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Conserved domains on  [gi|494404862|ref|WP_007213864|]
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MULTISPECIES: ParB/RepB/Spo0J family partition protein [Bacteroides]

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 ...
 7-107 9.99e-59

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: 178.53  E-value: 9.99e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862   7 PVYAVKAVPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCYYDNETDRYILVDGYHRYSVLRSSKRIyQRENGL 86
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDKYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                         90       100
                 ....*....|....*....|.
gi 494404862  87 LPVVVIDKELSNRMASTIRHN 107
Cdd:cd16397   80 LPVVVLDKDLEERMASTIRHN 100
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 7-107 9.99e-59

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: 178.53  E-value: 9.99e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862   7 PVYAVKAVPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCYYDNETDRYILVDGYHRYSVLRSSKRIyQRENGL 86
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDKYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                         90       100
                 ....*....|....*....|.
gi 494404862  87 LPVVVIDKELSNRMASTIRHN 107
Cdd:cd16397   80 LPVVVLDKDLEERMASTIRHN 100
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 10-153 7.44e-11

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: 58.85  E-value: 7.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  10 AVKAVPLEKIVANDYNPNIVAPPEmKLLEL--SIWEDGFTMPCVCyYDNETDRYILVDGYHRysvLRSSKRIYQREnglL 87
Cdd:COG1475    6 EIREIPIDKIVPSPYNPRRTFDEE-ALEELaaSIREHGLLQPILV-RPLGDGRYEIIAGERR---LRAAKLLGLET---V 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  88 PVVVIDKELSNRMASTIRHNRARGSHN-IELMCHIVAELDKAGMSDQWIMKNIGMDRDE---LLRLKQIS 153
Cdd:COG1475   78 PAIVRDLDDEEALELALIENLQREDLNpLEEARAYQRLLEEFGLTQEEIAERLGKSRSEvsnLLRLLKLP 147
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 14-108 3.21e-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: 48.81  E-value: 3.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862   14 VPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCyYDNETDRYILVDGYHRysvLRSSKRIYQREnglLPVVVID 93
Cdd:pfam02195   3 VPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIV-RKTPDGRYEIIAGERR---LRAAKLLGLKE---VPVIVRE 75

                          90
                  ....*....|....*
gi 494404862   94 KELSNRMASTIRHNR 108
Cdd:pfam02195  76 IDDEEAIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 14-108 1.44e-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: 44.22  E-value: 1.44e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862    14 VPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCyyDNETDRYILVDGYHRysvLRSSKRIYQREnglLPVVVID 93
Cdd:smart00470   3 VPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIV--RPNDGRYEIIDGERR---LRAAKLLGLKE---VPVIVRD 74

                           90
                   ....*....|....*
gi 494404862    94 KELSNRMASTIRHNR 108
Cdd:smart00470  75 LDDEEAIALSLEENI 89
 
Name Accession Description Interval E-value
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 7-107 9.99e-59

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: 178.53  E-value: 9.99e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862   7 PVYAVKAVPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCYYDNETDRYILVDGYHRYSVLRSSKRIyQRENGL 86
Cdd:cd16397    1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDKYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                         90       100
                 ....*....|....*....|.
gi 494404862  87 LPVVVIDKELSNRMASTIRHN 107
Cdd:cd16397   80 LPVVVLDKDLEERMASTIRHN 100
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 10-153 7.44e-11

