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Conserved domains on  [gi|491890840|ref|WP_005655458|]
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MULTISPECIES: ParB/RepB/Spo0J family partition protein [Bacteroidales]

Protein Classification

ParB/RepB/Spo0J family partition protein( domain architecture ID 11445026)

ParB/RepB/Spo0J family partition protein may be involved in segregation and competition between plasmids and chromosomes, such as the ParB/SpoJ-type DNA-binding component of the prokaryotic parABS partitioning system

CATH:  1.10.10.2830
Gene Ontology:  GO:0003677
SCOP:  4002475

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
14-254 3.66e-34

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: 123.56  E-value: 3.66e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  14 IDPRNIVVvDGFNVRRDFD---LDELKEQIKAKGVLNPLTVIAfkddEGNEKYKLVDGERRYRATMLAisEGADIP-YVR 89
Cdd:COG1475   10 IPIDKIVP-SPYNPRRTFDeeaLEELAASIREHGLLQPILVRP----LGDGRYEIIAGERRLRAAKLL--GLETVPaIVR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  90 amkarkDASTEELYIQQMMRNEGKK-FTEYECAIMFRRFKEEFGYSQVEIADKFKKSPAFISKCLSLLDLPPYIQERIMK 168
Cdd:COG1475   83 ------DLDDEEALELALIENLQREdLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALRE 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840 169 GELSVKAAKEIAAnYGSEKEQVKAAKSAVdnaKENGRVTATNKEVLNSLKDSKE-AKAIAEALRKVWAYLDGEVIVDVDK 247
Cdd:COG1475  157 GKLSLGHARALAA-LSDPERQEELAEKII---EEGLSVRETEELVKALAKDLARlERRLSELGTKVKIELEKKGKISLED 232

                 ....*..
gi 491890840 248 LARLLDK 254
Cdd:COG1475  233 LDRLLER 239
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
14-254 3.66e-34

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: 123.56  E-value: 3.66e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  14 IDPRNIVVvDGFNVRRDFD---LDELKEQIKAKGVLNPLTVIAfkddEGNEKYKLVDGERRYRATMLAisEGADIP-YVR 89
Cdd:COG1475   10 IPIDKIVP-SPYNPRRTFDeeaLEELAASIREHGLLQPILVRP----LGDGRYEIIAGERRLRAAKLL--GLETVPaIVR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  90 amkarkDASTEELYIQQMMRNEGKK-FTEYECAIMFRRFKEEFGYSQVEIADKFKKSPAFISKCLSLLDLPPYIQERIMK 168
Cdd:COG1475   83 ------DLDDEEALELALIENLQREdLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALRE 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840 169 GELSVKAAKEIAAnYGSEKEQVKAAKSAVdnaKENGRVTATNKEVLNSLKDSKE-AKAIAEALRKVWAYLDGEVIVDVDK 247
Cdd:COG1475  157 GKLSLGHARALAA-LSDPERQEELAEKII---EEGLSVRETEELVKALAKDLARlERRLSELGTKVKIELEKKGKISLED 232

                 ....*..
gi 491890840 248 LARLLDK 254
Cdd:COG1475  233 LDRLLER 239
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
10-196 1.97e-23

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: 93.98  E-value: 1.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   10 DLFLIDPRNivvvdgFNVRRDF---DLDELKEQIKAKGVLNPLTVIAFKDDEGneKYKLVDGERRYRATMLAisEGADIP 86
Cdd:TIGR00180   9 DIDLLQPNP------YQPRKDFseeSLAELIESIKEQGQLQPILVRKHPDQPG--RYEIIAGERRWRAAKLA--GLKTIP 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   87 yvramkarkdASTEELYIQQMMR------NEGKKFTEYECAIMFRRFKEEFGYSQVEIADKFKKSPAFISKCLSLLDLPP 160
Cdd:TIGR00180  79 ----------AIVRELDDEQMLAdalienIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPS 148
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 491890840  161 YIQERIM--KGELSVKAAKEIAANYGSEKEQVKAAKSA 196
Cdd:TIGR00180 149 EIQSAIPeaSGLLSSGHARLLLALKKKPKLQELLASII 186
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
20-78 4.15e-11

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: 58.26  E-value: 4.15e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491890840  20 VVVDGFNVRRDFD---LDELKEQIKAKGVLNPLTViaFKDDEGneKYKLVDGERRYRATMLA 78
Cdd:cd16393    9 IRPNPYQPRKEFDeeaLKELAESIKEHGLLQPIVV--RKVGDG--RYEIIAGERRWRAAKLA 66
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
32-78 7.09e-07

