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 1417810556  20 KVADLRPDPDNPRVNSGAVAYVVESIRQFGFQVPIVIGTDNLIRAGHTRYRAAVQLGLTEVPCIDASHLTDEQQRAFAIA 99
Cdd:cd16402     1 KISELKPYENNPRNNDKAVEKVAESIKEFGFLVPIVVDKNNVIVAGHTRYKAAKRLGLEEVPCIVADDLTEEQIKAFRLA 80

                  ....*..
gi 1417810556 100 ENRTSDF 106
Cdd:cd16402    81 DNKTSEF 87

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417810556  20 KVADLRPDPDNPRVNSGAVAYVVESIRQFGFQVPIVIGTDNLIRAGHTRYRAAVQLGLTEVPCIDASHLTDEQQRAFAIA 99
Cdd:cd16402     1 KISELKPYENNPRNNDKAVEKVAESIKEFGFLVPIVVDKNNVIVAGHTRYKAAKRLGLEEVPCIVADDLTEEQIKAFRLA 80

                  ....*..
gi 1417810556 100 ENRTSDF 106
Cdd:cd16402    81 DNKTSEF 87

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 1417810556   17 RMVKVADLRPDPDNPRVNS-GAVAYVVESIRQFGFQVPI-VIGTDNLIR--AGHTRYRAAVQLGLTEVPCIdASHLTDEQ 92
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLTSeESLEELAESIKENGLLQPIiVRPNDGRYEiiDGERRLRAAKLLGLKEVPVI-VRDLDDEE 79

                           90
                   ....*....|
gi 1417810556   93 QRAFAIAENR 102
Cdd:smart00470  80 AIALSLEENI 89

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 1417810556  16 IRMVKVADLRPDPDNPR--VNSGAVAYVVESIRQFGFQVPIVI----GTDN--LIRAGHTRYRAAVQLGLTEVPCIdASH 87
Cdd:TIGR00180   5 LIEIDIDLLQPNPYQPRkdFSEESLAELIESIKEQGQLQPILVrkhpDQPGryEIIAGERRWRAAKLAGLKTIPAI-VRE 83

                          90
                  ....*....|....
gi 1417810556  88 LTDEQQRAFAIAEN 101
Cdd:TIGR00180  84 LDDEQMLADALIEN 97

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417810556  20 KVADLRPDPDNPRVNSGAVAYVVESIRQFGFQVPIVIGTDNLIRAGHTRYRAAVQLGLTEVPCIDASHLTDEQQRAFAIA 99
Cdd:cd16402     1 KISELKPYENNPRNNDKAVEKVAESIKEFGFLVPIVVDKNNVIVAGHTRYKAAKRLGLEEVPCIVADDLTEEQIKAFRLA 80

                  ....*..
gi 1417810556 100 ENRTSDF 106
Cdd:cd16402    81 DNKTSEF 87

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 1417810556  13 APSIRMVKVADLRPDPDNPR--VNSGAVAYVVESIRQFGFQVPIVI----GTDNLIRAGHTRYRAAVQLGLTEVPCIDAS 86
Cdd:COG1475     4 GEEIREIPIDKIVPSPYNPRrtFDEEALEELAASIREHGLLQPILVrplgDGRYEIIAGERRLRAAKLLGLETVPAIVRD 83

                          90
                  ....*....|....*
gi 1417810556  87 hLTDEQQRAFAIAEN 101
Cdd:COG1475    84 -LDDEEALELALIEN 97

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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1417810556  34 NSGAVAYVVESIRQFGFQVPIVIGTDNLIRAGHTRYRAAVQLGLTEVPCIDAS 86
Cdd:cd16844     2 NDAQIERVAASIREFGFRVPVLIDKDGEIVDGHLRLEAARRLGLETVPVIRVD 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 1417810556  16 IRMVKVADLRPDPDNPR--VNSGAVAYVVESIRQFGFQVPIVIGTDNLIR----AGHTRYRAAVQLGLTEVPCIDAsHLT 89
Cdd:cd16393     1 VQEIPIDKIRPNPYQPRkeFDEEALKELAESIKEHGLLQPIVVRKVGDGRyeiiAGERRWRAAKLAGLTEIPAIVR-DLD 79

                          90
                  ....*....|..
gi 1417810556  90 DEQQRAFAIAEN 101
Cdd:cd16393    80 DEEALELALIEN 91

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417810556  26 PDPDNPRVN--SGAVAY--VVESIRQFGFQVPIVI-GTDNLIRAGHTRYRAAVQLGLTEVPCIdASHLTDEQQRAFAIAE 100
Cdd:cd16401     1 PAPYNPRKDlkPGDKEYekLKESIEEFGLVDPLIVnKRTNVLIGGHQRLKVLKELGYTEVPVV-VVDLDEEKEKALNIAL 79

                  ....
gi 1417810556 101 NRTS 104
Cdd:cd16401    80 NKIS 83

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417810556  18 MVKVADLRPDPDNPR--VNSGAVAYVVESIRQFGFQVPIVI----GTDNLIRAGHTRYRAAVQLGLTEVPCIDAShLTDE 91
Cdd:cd16396     5 EIPVADIIPNPYQPRkeFDEEEIEELAESIKEHGLLQPIVVrktkDGGYEIVAGERRWRAAKLLGWEKIPAIIRD-LSDK 83

                          90
                  ....*....|
gi 1417810556  92 QQRAFAIAEN 101
Cdd:cd16396    84 EALEIALIEN 93

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
                  ....*....|....*....|....*....|....*....|....*.
gi 1417810556  42 VESIRQFGFQVPIVI----GTDNLIRAGHTRYRAAVQLGLTEVPCI 83
Cdd:cd16387     9 AESIREHGVLQPIIVrplpDGRYEIIAGERRWRAAKLAGLTTIPVV 54

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417810556  32 RVNSGAVAYVVESIRQFGFQVPIVIGTDNLIRAGHTRYRAAVQLGLTEVPCIDASHLTDEQQRAFAIAEN 101
Cdd:cd16410    11 RKDLGDIEALAESIKRHGLLNPIVVTPDNELIAGERRLEAAKLLGWETIEVRVMDIEDEKEKLELEIEEN 80

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417810556  18 MVKVADLRPDPDnprVNSGAVAYVVESIRQFG-FQVPIVIGTD-NLIRAGHTRYRAAVQLGLTEVPCI 83
Cdd:cd16400     1 LLPISDLRPHEE---VDPDRVEELIEKILEEGvWTKPIIVDKNtGIILDGHHRLEAAKRLGLKRVPCV 65