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Conserved domains on  [gi|504278873|ref|WP_014465975|]
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nucleoid occlusion protein [Alicyclobacillus acidocaldarius]

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 ...
 20-276 8.26e-157

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: 437.33  E-value: 8.26e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   20 QVVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  100 AQTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  180 LLALPSEELQIELLNECIEKGWNVKQMEERVKAKLESlgSAVERRRKPRKRGLSKDVRLAVNTIRQSLQMIEQTGLQVVC 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEK--PEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKT 238

                         250
                  ....*....|....*..
gi 504278873  260 EEVDDEEYYQFTIRVPK 276
Cdd:TIGR04285 239 KEEDLDDYYEITIRIPK 255
 
Name Accession Description Interval E-value
nucleoid_noc TIGR04285
nucleoid occlusion protein; This model describes nucleoid occlusion protein, a close homolog ...
 20-276 8.26e-157

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: 437.33  E-value: 8.26e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   20 QVVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  100 AQTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  180 LLALPSEELQIELLNECIEKGWNVKQMEERVKAKLESlgSAVERRRKPRKRGLSKDVRLAVNTIRQSLQMIEQTGLQVVC 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEK--PEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKT 238

                         250
                  ....*....|....*..
gi 504278873  260 EEVDDEEYYQFTIRVPK 276
Cdd:TIGR04285 239 KEEDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 17-226 1.70e-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: 248.36  E-value: 1.70e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  17 AQTQVVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGD-VYELIAGERRLRAVRHLGWTTIPAIVR 95
Cdd:COG1475    3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLGDgRYEIIAGERRLRAAKLLGLETVPAIVR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  96 DLNDAQTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITER 175
Cdd:COG1475   83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504278873 176 HARALLALPSEELQIELLNECIEKGWNVKQMEERVKAKLESLGSAVERRRK 226
Cdd:COG1475  163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKDLARLERRLSE 213
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 21-116 1.90e-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: 146.09  E-value: 1.90e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  21 VVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDV-YELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:cd16393    1 VQEIPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGDGrYEIIAGERRWRAAKLAGLTEIPAIVRDLDD 80

                         90
                 ....*....|....*..
gi 504278873 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 9.65e-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: 100.07  E-value: 9.65e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873    22 VDIPVERIVPNPYQPRAIFhQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQ 101
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTS-EESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79

                           90
                   ....*....|
gi 504278873   102 TASAALIENL 111
Cdd:smart00470  80 AIALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 24-111 2.70e-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: 96.58  E-value: 2.70e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   24 IPVERIVPNPYQPRAIfHQESIEELAKTIHTHGVIQPVVVRK-KGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQT 102
Cdd:pfam02195   3 VPISKLRPNPDQPRKD-SEESLEELAASIKKRGLLQPIIVRKtPDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDEEA 81


                  ....*....
gi 504278873  103 ASAALIENL 111
Cdd:pfam02195  82 IALSLIENI 90
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 31-157 1.27e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 67.81  E-value: 1.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  31 PNPYQPRAI-FHQESIEELAKTIHTHGVIQPVVVRKK---GDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQTASAA 106
Cdd:PRK13832  13 DNPDNTRRSkSSPQSDALLLATIKAVGIVQPPVVSPEedgGNGYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRS 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504278873 107 LIENLQREGLTPIEEAVAYQQLMELhGLTQESLAQRLGKGQSTIaNKLRLL 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 ...
 20-276 8.26e-157

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: 437.33  E-value: 8.26e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   20 QVVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:TIGR04285   1 EVQQIPIDKIVPNPYQPRKVFDEESIEELAQSIKEHGLIQPIVVRKKDDKYEIIAGERRFRACKLLGWEEVPAIVREMND 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  100 AQTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITERHARA 179
Cdd:TIGR04285  81 EETASIALIENLQRENLTAIEEAEAYQQLIELHGLTQEELAQRLGKSQSTIANKLRLLKLPEEVQEALLERKITERHARA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  180 LLALPSEELQIELLNECIEKGWNVKQMEERVKAKLESlgSAVERRRKPRKRGLSKDVRLAVNTIRQSLQMIEQTGLQVVC 259
Cdd:TIGR04285 161 LLKLPDEELQLEVLNEIIEKGLNVKQTEELIKKLLEK--PEKKKKKKKRRKGFSKDVRIAVNTIKQSVKMIKKTGIKVKT 238

