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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560  16 IDRLTPYERNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNGVIIAGHGRRLAALKLGLKKVPVLVRDDLTDDQVIALRLA 95
Cdd:cd16403    2 IDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRIA 81

                 ....*
gi 380681560  96 DNKVS 100
Cdd:cd16403   82 DNRLA 86

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560  16 IDRLTPYERNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNGVIIAGHGRRLAALKLGLKKVPVLVRDDLTDDQVIALRLA 95
Cdd:cd16403    2 IDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRIA 81

                 ....*
gi 380681560  96 DNKVS 100
Cdd:cd16403   82 DNRLA 86

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 380681560   15 EIDRLTPYERNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNG----VIIAGHGRRLAALKLGLKKVPVLVRDDlTDDQVI 90
Cdd:pfam02195   4 PISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIVRKTPdgryEIIAGERRLRAAKLLGLKEVPVIVREI-DDEEAI 82

                  ....*..
gi 380681560   91 ALRLADN 97
Cdd:pfam02195  83 ALSLIEN 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 380681560   15 EIDRLTPYE-RNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNGV------IIAGHGRRLAALKLGLKKVPVLVRdDLTDD 87
Cdd:TIGR00180   9 DIDLLQPNPyQPRKDFSEESLAELIESIKEQGQLQPILVRKHPDqpgryeIIAGERRWRAAKLAGLKTIPAIVR-ELDDE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560   88 QVIALRLADnkvsstdydtNLLQLDLSDLHLADFDLSAIgfneKELSFLIEDLAEMNG----------------EALVED 151
Cdd:TIGR00180  88 QMLADALIE----------NIQREDLSPIEEAQAYKRLL----EKFSMTQEDLAKKIGksrahitnllrllklpSEIQSA 153

                         170       180
                  ....*....|....*....|...
gi 380681560  152 ITEAIETQKAEHEKAFKATDERP 174
Cdd:TIGR00180 154 IPEASGLLSSGHARLLLALKKKP 176

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560  16 IDRLTPYERNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNGVIIAGHGRRLAALKLGLKKVPVLVRDDLTDDQVIALRLA 95
Cdd:cd16403    2 IDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRIA 81

                 ....*
gi 380681560  96 DNKVS 100
Cdd:cd16403   82 DNRLA 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 380681560    15 EIDRLTPYERNAKKHSDEQVETLAKAIQSLGWTAPIVVDKNG---VIIAGHGRRLAALKLGLKKVPVLVRdDLTDDQVIA 91
Cdd:smart00470   4 PIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDgryEIIDGERRLRAAKLLGLKEVPVIVR-DLDDEEAIA 82

                   ....*.
gi 380681560    92 LRLADN 97
Cdd:smart00470  83 LSLEEN 88

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 380681560  12 QIWEIDRLTPYERNAKKH-SDEQVETLAKAIQSLGWTAPIVVDKNG----VIIAGHGRRLAALKLGLKKVPVLVRdDLTD 86
Cdd:COG1475    8 REIPIDKIVPSPYNPRRTfDEEALEELAASIREHGLLQPILVRPLGdgryEIIAGERRLRAAKLLGLETVPAIVR-DLDD 86

                         90
                 ....*....|.
gi 380681560  87 DQVIALRLADN 97
Cdd:COG1475   87 EEALELALIEN 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. 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 380681560  24 RNAKKHSDEQVETLAKAIQSLGWTAPIVVDK-NGVIIAGHGRRLAALKLGLKKVPVlVRDDLTDDQVIALRLADNKVS 100
Cdd:cd16401    7 RKDLKPGDKEYEKLKESIEEFGLVDPLIVNKrTNVLIGGHQRLKVLKELGYTEVPV-VVVDLDEEKEKALNIALNKIS 83

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560  16 IDRLTPYERNA-KKHSDEQVETLAKAIQSLGWTAPIVV--DKNG--VIIAGHGRRLAALKLGLKKVPVLVRdDLTDDQ-V 89
Cdd:cd16407    1 LSELHPFPNHPfKVRDDEEMEELVESIKENGVLTPIIVrpREDGgyEIISGHRRKRACELAGLETIPVIVR-EMDDDEaV 79

                 ...
gi 380681560  90 IAL 92
Cdd:cd16407   80 IAM 82

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 380681560  15 EIDRLTPYERNAKKHSDEQ-VETLAKAIQSLGWTAPIVVDKNGV----IIAGHGRRLAALKLGLKKVPVLVRdDLTDDQV 89
Cdd:cd16393    5 PIDKIRPNPYQPRKEFDEEaLKELAESIKEHGLLQPIVVRKVGDgryeIIAGERRWRAAKLAGLTEIPAIVR-DLDDEEA 83

                 ....*...
gi 380681560  90 IALRLADN 97
Cdd:cd16393   84 LELALIEN 91

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 380681560   6 EHKLAPQIWEIDRLTPYERnaKKHSDEQVETLAKAIQSLGWTAPIVVDKNGV----IIAGHGRRLAALKLGLKKVPVLVR 81
Cdd:cd16396    1 GEVLEIPVADIIPNPYQPR--KEFDEEEIEELAESIKEHGLLQPIVVRKTKDggyeIVAGERRWRAAKLLGWEKIPAIIR 78

                         90
                 ....*....|....*.
gi 380681560  82 dDLTDDQVIALRLADN 97
Cdd:cd16396   79 -DLSDKEALEIALIEN 93

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 380681560  19 LTPYERNA-KKHSDEQVETLAKAIQSLGWTAPIVVDKNGV----IIAGHGRRLAALKLGLKKVPVLVRDDLTDDQ 88
Cdd:cd16408    1 LVPFSDHPfKLYTGERLEDMVESIKENGVLQPIIVRPIEDgkyeILAGHNRVNAAKLAGLTTIPAIIKENLTDEE 75

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380681560  16 IDRLTPYERNAKKHSDEQ-VETLAKAIQSLGWTAPIVV----DKNG--VIIAGHGRRLAALKLGLKKVPVLVRDDLTD-D 87
Cdd:cd16398    1 LDKIDEDPDNPRTEFDEEkIEELAASIKERGVKSPISVrphpEKPGkyIINHGARRYRASKWAGLKTIPAFIDNDHDDfD 80

                 ...
gi 380681560  88 QVI 90
Cdd:cd16398   81 QVI 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 380681560  31 DEQVETLAKAIQSLGWTAPIVV----DKNGV--IIAGHgRRLAALKLGLKKVPVLVRdDLTDDQVIAL 92
Cdd:cd16405   21 DDEFEELKESIRESGQQVPILVrphpEEGGRyeIVYGH-RRLRACRELGLPVRAIVR-ELSDEELVVA 86