFQPRTVFD-ESGISELAATIRTHGVIQPIIVRRN---NGRYELIAGERRWRAVRSLGwSTIPAIVKV 96
Cdd:PRK13866   65 VVSLDPSMIDGSPIADRLPADvDPKFEQLEASISQEGQQVPILVRPHpeaAGRYQIVYGRRRLRAAVNLR-REVSAIVRN 143

                          90       100
                  ....*....|....*....|....*.
gi 1998284959  97 MNDAQTASAALIENLQREGLTPIEEA 122
Cdd:PRK13866  144 LTDRELVVAQGRENLDRADLSFIEKA 169
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
 24-111 5.48e-07

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: 46.82  E-value: 5.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998284959  24 IGVDEI-VSNP-FQPRTVFDEsgiseLAATIRTHGVIQPIIVRRNNG-----RYELIAGERRWRAVRSLGWSTIPAIVKV 96
Cdd:cd16411     1 IPIDDIrVLNPrSRNRKIFRE-----IVESIATVGLKRPITVRRRSSddggyKYDLVCGQGRLEAFKALGETEIPAIVVD 75

                          90
                  ....*....|....*
gi 1998284959  97 MNDAQTASAALIENL 111
Cdd:cd16411    76 VDEEDALLMSLVENI 90
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 32-94 7.14e-07

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: 46.06  E-value: 7.14e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1998284959  32 NPFQPRTV--FDESGISELAATIRTHGVIQPIIVRRNNGRyeLIAGERRWRAVRSLGWSTIPAIV 94
Cdd:cd16401     2 APYNPRKDlkPGDKEYEKLKESIEEFGLVDPLIVNKRTNV--LIGGHQRLKVLKELGYTEVPVVV 64
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 47-94 4.40e-06

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: 43.42  E-value: 4.40e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1998284959  47 ELAATIRTHGVIQPIIVrrnNGRYELIAGERRWRAVRSLGWSTIPAIV 94
Cdd:cd16404    19 ELKESIRKNGIIVPIIV---DQDGVIIDGHHRYRIAKELGIKEVPVIV 63
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 31-81 1.99e-05

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: 41.42  E-value: 1.99e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998284959  31 SNPFQPRTVFDESGISELAATIRTHGVIQPIIVRRNNGRYELIAGERRWRA 81
Cdd:cd16394     3 SLNGRDQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRA 53
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 45-94 2.75e-05

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: 40.71  E-value: 2.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1998284959  45 ISELAATIRTHGVIQPIIVRRNNgryELIAGERRWRAVRSLGWSTIPAIV 94
Cdd:cd16844     6 IERVAASIREFGFRVPVLIDKDG---EIVDGHLRLEAARRLGLETVPVIR 52
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 40-93 1.10e-03

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: 36.76  E-value: 1.10e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1998284959  40 FDESGISELAATIRTHGV-IQPIIVRRNNGRyeLIAGERRWRAVRSLGWSTIPAI 93
Cdd:cd16400    13 VDPDRVEELIEKILEEGVwTKPIIVDKNTGI--ILDGHHRLEAAKRLGLKRVPCV 65
 
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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