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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209  13 IEIAKIKFLNPRTRNKVVHEEIKESIKKRGLSKPISVRAI--DEGDFKYALICGQGRIEALVALGETIIPAIIRDVSEED 90
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRssDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                         90
                 ....*....|
gi 446859209  91 AYVMSLVENI 100
Cdd:cd16411   81 ALLMSLVENI 90

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209  13 IEIAKIKFLNPRTRNKVVHEEIKESIKKRGLSKPISVRAI--DEGDFKYALICGQGRIEALVALGETIIPAIIRDVSEED 90
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRssDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                         90
                 ....*....|
gi 446859209  91 AYVMSLVENI 100
Cdd:cd16411   81 ALLMSLVENI 90

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209    11 IQIEIAKIKF--LNPRTRNKVVHEEIKESIKKRGLSKPISVRaidEGDFKYALICGQGRIEALVALGETIIPAIIRDVSE 88
Cdd:smart00470   1 VEVPIEKLRPnpDQPRLTSEESLEELAESIKENGLLQPIIVR---PNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDD 77

                           90
                   ....*....|..
gi 446859209    89 EDAYVMSLVENI 100
Cdd:smart00470  78 EEAIALSLEENI 89

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209   12 QIEIAKIKF--LNPRTRNKVVHEEIKESIKKRGLSKPISVRAIDEGdfKYALICGQGRIEALVALGETIIPAIIRDVSEE 89
Cdd:pfam02195   2 EVPISKLRPnpDQPRKDSEESLEELAASIKKRGLLQPIIVRKTPDG--RYEIIAGERRLRAAKLLGLKEVPVIVREIDDE 79

                          90
                  ....*....|.
gi 446859209   90 DAYVMSLVENI 100
Cdd:pfam02195  80 EAIALSLIENI 90

plasmid partitioning protein; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446859209  37 SIKKRGLSKPISVRAIDEGDFKYALICGQGRIEALVALGETIIPAIIRDVSEEDAYVMSLVENIAR 102
Cdd:PRK13832  34 TIKAVGIVQPPVVSPEEDGGNGYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRSMVENIAR 99

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209  13 IEIAKIKFLNPRTRNKVVHEEIKESIKKRGLSKPISVRAI--DEGDFKYALICGQGRIEALVALGETIIPAIIRDVSEED 90
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRssDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                         90
                 ....*....|
gi 446859209  91 AYVMSLVENI 100
Cdd:cd16411   81 ALLMSLVENI 90

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446859209  32 EEIKESIKKRGLSKPISVRAIDEGdfKYALICGQGRIEALVALGETIIPAIIRDVSEEDAYVMSLVENIAR 102
Cdd:cd16393   26 KELAESIKEHGLLQPIVVRKVGDG--RYEIIAGERRWRAAKLAGLTEIPAIVRDLDDEEALELALIENIQR 94

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209    11 IQIEIAKIKF--LNPRTRNKVVHEEIKESIKKRGLSKPISVRaidEGDFKYALICGQGRIEALVALGETIIPAIIRDVSE 88
Cdd:smart00470   1 VEVPIEKLRPnpDQPRLTSEESLEELAESIKENGLLQPIIVR---PNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDD 77

                           90
                   ....*....|..
gi 446859209    89 EDAYVMSLVENI 100
Cdd:smart00470  78 EEAIALSLEENI 89

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209   22 NPRTR-NKVVHEEIKESIKKRGLSKPISVRAIDEGDFkYALICGQGRIEA-LVALGETI-IPAIIRDVSEEDAYVMSLVE 98
Cdd:TIGR03734   7 NPRRYfDPAEMAELVESIRAKGVLQPILVRPVPGSDL-YEVVAGERRYRAaLEVFGEDYdIPALIKVLTDEEAEAAALIE 85

                  ....
gi 446859209   99 NIAR 102
Cdd:TIGR03734  86 NVQR 89

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209  32 EEIKESIKKRGLSKPISVRAIDEGDFKYALICGQGRIEALVALGetiIP--AIIRDVSEEDAYVMSLVEN 99
Cdd:cd16405   25 EELKESIRESGQQVPILVRPHPEEGGRYEIVYGHRRLRACRELG---LPvrAIVRELSDEELVVAQGQEN 91

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446859209  32 EEIKESIKKRGLSKPISVRAIDEGdfKYALICGQGRIEALVALGETIIPAIIRDVSEEDAYVMSLVEN 99
Cdd:cd16409    7 EALAQSIAEHGLLTPITVRQDPGG--RYTLIAGAHRLAAAKLLGWDTIDAIIVKADDLEAELLEIDEN 72

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446859209  32 EEIKESIKKRGLSKPISVRAIDEGdfKYALICGQGRIEALVALGETIIPAIIR-DVSEEDAYVM 94
Cdd:cd16408   18 EDMVESIKENGVLQPIIVRPIEDG--KYEILAGHNRVNAAKLAGLTTIPAIIKeNLTDEEAKLI 79

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446859209  22 NPRTRNKVVHEEIKESIKKRGLSKPIsvrAIDEGDFkyaLICGQGRIEALVALGETIIPAIIRD-VSEED--AYVM 94
Cdd:cd16403   11 NARTHSEKQIEQLAASIREFGFTNPI---LVDEDGV---IIAGHGRLLAAKLLGLKEVPVIRLDhLSEAQkrAYRI 80

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446859209  22 NPRTRNKVVhEEIKESIKKRGLSKPISVraidegDFKYALICGQGRIEALVALGETIIPAII-RDVSEEDAYVMSLVEN 99
Cdd:cd16402   11 NPRNNDKAV-EKVAESIKEFGFLVPIVV------DKNNVIVAGHTRYKAAKRLGLEEVPCIVaDDLTEEQIKAFRLADN 82

RepB plasmid partitioning protein; This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859209  101 ARRRPRSNELLQVIKDMKIRGLSDSEISEITGYSSNWVS-----SINMLLDKGEHKLLSAVERGNLPLYLAVQFARCETE 175
Cdd:pfam07506   1 ARADLSFIERARFAARLLERGVPRAEIAAALGLDPQTVSkmvarAIPEGICPEEEALLKDVETGIAAFGLARKIGRDRWV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 446859209  176 EAQDIL------TEAYDKKLIKSRDIIKIKHILNQRTVGNKGAKAAG 216
Cdd:pfam07506  81 ELAELLaaaknvESAYFRALLADTRFSQLVKPLRPKRIKGVSGKSAA 127

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446859209  32 EEIKESIKKRGLSKPISVraidegDFKYALICGQGRIEALVALGETIIPAIIRDVSEE 89
Cdd:cd16404   18 EELKESIRKNGIIVPIIV------DQDGVIIDGHHRYRIAKELGIKEVPVIVYDFDDE 69