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Conserved domains on  [gi|496088835|ref|WP_008813342|]
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MULTISPECIES: ParB/RepB/Spo0J family partition protein [Hafnia]

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 ...
 43-147 2.14e-48

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: 153.50  E-value: 2.14e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835  43 PIDCVLWKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVTAQIKDDDKdYVIVDGFHRRELAADrPKLRKRVRG 122
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDK-YVIVDGFHRYTLAKK-KPLIERLKG 78

                         90       100
                 ....*....|....*....|....*.
gi 496088835 123 YLPVVILN-DLENekshRIAATIRHN 147
Cdd:cd16397   79 YLPVVVLDkDLEE----RMASTIRHN 100
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 43-147 2.14e-48

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: 153.50  E-value: 2.14e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835  43 PIDCVLWKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVTAQIKDDDKdYVIVDGFHRRELAADrPKLRKRVRG 122
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDK-YVIVDGFHRYTLAKK-KPLIERLKG 78

                         90       100
                 ....*....|....*....|....*.
gi 496088835 123 YLPVVILN-DLENekshRIAATIRHN 147
Cdd:cd16397   79 YLPVVVLDkDLEE----RMASTIRHN 100
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 48-148 1.51e-08

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: 50.36  E-value: 1.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835   48 LWKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVtaQIKDDDKDYVIVDGFHRRElAADRPKLRKrvrgyLPVV 127
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPII--VRKTPDGRYEIIAGERRLR-AAKLLGLKE-----VPVI 72

                          90       100
                  ....*....|....*....|.
gi 496088835  128 ILNDLENEkshRIAATIRHNR 148
Cdd:pfam02195  73 VREIDDEE---AIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 49-148 4.01e-06

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: 43.83  E-value: 4.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835    49 WKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVTAQIKDDdkdYVIVDGFHRRElAADRPKLRKrvrgyLPVVI 128
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGR---YEIIDGERRLR-AAKLLGLKE-----VPVIV 72

                           90       100
                   ....*....|....*....|
gi 496088835   129 LNDLENEkshRIAATIRHNR 148
Cdd:smart00470  73 RDLDDEE---AIALSLEENI 89
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 51-206 1.17e-05

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: 44.59  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835  51 SIEDVVANDYNPNNVAPPEK-RLLYTSLLRDGYTQPIVTAqiKDDDKDYVIVDGfHRRELAADRPKLRKrvrgyLPVVIL 129
Cdd:COG1475   11 PIDKIVPSPYNPRRTFDEEAlEELAASIREHGLLQPILVR--PLGDGRYEIIAG-ERRLRAAKLLGLET-----VPAIVR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835 130 nDLENEKSHRIAATIrhNRARGkhQISIMsDIVRELYRL----GWSDEKISEELGMDADEV---LRLKQIS-GLMELFQD 201
Cdd:COG1475   83 -DLDDEEALELALIE--NLQRE--DLNPL-EEARAYQRLleefGLTQEEIAERLGKSRSEVsnlLRLLKLPpEVQEALRE 156


                 ....*
gi 496088835 202 REFSE 206
Cdd:COG1475  157 GKLSL 161
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 43-147 2.14e-48

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: 153.50  E-value: 2.14e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835  43 PIDCVLWKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVTAQIKDDDKdYVIVDGFHRRELAADrPKLRKRVRG 122
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDK-YVIVDGFHRYTLAKK-KPLIERLKG 78

                         90       100
                 ....*....|....*....|....*.
gi 496088835 123 YLPVVILN-DLENekshRIAATIRHN 147
Cdd:cd16397   79 YLPVVVLDkDLEE----RMASTIRHN 100
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 48-148 1.51e-08

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: 50.36  E-value: 1.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835   48 LWKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVtaQIKDDDKDYVIVDGFHRRElAADRPKLRKrvrgyLPVV 127
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPII--VRKTPDGRYEIIAGERRLR-AAKLLGLKE-----VPVI 72

                          90       100
                  ....*....|....*....|.
gi 496088835  128 ILNDLENEkshRIAATIRHNR 148
Cdd:pfam02195  73 VREIDDEE---AIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 49-148 4.01e-06

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: 43.83  E-value: 4.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835    49 WKSIEDVVANDYNPNNVAPPEKRLLYTSLLRDGYTQPIVTAQIKDDdkdYVIVDGFHRRElAADRPKLRKrvrgyLPVVI 128
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGR---YEIIDGERRLR-AAKLLGLKE-----VPVIV 72

                           90       100
                   ....*....|....*....|
gi 496088835   129 LNDLENEkshRIAATIRHNR 148
Cdd:smart00470  73 RDLDDEE---AIALSLEENI 89
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 51-206 1.17e-05

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: 44.59  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835  51 SIEDVVANDYNPNNVAPPEK-RLLYTSLLRDGYTQPIVTAqiKDDDKDYVIVDGfHRRELAADRPKLRKrvrgyLPVVIL 129
Cdd:COG1475   11 PIDKIVPSPYNPRRTFDEEAlEELAASIREHGLLQPILVR--PLGDGRYEIIAG-ERRLRAAKLLGLET-----VPAIVR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496088835 130 nDLENEKSHRIAATIrhNRARGkhQISIMsDIVRELYRL----GWSDEKISEELGMDADEV---LRLKQIS-GLMELFQD 201
Cdd:COG1475   83 -DLDDEEALELALIE--NLQRE--DLNPL-EEARAYQRLleefGLTQEEIAERLGKSRSEVsnlLRLLKLPpEVQEALRE 156


                 ....*
gi 496088835 202 REFSE 206
Cdd:COG1475  157 GKLSL 161
 
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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