                         250
                  ....*....|....*..
gi 504278873  260 EEVDDEEYYQFTIRVPK 276
Cdd:TIGR04285 239 KEEDLDDYYEITIRIPK 255
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 17-226 1.70e-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: 248.36  E-value: 1.70e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  17 AQTQVVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGD-VYELIAGERRLRAVRHLGWTTIPAIVR 95
Cdd:COG1475    3 EGEEIREIPIDKIVPSPYNPRRTFDEEALEELAASIREHGLLQPILVRPLGDgRYEIIAGERRLRAAKLLGLETVPAIVR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  96 DLNDAQTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITER 175
Cdd:COG1475   83 DLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALREGKLSLG 162

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504278873 176 HARALLALPSEELQIELLNECIEKGWNVKQMEERVKAKLESLGSAVERRRK 226
Cdd:COG1475  163 HARALAALSDPERQEELAEKIIEEGLSVRETEELVKALAKDLARLERRLSE 213
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 24-197 5.39e-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: 194.13  E-value: 5.39e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   24 IPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRK---KGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDA 100
Cdd:TIGR00180   8 IDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKhpdQPGRYEIIAGERRWRAAKLAGLKTIPAIVRELDDE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  101 QTASAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQ--ITERHAR 178
Cdd:TIGR00180  88 QMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASglLSSGHAR 167

                         170       180
                  ....*....|....*....|
gi 504278873  179 ALLALP-SEELQIELLNECI 197
Cdd:TIGR00180 168 LLLALKkKPKLQELLASIII 187
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 21-116 1.90e-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: 146.09  E-value: 1.90e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  21 VVDIPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDV-YELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:cd16393    1 VQEIPIDKIRPNPYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGDGrYEIIAGERRWRAAKLAGLTEIPAIVRDLDD 80

                         90
                 ....*....|....*..
gi 504278873 100 AQTASAALIENLQREGL 116
Cdd:cd16393   81 EEALELALIENIQREDL 97
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 24-112 1.97e-37

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: 128.11  E-value: 1.97e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  24 IPVERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDV-YELIAGERRLRAVRHLGWTTIPAIVRDLNDAQT 102
Cdd:cd16396    6 IPVADIIPNPYQPRKEFDEEEIEELAESIKEHGLLQPIVVRKTKDGgYEIVAGERRWRAAKLLGWEKIPAIIRDLSDKEA 85

                         90
                 ....*....|
gi 504278873 103 ASAALIENLQ 112
Cdd:cd16396   86 LEIALIENLQ 95
PRTRC_parB TIGR03734
PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ...
 28-221 2.50e-36

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: 136.38  E-value: 2.50e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   28 RIVPNpYQPRAIFHQESIEELAKTIHTHGVIQPVVVR--KKGDVYELIAGERRLRAVRHLGWT--TIPAIVRDLNDAQTA 103
Cdd:TIGR03734   1 LIVPG-NNPRRYFDPAEMAELVESIRAKGVLQPILVRpvPGSDLYEVVAGERRYRAALEVFGEdyDIPALIKVLTDEEAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  104 SAALIENLQREGLTPIEEAVAYQQLMELHGLTQESLAQRLGKGQSTIANKLRLLHLPQAVQDALLTRQITERHARALLAL 183
Cdd:TIGR03734  80 AAALIENVQRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLALMNCTDEVRQALIDRKILLGHAELLAGL 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 504278873  184 PsEELQIELLNECIEKGWNVKQMEERVKAKLESLGSAV 221
Cdd:TIGR03734 160 P-KDKQDNVLTAILAEKPTVAELKKMIESAALSLSAAI 196
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 22-111 9.65e-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: 100.07  E-value: 9.65e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873    22 VDIPVERIVPNPYQPRAIFhQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQ 101
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTS-EESLEELAESIKENGLLQPIIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79

                           90
                   ....*....|
gi 504278873   102 TASAALIENL 111
Cdd:smart00470  80 AIALSLEENI 89
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 24-111 2.70e-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: 96.58  E-value: 2.70e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873   24 IPVERIVPNPYQPRAIfHQESIEELAKTIHTHGVIQPVVVRK-KGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQT 102
Cdd:pfam02195   3 VPISKLRPNPDQPRKD-SEESLEELAASIKKRGLLQPIIVRKtPDGRYEIIAGERRLRAAKLLGLKEVPVIVREIDDEEA 81


