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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 100 IDPATVRPSRWANRHPASFESAEFAGLKADIElAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwlDE 179
Cdd:cd16405     1 LDPDLIDPSFIADRLEDDFDDDEFEELKESIR-ESGQQVPILVRPHPEEGGRYEIVYGHRRLRACRELGLPVRAIV--RE 77

                          90
                  ....*....|....
gi 1372068509 180 LGDAELFAAMDREN 193
Cdd:cd16405    78 LSDEELVVAQGQEN 91

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 100 IDPATVRPSRWANRHPASFESAEFAGLKADIElAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwlDE 179
Cdd:cd16405     1 LDPDLIDPSFIADRLEDDFDDDEFEELKESIR-ESGQQVPILVRPHPEEGGRYEIVYGHRRLRACRELGLPVRAIV--RE 77

                          90
                  ....*....|....
gi 1372068509 180 LGDAELFAAMDREN 193
Cdd:cd16405    78 LSDEELVVAQGQEN 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 1372068509  98 RKIDPATVRPSRWANRHpaSFESAEFAGLKADIeLAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwL 177
Cdd:TIGR00180   6 IEIDIDLLQPNPYQPRK--DFSEESLAELIESI-KEQGQLQPILVRKHPDQPGRYEIIAGERRWRAAKLAGLKTIPAI-V 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 178 DELGDAELFAAMDRENRERADLSPYEQGVMYQRALEEqLFPTQRQLAEKLGVSHTWIRKALMVAQLPSAVLECFRSPLEV 257
Cdd:TIGR00180  82 RELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEK-FSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGL 160

                         170       180
                  ....*....|....*....|....*.
gi 1372068509 258 -QHRHAEQLNA--ALDKDRRSVLKRA 280
Cdd:TIGR00180 161 lSSGHARLLLAlkKKPKLQELLASII 186

plasmid partitioning protein RepB; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 100 IDPATVRPSRWANRHPASFESAeFAGLKADIELAGGNVqPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwlDE 179
Cdd:PRK13866   68 LDPSMIDGSPIADRLPADVDPK-FEQLEASISQEGQQV-PILVRPHPEAAGRYQIVYGRRRLRAAVNLRREVSAIV--RN 143

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1372068509 180 LGDAELFAAMDRENRERADLSPYEQGVMYQRaLEEQLF 217
Cdd:PRK13866  144 LTDRELVVAQGRENLDRADLSFIEKALFALR-LEDAGF 180

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 1372068509  98 RKIDPATVRPSRWANRhpaSFESAEFAGLKADIElAGGNVQPILVRPLvdEPGQYELVFGHRRHRACLELGIPVLAAIwL 177
Cdd:pfam02195   1 EEVPISKLRPNPDQPR---KDSEESLEELAASIK-KRGLLQPIIVRKT--PDGRYEIIAGERRLRAAKLLGLKEVPVI-V 73

                          90
                  ....*....|....*..
gi 1372068509 178 DELGDAELFAAMDRENR 194
Cdd:pfam02195  74 REIDDEEAIALSLIENI 90

ParB/RepB/Spo0J family plasmid partition protein;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 179 ELGDAELfAAMDRENRERADLSPYEQGVMYQRALEEQLFPTQRQLAEKLGVSHTWIRKALMVAQLPSAVLECFRSPLEVQ 258
Cdd:PRK13698  139 ELDDEQM-AALSRLGNDYRPTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELS 217

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1372068509 259 HRHAEQLNAALDKDRRSVLKRAEKVRGMKLA 289
Cdd:PRK13698  218 ARSGEALQKAFTDKEELLKQQTSNLHEQKKA 248

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 100 IDPATVRPSRWANRHPASFESAEFAGLKADIElAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwlDE 179
Cdd:cd16405     1 LDPDLIDPSFIADRLEDDFDDDEFEELKESIR-ESGQQVPILVRPHPEEGGRYEIVYGHRRLRACRELGLPVRAIV--RE 77