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: 58.85  E-value: 7.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  10 AVKAVPLEKIVANDYNPNIVAPPEmKLLEL--SIWEDGFTMPCVCyYDNETDRYILVDGYHRysvLRSSKRIYQREnglL 87
Cdd:COG1475    6 EIREIPIDKIVPSPYNPRRTFDEE-ALEELaaSIREHGLLQPILV-RPLGDGRYEIIAGERR---LRAAKLLGLET---V 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  88 PVVVIDKELSNRMASTIRHNRARGSHN-IELMCHIVAELDKAGMSDQWIMKNIGMDRDE---LLRLKQIS 153
Cdd:COG1475   78 PAIVRDLDDEEALELALIENLQREDLNpLEEARAYQRLLEEFGLTQEEIAERLGKSRSEvsnLLRLLKLP 147
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 14-108 3.21e-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: 48.81  E-value: 3.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862   14 VPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCyYDNETDRYILVDGYHRysvLRSSKRIYQREnglLPVVVID 93
Cdd:pfam02195   3 VPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIV-RKTPDGRYEIIAGERR---LRAAKLLGLKE---VPVIVRE 75

                          90
                  ....*....|....*
gi 494404862   94 KELSNRMASTIRHNR 108
Cdd:pfam02195  76 IDDEEAIALSLIENI 90
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 14-108 1.44e-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: 44.22  E-value: 1.44e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862    14 VPLEKIVANDYNPNIVAPPEMKLLELSIWEDGFTMPCVCyyDNETDRYILVDGYHRysvLRSSKRIYQREnglLPVVVID 93
Cdd:smart00470   3 VPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIV--RPNDGRYEIIDGERR---LRAAKLLGLKE---VPVIVRD 74

                           90
                   ....*....|....*
gi 494404862    94 KELSNRMASTIRHNR 108
Cdd:smart00470  75 LDDEEAIALSLEENI 89
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 21-111 2.11e-04

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.


Pssm-ID: 319258 [Multi-domain]  Cd Length: 85  Bit Score: 38.36  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  21 ANDYNPNIVAPP---EMKLLELSIWEDGFTMPCVCyydNETDRyILVDGYHRYSVLRsskriyqrENGL--LPVVVIDKE 95
Cdd:cd16401    1 PAPYNPRKDLKPgdkEYEKLKESIEEFGLVDPLIV---NKRTN-VLIGGHQRLKVLK--------ELGYteVPVVVVDLD 68

                         90
                 ....*....|....*.
gi 494404862  96 LSNRMASTIRHNRARG 111
Cdd:cd16401   69 EEKEKALNIALNKISG 84
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 11-104 3.09e-04

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.


Pssm-ID: 319251 [Multi-domain]  Cd Length: 97  Bit Score: 38.23  E-value: 3.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494404862  11 VKAVPLEKIVANDYNPNIVAPPEmKLLEL--SIWEDGFTMPCVCYYdNETDRYILVDGYHRYsvlRSSKriyqrENGLLP 88
Cdd:cd16393    1 VQEIPIDKIRPNPYQPRKEFDEE-ALKELaeSIKEHGLLQPIVVRK-VGDGRYEIIAGERRW---RAAK-----LAGLTE 70

                         90
                 ....*....|....*.
gi 494404862  89 VVVIDKELSNRMASTI 104
Cdd:cd16393   71 IPAIVRDLDDEEALEL 86
Glyco_hydro_57 pfam03065
Glycosyl hydrolase family 57; This family includes alpha-amylase (EC:3.2.1.1), ...
 60-98 2.01e-03

Glycosyl hydrolase family 57; This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes.


Pssm-ID: 397267 [Multi-domain]  Cd Length: 293  Bit Score: 37.73  E-value: 2.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 494404862   60 RYILVDGYHRYSVLRSSKRIYQRENGLLPVVVIDKELSN 98
Cdd:pfam03065 167 EYVFTDGYAFILAGLSPYRPYYIENGGLAVFFRNYELSD 205
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 31-92 3.64e-03

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: 34.10  E-value: 3.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494404862  31 PPEMKLLELSIWEDGFTMPCVCYYdNETDRYILVDGYHRYsvlRSSKRIyqrenGLLPVVVI 92
Cdd:cd16387    2 EEELEELAESIREHGVLQPIIVRP-LPDGRYEIIAGERRW---RAAKLA-----GLTTIPVV 54
 
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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