Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504108157   9 MDVKITILQVEIARLRPNPWNTNSV-GAQNFEKLKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVI 87
Cdd:COG1475    1 MKEGEEIREIPIDKIVPSPYNPRRTfDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLGLETVPAI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 504108157  88 sVGKISDLVAKQMSLVDNERYGEDDQVALQRLIEEIQSELDYQLSEIA 135
Cdd:COG1475   81 -VRDLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIA 127

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 504108157  36 QNFEKLKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVI 87
Cdd:cd16387    3 EELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERRWRAAKLAGLTTIPVV 54

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504108157   9 MDVKITILQVEIARLRPNPWNTNSV-GAQNFEKLKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVI 87
Cdd:COG1475    1 MKEGEEIREIPIDKIVPSPYNPRRTfDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLGLETVPAI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 504108157  88 sVGKISDLVAKQMSLVDNERYGEDDQVALQRLIEEIQSELDYQLSEIA 135
Cdd:COG1475   81 -VRDLDDEEALELALIENLQREDLNPLEEARAYQRLLEEFGLTQEEIA 127

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 504108157  36 QNFEKLKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVI 87
Cdd:cd16387    3 EELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERRWRAAKLAGLTTIPVV 54

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 504108157  15 ILQVEIARLRPNPWNTNsvgaQNFEK-----LKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVIsV 89
Cdd:cd16393    1 VQEIPIDKIRPNPYQPR----KEFDEealkeLAESIKEHGLLQPIVVRKVGDGRYEIIAGERRWRAAKLAGLTEIPAI-V 75

                         90
                 ....*....|....*.
gi 504108157  90 GKISDLVAKQMSLVDN 105
Cdd:cd16393   76 RDLDDEEALELALIEN 91

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504108157   15 ILQVEIARLRPNPW-NTNSVGAQNFEKLKGSIEKLGFFKPILARELDG--GQFEILGGEHRWRAAMEQGISTVPVIsVGK 91
Cdd:TIGR00180   5 LIEIDIDLLQPNPYqPRKDFSEESLAELIESIKEQGQLQPILVRKHPDqpGRYEIIAGERRWRAAKLAGLKTIPAI-VRE 83

                          90
                  ....*....|....
gi 504108157   92 ISDLVAKQMSLVDN 105
Cdd:TIGR00180  84 LDDEQMLADALIEN 97

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 504108157  36 QNFEKLKGSIEKLGFFKPILARELDGGQFEILGGEHRWRAAMEQGISTVPVISVGKISDLVAKQM 100
Cdd:cd16408   15 ERLEDMVESIKENGVLQPIIVRPIEDGKYEILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKLI 79

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504108157  18 VEIARLRPNPWNTNSVGAQNFEKLKGSIEKLGFFKPILA-RELDGGQFEILGGEHRWR 74
Cdd:cd16397    8 VPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVyYDEEDDKYVIVDGFHRYT 65

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 504108157  39 EKLKGSIEKLGFFKPILareLDGgQFEILGGEHRWRAAMEQGISTVPVISVGKISDLVAKQMSLVDN 105
Cdd:cd16402   20 EKVAESIKEFGFLVPIV---VDK-NNVIVAGHTRYKAAKRLGLEEVPCIVADDLTEEQIKAFRLADN 82

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504108157  18 VEIARLRPnpwnTNSVGAQNFEKLKGSIEKLGFF-KPILareLDGGQFEILGGEHRWRAAMEQGISTVPVI 87
Cdd:cd16400    2 LPISDLRP----HEEVDPDRVEELIEKILEEGVWtKPII---VDKNTGIILDGHHRLEAAKRLGLKRVPCV 65

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
                 ....*....|....*....|....*....|....*....|....*.
gi 504108157  38 FEKLKGSIEKLGFFKPILAREL--DGGQFEILGGEHRWRAAMEQGI 81
Cdd:cd16405   24 FEELKESIRESGQQVPILVRPHpeEGGRYEIVYGHRRLRACRELGL 69