                          90
                  ....*....|....
gi 1372068509 180 LGDAELFAAMDREN 193
Cdd:cd16405    78 LSDEELVVAQGQEN 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 1372068509  98 RKIDPATVRPSRWANRHpaSFESAEFAGLKADIeLAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwL 177
Cdd:TIGR00180   6 IEIDIDLLQPNPYQPRK--DFSEESLAELIESI-KEQGQLQPILVRKHPDQPGRYEIIAGERRWRAAKLAGLKTIPAI-V 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 178 DELGDAELFAAMDRENRERADLSPYEQGVMYQRALEEqLFPTQRQLAEKLGVSHTWIRKALMVAQLPSAVLECFRSPLEV 257
Cdd:TIGR00180  82 RELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEK-FSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGL 160

                         170       180
                  ....*....|....*....|....*.
gi 1372068509 258 -QHRHAEQLNA--ALDKDRRSVLKRA 280
Cdd:TIGR00180 161 lSSGHARLLLAlkKKPKLQELLASII 186

plasmid partitioning protein RepB; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372068509 100 IDPATVRPSRWANRHPASFESAeFAGLKADIELAGGNVqPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwlDE 179
Cdd:PRK13866   68 LDPSMIDGSPIADRLPADVDPK-FEQLEASISQEGQQV-PILVRPHPEAAGRYQIVYGRRRLRAAVNLRREVSAIV--RN 143

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1372068509 180 LGDAELFAAMDRENRERADLSPYEQGVMYQRaLEEQLF 217
Cdd:PRK13866  144 LTDRELVVAQGRENLDRADLSFIEKALFALR-LEDAGF 180

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 1372068509 118 FESAEFAGLKADIElAGGNVQPILVRPlVDEPGQYELVFGHRRHRACLELG-----IPVLaaiwLDELGDAELFAAMDRE 192
Cdd:TIGR03734  12 FDPAEMAELVESIR-AKGVLQPILVRP-VPGSDLYEVVAGERRYRAALEVFgedydIPAL----IKVLTDEEAEAAALIE 85

                          90       100
                  ....*....|....*....|
gi 1372068509 193 NRERADLSPYEQGVMYQRAL 212
Cdd:TIGR03734  86 NVQRADMSPAEEAEAAARLL 105

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 1372068509 114 HPasF---ESAEFAGLKADIElAGGNVQPILVRPlvDEPGQYELVFGHRRHRACLELGIPVLAAI 175
Cdd:cd16407    10 HP--FkvrDDEEMEELVESIK-ENGVLTPIIVRP--REDGGYEIISGHRRKRACELAGLETIPVI 69

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 1372068509 121 AEFAGLKADIElAGGNVQPILVRPLVDepGQYELVFGHRRHRACLELG---IPVL 172
Cdd:cd16387     3 EELEELAESIR-EHGVLQPIIVRPLPD--GRYEIIAGERRWRAAKLAGlttIPVV 54

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1372068509 126 LKADIeLAGGNVQPILVRPLVDEPGQYELVFGHRRHRACLELGIPVLAAIwLDELGDaELFAAMdrENRERADL 199
Cdd:cd16398    23 LAASI-KERGVKSPISVRPHPEKPGKYIINHGARRYRASKWAGLKTIPAF-IDNDHD-DFDQVI--ENIQREDL 91

Centromere-binding protein HTH domain; This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1372068509 199 LSPYEQGVMYQRALEEQLFPTQRQLAEKLGVSHTWIRKALMVAQLPSAVLECFRSPLEVQHRHAEQLNAALD 270
Cdd:pfam18090   1 TSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFT 72

TyrR family helix-turn-helix domain; This model describes the C-terminal DNA-binding helix-turn-helix domain of several regulators of aromatic amino acid metabolism. Examples include TyrR in Escherichia coli and PhhR in Pseudomonas putida. Most members of this family have a sigma-54 interaction domain. [Regulatory functions, DNA interactions]

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1372068509 208 YQRALEEQL---FPTQRQLAEKLGVSHTWIRKAL 238
Cdd:TIGR04381   9 FEASLLRRLyasYPSTRQLAKRLGVSHTAIANKL 42

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1372068509 135 GNVQPILVrplvDEpgQYELVFGHRRHRACLELG---IPVLAAIWLDE 179
Cdd:cd16402    30 GFLVPIVV----DK--NNVIVAGHTRYKAAKRLGleeVPCIVADDLTE 71