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: 46.14  E-value: 7.09e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 491890840    32 DLDELKEQIKAKGVLNPLTViafkdDEGNEKYKLVDGERRYRATMLA 78
Cdd:smart00470  22 SLEELAESIKENGLLQPIIV-----RPNDGRYEIIDGERRLRAAKLL 63
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
10-78 6.51e-06

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: 43.42  E-value: 6.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491890840   10 DLFLIDPRNivvvdgFNVRRDF--DLDELKEQIKAKGVLNPLTViafkDDEGNEKYKLVDGERRYRATMLA 78
Cdd:pfam02195   4 PISKLRPNP------DQPRKDSeeSLEELAASIKKRGLLQPIIV----RKTPDGRYEIIAGERRLRAAKLL 64
 
Name Accession Description Interval E-value
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
14-254 3.66e-34

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: 123.56  E-value: 3.66e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  14 IDPRNIVVvDGFNVRRDFD---LDELKEQIKAKGVLNPLTVIAfkddEGNEKYKLVDGERRYRATMLAisEGADIP-YVR 89
Cdd:COG1475   10 IPIDKIVP-SPYNPRRTFDeeaLEELAASIREHGLLQPILVRP----LGDGRYEIIAGERRLRAAKLL--GLETVPaIVR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840  90 amkarkDASTEELYIQQMMRNEGKK-FTEYECAIMFRRFKEEFGYSQVEIADKFKKSPAFISKCLSLLDLPPYIQERIMK 168
Cdd:COG1475   83 ------DLDDEEALELALIENLQREdLNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSNLLRLLKLPPEVQEALRE 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840 169 GELSVKAAKEIAAnYGSEKEQVKAAKSAVdnaKENGRVTATNKEVLNSLKDSKE-AKAIAEALRKVWAYLDGEVIVDVDK 247
Cdd:COG1475  157 GKLSLGHARALAA-LSDPERQEELAEKII---EEGLSVRETEELVKALAKDLARlERRLSELGTKVKIELEKKGKISLED 232

                 ....*..
gi 491890840 248 LARLLDK 254
Cdd:COG1475  233 LDRLLER 239
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
10-196 1.97e-23

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: 93.98  E-value: 1.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   10 DLFLIDPRNivvvdgFNVRRDF---DLDELKEQIKAKGVLNPLTVIAFKDDEGneKYKLVDGERRYRATMLAisEGADIP 86
Cdd:TIGR00180   9 DIDLLQPNP------YQPRKDFseeSLAELIESIKEQGQLQPILVRKHPDQPG--RYEIIAGERRWRAAKLA--GLKTIP 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   87 yvramkarkdASTEELYIQQMMR------NEGKKFTEYECAIMFRRFKEEFGYSQVEIADKFKKSPAFISKCLSLLDLPP 160
Cdd:TIGR00180  79 ----------AIVRELDDEQMLAdalienIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPS 148
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 491890840  161 YIQERIM--KGELSVKAAKEIAANYGSEKEQVKAAKSA 196
Cdd:TIGR00180 149 EIQSAIPeaSGLLSSGHARLLLALKKKPKLQELLASII 186
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
20-78 4.15e-11

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: 58.26  E-value: 4.15e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491890840  20 VVVDGFNVRRDFD---LDELKEQIKAKGVLNPLTViaFKDDEGneKYKLVDGERRYRATMLA 78
Cdd:cd16393    9 IRPNPYQPRKEFDeeaLKELAESIKEHGLLQPIVV--RKVGDG--RYEIIAGERRWRAAKLA 66
PRTRC_parB TIGR03734
PRTRC system ParB family protein; A novel genetic system characterized by six major proteins, ...
21-169 2.22e-10

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: 60.49  E-value: 2.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   21 VVDGFNVRRDFD---LDELKEQIKAKGVLNPLTViafKDDEGNEKYKLVDGERRYRATMLAISEGADIPYVraMKARKDA 97
Cdd:TIGR03734   2 IVPGNNPRRYFDpaeMAELVESIRAKGVLQPILV---RPVPGSDLYEVVAGERRYRAALEVFGEDYDIPAL--IKVLTDE 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491890840   98 STEEL-YIQQMMRNEGKKFTEYECAimfrrfKEEFGYSQV---EIADKFKKSPAFISKCLSLLDLPP-----YIQERIMK 168
Cdd:TIGR03734  77 EAEAAaLIENVQRADMSPAEEAEAA------ARLLGRCKGdreEAARRLGWSPATLDRRLALMNCTDevrqaLIDRKILL 150

