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Conserved domains on  [gi|490997742|ref|WP_004859468|]
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MULTISPECIES: ParB/RepB/Spo0J family partition protein [Raoultella]

Protein Classification

IbrB-like domain-containing protein( domain architecture ID 11611634)

IbrB-like domain-containing protein, a member of the ParB/Srx superfamily; similar to Escherichia coli IbrB which along with IbrA activates immunoglobulin-binding eib genes

CATH:  1.10.10.2830
Gene Ontology:  GO:0071453|GO:0003677
PubMed:  25358815

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 42-144 1.28e-49

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.


:

Pssm-ID: 319255 [Multi-domain]  Cd Length: 100  Bit Score: 156.58  E-value: 1.28e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742  42 PVDCVLWVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVLRQDEA-RYTIVDGFHRHELARNKvPLKKQLNGY 120
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDdKYVIVDGFHRYTLAKKK-PLIERLKGY 79

                         90       100
                 ....*....|....*....|....
gi 490997742 121 LPVTCLEnpsPGRDTLMAATIRHN 144
Cdd:cd16397   80 LPVVVLD---KDLEERMASTIRHN 100
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 42-144 1.28e-49

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.


Pssm-ID: 319255 [Multi-domain]  Cd Length: 100  Bit Score: 156.58  E-value: 1.28e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742  42 PVDCVLWVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVLRQDEA-RYTIVDGFHRHELARNKvPLKKQLNGY 120
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDdKYVIVDGFHRYTLAKKK-PLIERLKGY 79

                         90       100
                 ....*....|....*....|....
gi 490997742 121 LPVTCLEnpsPGRDTLMAATIRHN 144
Cdd:cd16397   80 LPVVVLD---KDLEERMASTIRHN 100
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 47-145 6.39e-14

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.


Pssm-ID: 426651 [Multi-domain]  Cd Length: 90  Bit Score: 64.61  E-value: 6.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742   47 LWVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELArnkvplKKQLNGYLPVTCL 126
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIVRKTPDGRYEIIAGERRLRAA------KLLGLKEVPVIVR 74

                          90
                  ....*....|....*....
gi 490997742  127 ENPspgRDTLMAATIRHNR 145
Cdd:pfam02195  75 EID---DEEAIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 48-145 3.71e-09

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.


Pssm-ID: 214678 [Multi-domain]  Cd Length: 89  Bit Score: 51.92  E-value: 3.71e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742    48 WVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVlRQDEARYTIVDGFHRHELArnkvplkkQLNG--YLPVTC 125
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIV-RPNDGRYEIIDGERRLRAA--------KLLGlkEVPVIV 72

                           90       100
                   ....*....|....*....|
gi 490997742   126 LENPspgRDTLMAATIRHNR 145
Cdd:smart00470  73 RDLD---DEEAIALSLEENI 89
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 52-202 1.08e-07

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


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 50.37  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742  52 ESVSPNDYNPNNLAPPEK-RLLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELArnkvplkkQLNGYLPVTCL-ENP 129
Cdd:COG1475   13 DKIVPSPYNPRRTFDEEAlEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAA--------KLLGLETVPAIvRDL 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490997742 130 SPgrDTLMAATIRHNRARGR-HQIPAMSAIVHELANLGWSDAKISQELGMDADEV---LRLKQIN-GLAELFGDRQFS 202
Cdd:COG1475   85 DD--EEALELALIENLQREDlNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVsnlLRLLKLPpEVQEALREGKLS 160
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 42-144 1.28e-49

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.


Pssm-ID: 319255 [Multi-domain]  Cd Length: 100  Bit Score: 156.58  E-value: 1.28e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742  42 PVDCVLWVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVLRQDEA-RYTIVDGFHRHELARNKvPLKKQLNGY 120
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDdKYVIVDGFHRYTLAKKK-PLIERLKGY 79

                         90       100
                 ....*....|....*....|....
gi 490997742 121 LPVTCLEnpsPGRDTLMAATIRHN 144
Cdd:cd16397   80 LPVVVLD---KDLEERMASTIRHN 100
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 47-145 6.39e-14

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.


Pssm-ID: 426651 [Multi-domain]  Cd Length: 90  Bit Score: 64.61  E-value: 6.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742   47 LWVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELArnkvplKKQLNGYLPVTCL 126
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIVRKTPDGRYEIIAGERRLRAA------KLLGLKEVPVIVR 74

                          90
                  ....*....|....*....
gi 490997742  127 ENPspgRDTLMAATIRHNR 145
Cdd:pfam02195  75 EID---DEEAIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 48-145 3.71e-09

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.


Pssm-ID: 214678 [Multi-domain]  Cd Length: 89  Bit Score: 51.92  E-value: 3.71e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742    48 WVKQESVSPNDYNPNNLAPPEKRLLLTSLETDGFTQPIVVlRQDEARYTIVDGFHRHELArnkvplkkQLNG--YLPVTC 125
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIV-RPNDGRYEIIDGERRLRAA--------KLLGlkEVPVIV 72

                           90       100
                   ....*....|....*....|
gi 490997742   126 LENPspgRDTLMAATIRHNR 145
Cdd:smart00470  73 RDLD---DEEAIALSLEENI 89
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 52-202 1.08e-07

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


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 50.37  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490997742  52 ESVSPNDYNPNNLAPPEK-RLLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELArnkvplkkQLNGYLPVTCL-ENP 129
Cdd:COG1475   13 DKIVPSPYNPRRTFDEEAlEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAA--------KLLGLETVPAIvRDL 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490997742 130 SPgrDTLMAATIRHNRARGR-HQIPAMSAIVHELANLGWSDAKISQELGMDADEV---LRLKQIN-GLAELFGDRQFS 202
Cdd:COG1475   85 DD--EEALELALIENLQREDlNPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVsnlLRLLKLPpEVQEALREGKLS 160
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 66-108 1.52e-04

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.


Pssm-ID: 319246 [Multi-domain]  Cd Length: 54  Bit Score: 38.34  E-value: 1.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 490997742  66 PPEKRLLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELAR 108
Cdd:cd16387    2 EEELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERRWRAAK 44
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 71-108 3.82e-03

ParB N-terminal-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.


Pssm-ID: 319266 [Multi-domain]  Cd Length: 74  Bit Score: 34.97  E-value: 3.82e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 490997742  71 LLLTSLETDGFTQPIVVLRQDEARYTIVDGFHRHELAR 108
Cdd:cd16409    8 ALAQSIAEHGLLTPITVRQDPGGRYTLIAGAHRLAAAK 45
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 53-103 7.96e-03

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.


Pssm-ID: 319254 [Multi-domain]  Cd Length: 95  Bit Score: 34.51  E-value: 7.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 490997742  53 SVSPNDYNPNNLAPPEKRL-LLTSLETDGFTQPIVVLRQDEARYTIVDGFHR 103
Cdd:cd16396   10 DIIPNPYQPRKEFDEEEIEeLAESIKEHGLLQPIVVRKTKDGGYEIVAGERR 61
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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