                  ....*....
gi 504278873  103 ASAALIENL 111
Cdd:pfam02195  82 IALSLIENI 90
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 26-101 2.45e-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: 80.64  E-value: 2.45e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504278873  26 VERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVR-KKGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQ 101
Cdd:cd16407    1 LSELHPFPNHPFKVRDDEEMEELVESIKENGVLTPIIVRpREDGGYEIISGHRRKRACELAGLETIPVIVREMDDDE 77
KorB_N_like cd16398
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ...
 26-116 3.07e-17

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: 75.00  E-value: 3.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  26 VERIVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDV---YELIAGERRLRAVRHLGWTTIPAIV-RDLNDAQ 101
Cdd:cd16398    1 LDKIDEDPDNPRTEFDEEKIEELAASIKERGVKSPISVRPHPEKpgkYIINHGARRYRASKWAGLKTIPAFIdNDHDDFD 80

                         90
                 ....*....|....*
gi 504278873 102 tasaALIENLQREGL 116
Cdd:cd16398   81 ----QVIENIQREDL 91
ParB_N_like cd16406
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 42-114 8.40e-17

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: 73.71  E-value: 8.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  42 QESIEELAKTIHTHGVIQPVVVR--KKGDVYELIAGERRLRAVRHL---GW----TTIPAIVRDLNDAQTASaaLIENLQ 112
Cdd:cd16406    3 PAGIEELAASIAAHGLLQNLVVRpaKKKGRYEVVAGGRRLRALQLLaerGRlpadYPVPVKVVPDADALEAS--LAENVQ 80


                 ..
gi 504278873 113 RE 114
Cdd:cd16406   81 RE 82
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 42-93 3.49e-16

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: 71.08  E-value: 3.49e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504278873  42 QESIEELAKTIHTHGVIQPVVVRK-KGDVYELIAGERRLRAVRHLGWTTIPAI 93
Cdd:cd16387    2 EEELEELAESIREHGVLQPIIVRPlPDGRYEIIAGERRWRAAKLAGLTTIPVV 54
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 42-111 1.42e-15

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: 70.02  E-value: 1.42e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504278873  42 QESIEELAKTIHTHGVIQPVVVRK-KGDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQTASAALIENL 111
Cdd:cd16409    3 PEHVEALAQSIAEHGLLTPITVRQdPGGRYTLIAGAHRLAAAKLLGWDTIDAIIVKADDLEAELLEIDENL 73
HTH_ParB pfam17762
HTH domain found in ParB protein;
161-210 2.00e-15

HTH domain found in ParB protein;


Pssm-ID: 465489  Cd Length: 50  Bit Score: 68.95  E-value: 2.00e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 504278873  161 QAVQDALLTRQITERHARALLALPSEELQIELLNECIEKGWNVKQMEERV 210
Cdd:pfam17762   1 PEVQELLREGKLSEGHARALLSLKDEEKQLELAKKIIEEGLSVRETEKLV 50
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 45-100 3.78e-15

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: 69.15  E-value: 3.78e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 504278873  45 IEELAKTIHTHGVIQPVVVRKKgdvYELIAGERRLRAVRHLGWTTIPAIVRDLNDA 100
Cdd:cd16410   17 IEALAESIKRHGLLNPIVVTPD---NELIAGERRLEAAKLLGWETIEVRVMDIEDE 69
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 24-110 1.77e-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: 1.77e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  24 IPVERIVPNPYQPR--AIFHQESIEELAKTIHTHGVIQPVVVRK---KGDVYELIAGERRLRAVRHLGWtTIPAIVRDLN 98
Cdd:cd16405    1 LDPDLIDPSFIADRleDDFDDDEFEELKESIRESGQQVPILVRPhpeEGGRYEIVYGHRRLRACRELGL-PVRAIVRELS 79

                         90
                 ....*....|..
gi 504278873  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 5.47e-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: 319265 [Multi-domain]  Cd Length: 84  Bit Score: 63.41  E-value: 5.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  29 IVPNPYQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKGD-VYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQTASAAL 107
Cdd:cd16408    1 LVPFSDHPFKLYTGERLEDMVESIKENGVLQPIIVRPIEDgKYEILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKLIV 80


                 ..
gi 504278873 108 IE 109
Cdd:cd16408   81 VE 82
PRK13832 PRK13832
plasmid partitioning protein; Provisional
 31-157 1.27e-12

plasmid partitioning protein; Provisional


Pssm-ID: 184353 [Multi-domain]  Cd Length: 520  Bit Score: 67.81  E-value: 1.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  31 PNPYQPRAI-FHQESIEELAKTIHTHGVIQPVVVRKK---GDVYELIAGERRLRAVRHLGWTTIPAIVRDLNDAQTASAA 106
Cdd:PRK13832  13 DNPDNTRRSkSSPQSDALLLATIKAVGIVQPPVVSPEedgGNGYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRS 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504278873 107 LIENLQREGLTPIEEAVAYQQLMELhGLTQESLAQRLGKGQSTIaNKLRLL 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 ...
 25-101 3.45e-12

