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 1939405845 13 IPISQIEVINPRERNGRVFDEIVSNIKTIGLKKPILVTPRATASGVEKYLLVCGEGRLKAFRSLGETTIPALVVSVSDED 92
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRSSDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                 ....
gi 1939405845 93 AFIM 96
Cdd:cd16411   81 ALLM 84

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 1939405845 13 IPISQIEVINPRERNGRVFDEIVSNIKTIGLKKPILVTPRATASGVEKYLLVCGEGRLKAFRSLGETTIPALVVSVSDED 92
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRSSDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                 ....
gi 1939405845 93 AFIM 96
Cdd:cd16411   81 ALLM 84

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 1939405845  11 RMIPISQIEVI--NPRERNGRVFDEIVSNIKTIGLKKPILVTPRATasgveKYLLVCGEGRLKAFRSLGETTIPALVVSV 88
Cdd:smart00470  1 VEVPIEKLRPNpdQPRLTSEESLEELAESIKENGLLQPIIVRPNDG-----RYEIIDGERRLRAAKLLGLKEVPVIVRDL 75

                  ....*...
gi 1939405845  89 SDEDAFIM 96
Cdd:smart00470 76 DDEEAIAL 83

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 1939405845 11 RMIPISQIEVINPRERNGRV--FDEIVSNIKTIGLKKPILVTPrataSGVEKYLLVCGEGRLKAFRSLGETTIPALVVSV 88
Cdd:pfam02195  1 EEVPISKLRPNPDQPRKDSEesLEELAASIKKRGLLQPIIVRK----TPDGRYEIIAGERRLRAAKLLGLKEVPVIVREI 76

                 ....*...
gi 1939405845 89 SDEDAFIM 96
Cdd:pfam02195 77 DDEEAIAL 84

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 1939405845 13 IPISQIEVINPRERNGRVFDEIVSNIKTIGLKKPILVTPRATASGVEKYLLVCGEGRLKAFRSLGETTIPALVVSVSDED 92
Cdd:cd16411    1 IPIDDIRVLNPRSRNRKIFREIVESIATVGLKRPITVRRRSSDDGGYKYDLVCGQGRLEAFKALGETEIPAIVVDVDEED 80

                 ....
gi 1939405845 93 AFIM 96
Cdd:cd16411   81 ALLM 84

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939405845 10 VRMIPISQIEVI--NPRerngRVFD-----EIVSNIKTIGLKKPILVTPrataSGVEKYLLVCGEGRLKAFRSLGETTIP 82
Cdd:cd16393    1 VQEIPIDKIRPNpyQPR----KEFDeealkELAESIKEHGLLQPIVVRK----VGDGRYEIIAGERRWRAAKLAGLTEIP 72

                         90
                 ....*....|....
gi 1939405845 83 ALVVSVSDEDAFIM 96
Cdd:cd16393   73 AIVRDLDDEEALEL 86

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 1939405845  11 RMIPISQIEVI--NPRERNGRVFDEIVSNIKTIGLKKPILVTPRATasgveKYLLVCGEGRLKAFRSLGETTIPALVVSV 88
Cdd:smart00470  1 VEVPIEKLRPNpdQPRLTSEESLEELAESIKENGLLQPIIVRPNDG-----RYEIIDGERRLRAAKLLGLKEVPVIVRDL 75

                  ....*...
gi 1939405845  89 SDEDAFIM 96
Cdd:smart00470 76 DDEEAIAL 83

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1939405845 31 FDEIVSNIKTIGLKKPILVTPRATASGveKYLLVCGEGRLKAFRSLGettIP--ALVVSVSDEDAFIM 96
Cdd:cd16405   24 FEELKESIRESGQQVPILVRPHPEEGG--RYEIVYGHRRLRACRELG---LPvrAIVRELSDEELVVA 86

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
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1939405845 31 FDEIVSNIKTIGLKKPILVTPRATasgvEKYLLVCGEGRLKAFRSLGETTIPAL 84
Cdd:cd16387    5 LEELAESIREHGVLQPIIVRPLPD----GRYEIIAGERRWRAAKLAGLTTIPVV 54

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 1939405845 18 IEVINPRERNGRVFDE-----IVSNIKTIGLKKPILVTpratasgvEKYLLVCGEGRLKAFRSLGETTIPALVVS 87
Cdd:cd16403    2 IDDLKPYPRNARTHSEkqieqLAASIREFGFTNPILVD--------EDGVIIAGHGRLLAAKLLGLKEVPVIRLD 68

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 1939405845 32 DEIVSNIKTIGLKKPILVTPratasgveKYLLVCGEGRLKAFRSLGETTIPALVVSVSDE 91
Cdd:cd16410   18 EALAESIKRHGLLNPIVVTP--------DNELIAGERRLEAAKLLGWETIEVRVMDIEDE 69

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 1939405845 31 FDEIVSNIKTIGLKKPILVTPRATasgvEKYLLVCGEGRLKAFRSLGETTIPALVVSV-SDEDAFIM 96
Cdd:cd16408   17 LEDMVESIKENGVLQPIIVRPIED----GKYEILAGHNRVNAAKLAGLTTIPAIIKENlTDEEAKLI 79

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939405845 10 VRMIPISQIEVINPRERNgRVFDeIVSNIKTIG-LKKPILVTPrataSGVEKYLLVCGEGRLKAFRSLGETTIPALVVSV 88
Cdd:cd16388    1 LKLVPIEQIRLHEEHEPN-RLEK-LVERIEAEGvLRNPPIVTP----LQDGRYLILDGAHRTTALKKLGCKRIPVQVVDE 74

                 ..
gi 1939405845 89 SD 90
Cdd:cd16388   75 ED 76

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1939405845 26 RNGRVFDEIVSNIKTIGLKKPILVTPRATasgvekylLVCGEGRLKAFRSLGETTIPALVVS 87
Cdd:cd16844    1 KNDAQIERVAASIREFGFRVPVLIDKDGE--------IVDGHLRLEAARRLGLETVPVIRVD 54