                  .
gi 491890840  169 G 169
Cdd:TIGR03734 151 G 151
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
32-88 9.95e-09

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: 50.28  E-value: 9.95e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491890840  32 DLDELKEQIKAKGVLNPLTVIAFKDDegneKYKLVDGERRYRATMLAISEgaDIPYV 88
Cdd:cd16387    4 ELEELAESIREHGVLQPIIVRPLPDG----RYEIIAGERRWRAAKLAGLT--TIPVV 54
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
10-74 1.72e-07

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: 47.99  E-value: 1.72e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491890840  10 DLFLIDPRNIVVVDGFNVRRDFD---LDELKEQIKAKGVLNPLTVIAFKDdegnEKYKLVDGERRYRA 74
Cdd:cd16396    1 GEVLEIPVADIIPNPYQPRKEFDeeeIEELAESIKEHGLLQPIVVRKTKD----GGYEIVAGERRWRA 64
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
32-78 7.09e-07

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: 46.14  E-value: 7.09e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 491890840    32 DLDELKEQIKAKGVLNPLTViafkdDEGNEKYKLVDGERRYRATMLA 78
Cdd:smart00470  22 SLEELAESIKENGLLQPIIV-----RPNDGRYEIIDGERRLRAAKLL 63
ParB_N_like cd16406
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
32-82 1.38e-06

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: 45.20  E-value: 1.38e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491890840  32 DLDELKEQIKAKGVLNPLTVIAFKDDegnEKYKLVDGERRYRATMLAISEG 82
Cdd:cd16406    5 GIEELAASIAAHGLLQNLVVRPAKKK---GRYEVVAGGRRLRALQLLAERG 52
KorB_N_like cd16398
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ...
26-78 1.52e-06

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: 45.34  E-value: 1.52e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 491890840  26 NVRRDFD---LDELKEQIKAKGVLNPLTVIAFKDDEGneKYKLVDGERRYRATMLA 78
Cdd:cd16398   10 NPRTEFDeekIEELAASIKERGVKSPISVRPHPEKPG--KYIINHGARRYRASKWA 63
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
10-78 6.51e-06

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: 43.42  E-value: 6.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491890840   10 DLFLIDPRNivvvdgFNVRRDF--DLDELKEQIKAKGVLNPLTViafkDDEGNEKYKLVDGERRYRATMLA 78
Cdd:pfam02195   4 PISKLRPNP------DQPRKDSeeSLEELAASIKKRGLLQPIIV----RKTPDGRYEIIAGERRLRAAKLL 64
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
27-74 6.68e-05

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: 40.65  E-value: 6.68e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 491890840  27 VRRDF-DLDELKEQIKAKGVLNPLTViafkddegNEKYKLVDGERRYRA 74
Cdd:cd16410   10 IRKDLgDIEALAESIKRHGLLNPIVV--------TPDNELIAGERRLEA 50
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
33-81 3.50e-04

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: 38.03  E-value: 3.50e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 491890840  33 LDELKEQIKAKGVLNPLTViafkddegNEKYKLVDGERRYR-ATMLAISE 81
Cdd:cd16404   17 FEELKESIRKNGIIVPIIV--------DQDGVIIDGHHRYRiAKELGIKE 58
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
34-110 1.03e-03

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: 37.19  E-value: 1.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491890840  34 DELKEQIKAKGVLNPLTVIAFKDDEGNEKYKLVDGERRYRATMLAiseGAD-IPyvramkAR-KDASTEELYIQQMMRN 110
Cdd:cd16411   20 REIVESIATVGLKRPITVRRRSSDDGGYKYDLVCGQGRLEAFKAL---GETeIP------AIvVDVDEEDALLMSLVEN 89
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
34-74 2.57e-03

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: 35.74  E-value: 2.57e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 491890840  34 DELKEQIKAKGVLNPLTVIAFKDdegnEKYKLVDGERRYRA 74
Cdd:cd16409    7 EALAQSIAEHGLLTPITVRQDPG----GRYTLIAGAHRLAA 43
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
31-78 9.97e-03

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: 34.52  E-value: 9.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491890840  31 FDLDELKEQIKAKGVLNPLTVIAFKDDegneKYKLVDGERRYRATMLA 78
Cdd:cd16408   15 ERLEDMVESIKENGVLQPIIVRPIEDG----KYEILAGHNRVNAAKLA 58
 
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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