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: 61.32  E-value: 3.45e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504278873  25 PVERIVPNPYQPRAifH-QESIEELAKTIHTHGVIQPVVVRKKGdvyELIAGERRLRAVRHLGWTTIPAIVRD-LNDAQ 101
Cdd:cd16403    1 PIDDLKPYPRNART--HsEKQIEQLAASIREFGFTNPILVDEDG---VIIAGHGRLLAAKLLGLKEVPVIRLDhLSEAQ 74
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
 24-111 5.09e-11

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: 57.99  E-value: 5.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  24 IPVERI-VPNPY-QPRAIFhqesiEELAKTIHTHGVIQPVVVRK-----KGDVYELIAGERRLRAVRHLGWTTIPAIVRD 96
Cdd:cd16411    1 IPIDDIrVLNPRsRNRKIF-----REIVESIATVGLKRPITVRRrssddGGYKYDLVCGQGRLEAFKALGETEIPAIVVD 75

                         90
                 ....*....|....*
gi 504278873  97 LNDAQTASAALIENL 111
Cdd:cd16411   76 VDEEDALLMSLVENI 90
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 31-97 1.66e-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. 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: 56.46  E-value: 1.66e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504278873  31 PNPYQPRAIFH--QESIEELAKTIHTHGVIQPVVVRKKGDVyeLIAGERRLRAVRHLGWTTIPAIVRDL 97
Cdd:cd16401    1 PAPYNPRKDLKpgDKEYEKLKESIEEFGLVDPLIVNKRTNV--LIGGHQRLKVLKELGYTEVPVVVVDL 67
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 25-110 5.49e-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: 54.93  E-value: 5.49e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  25 PVERIVPNPYQPRAifHQESIEELAKTIHTHGVIQPVVVRKKGdvyELIAGERRLRAVRHLGWTTIPAIV-RDLNDAQTA 103
Cdd:cd16402    1 KISELKPYENNPRN--NDKAVEKVAESIKEFGFLVPIVVDKNN---VIVAGHTRYKAAKRLGLEEVPCIVaDDLTEEQIK 75


                 ....*..
gi 504278873 104 SAALIEN 110
Cdd:cd16402   76 AFRLADN 82
PRK13866 PRK13866
plasmid partitioning protein RepB; Provisional
 46-122 9.13e-07

plasmid partitioning protein RepB; Provisional


Pssm-ID: 172387 [Multi-domain]  Cd Length: 336  Bit Score: 49.57  E-value: 9.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504278873  46 EELAKTIHTHGVIQPVVVRKKGDV---YELIAGERRLRAVRHLGwTTIPAIVRDLNDAQTASAALIENLQREGLTPIEEA 122
Cdd:PRK13866  91 EQLEASISQEGQQVPILVRPHPEAagrYQIVYGRRRLRAAVNLR-REVSAIVRNLTDRELVVAQGRENLDRADLSFIEKA 169
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 34-99 4.12e-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: 43.80  E-value: 4.12e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504278873  34 YQPRAIFHQESIEELAKTIHTHGVIQPVVVRKKgdvYELIAGERRLRAVRHLGWTTIPAIVRDLND 99
Cdd:cd16404    6 EFRTPNPTNEEFEELKESIRKNGIIVPIIVDQD---GVIIDGHHRYRIAKELGIKEVPVIVYDFDD 68
sopB_N cd16394
N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid; ...
 36-86 1.93e-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: 41.81  E-value: 1.93e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504278873  36 PRAIFHQESIEELAKTIHTHGVIQPVVVRKKGDVYELIAGERRLRAVRHLG 86
Cdd:cd16394    8 DQELLTEEAVSDIIPSIKENGQFVPAIGYRVDGKIELLDGSRRRRAAILAG 58
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 20-80 1.17e-03

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: 37.55  E-value: 1.17e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504278873  20 QVVDIPVERIVPNPYQPRAIFHQESieELAKT-IHTHGVIQPVVVR--KKGDVYELIAGERRLR 80
Cdd:cd16397    4 NVQWVPIEKVQANDYNPNKVAPPEM--KLLKLsILEDGFTQPIVVYydEEDDKYVIVDGFHRYT 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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