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Conserved domains on  [gi|1148323821|gb|AQR76899|]
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hypothetical protein BXP28_05505 [Paenibacillus larvae subsp. larvae]

Protein Classification

ParB N-terminal domain-containing protein; ParB/RepB/Spo0J family partition protein( domain architecture ID 11611584)

ParB N-terminal domain-containing protein; ParB/RepB/Spo0J family partition protein which may be involved in segregation and competition between plasmids and chromosomes such as the ParB/SpoJ-type DNA-binding component of the prokaryotic parABS partitioning system

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SbnI_like_N cd16388
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ...
 8-83 6.17e-33

N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression.


:

Pssm-ID: 319247 [Multi-domain]  Cd Length: 77  Bit Score: 114.91  E-value: 6.17e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1148323821   8 LELVDIEFIDVHEKCEPKRLTKTVQTIQDDGFIKNSVLAIKI-DNRYLIIDGTHRTSALKTLGCRRIPIQVVDPKEL 83
Cdd:cd16388     1 LKLVPIEQIRLHEEHEPNRLEKLVERIEAEGVLRNPPIVTPLqDGRYLILDGAHRTTALKKLGCKRIPVQVVDEEDP 77
 
Name Accession Description Interval E-value
SbnI_like_N cd16388
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ...
 8-83 6.17e-33

N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression.


Pssm-ID: 319247 [Multi-domain]  Cd Length: 77  Bit Score: 114.91  E-value: 6.17e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1148323821   8 LELVDIEFIDVHEKCEPKRLTKTVQTIQDDGFIKNSVLAIKI-DNRYLIIDGTHRTSALKTLGCRRIPIQVVDPKEL 83
Cdd:cd16388     1 LKLVPIEQIRLHEEHEPNRLEKLVERIEAEGVLRNPPIVTPLqDGRYLILDGAHRTTALKKLGCKRIPVQVVDEEDP 77
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 9-89 2.64e-08

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: 50.00  E-value: 2.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148323821    9 ELVDIEFIDVHE----KCEPKRLTKTVQTIQDDGFIKNsVLAIKIDNRYLIIDGTHRTSALKTLGCRRIPIQVVDPKELK 84
Cdd:smart00470   1 VEVPIEKLRPNPdqprLTSEESLEELAESIKENGLLQP-IIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79


                   ....*
gi 1148323821   85 IEYWS 89
Cdd:smart00470  80 AIALS 84
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 31-79 5.29e-05

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: 41.11  E-value: 5.29e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1148323821  31 VQTIQDDGFIKNsVLAIKI-DNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:pfam02195  27 AASIKKRGLLQP-IIVRKTpDGRYEIIAGERRLRAAKLLGLKEVPVIVRE 75
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 6-79 9.78e-04

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: 39.59  E-value: 9.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1148323821   6 SNLELVDIEFIDVHEK-----CEPKRLTKTVQTIQDDGFIKNSVLAIKIDNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:COG1475     5 EEIREIPIDKIVPSPYnprrtFDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLGLETVPAIVRD 83
 
Name Accession Description Interval E-value
SbnI_like_N cd16388
N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin ...
 8-83 6.17e-33

N-terminal domain of transcriptional regulators similar to SbnI; Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression.


Pssm-ID: 319247 [Multi-domain]  Cd Length: 77  Bit Score: 114.91  E-value: 6.17e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1148323821   8 LELVDIEFIDVHEKCEPKRLTKTVQTIQDDGFIKNSVLAIKI-DNRYLIIDGTHRTSALKTLGCRRIPIQVVDPKEL 83
Cdd:cd16388     1 LKLVPIEQIRLHEEHEPNRLEKLVERIEAEGVLRNPPIVTPLqDGRYLILDGAHRTTALKKLGCKRIPVQVVDEEDP 77
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 9-89 2.64e-08

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: 50.00  E-value: 2.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148323821    9 ELVDIEFIDVHE----KCEPKRLTKTVQTIQDDGFIKNsVLAIKIDNRYLIIDGTHRTSALKTLGCRRIPIQVVDPKELK 84
Cdd:smart00470   1 VEVPIEKLRPNPdqprLTSEESLEELAESIKENGLLQP-IIVRPNDGRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDEE 79


                   ....*
gi 1148323821   85 IEYWS 89
Cdd:smart00470  80 AIALS 84
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 10-79 4.14e-07

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.


Pssm-ID: 319257 [Multi-domain]  Cd Length: 72  Bit Score: 46.39  E-value: 4.14e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148323821  10 LVDIEFIDVHEKCEPKRLTKTVQTIQDDGFIKNSVLAIKidNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:cd16400     1 LLPISDLRPHEEVDPDRVEELIEKILEEGVWTKPIIVDK--NTGIILDGHHRLEAAKRLGLKRVPCVLLD 68
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 31-79 5.29e-05

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: 41.11  E-value: 5.29e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1148323821  31 VQTIQDDGFIKNsVLAIKI-DNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:pfam02195  27 AASIKKRGLLQP-IIVRKTpDGRYEIIAGERRLRAAKLLGLKEVPVIVRE 75
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 6-79 9.78e-04

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: 39.59  E-value: 9.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1148323821   6 SNLELVDIEFIDVHEK-----CEPKRLTKTVQTIQDDGFIKNSVLAIKIDNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:COG1475     5 EEIREIPIDKIVPSPYnprrtFDEEALEELAASIREHGLLQPILVRPLGDGRYEIIAGERRLRAAKLLGLETVPAIVRD 83
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 34-79 3.66e-03

pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins.


Pssm-ID: 319261 [Multi-domain]  Cd Length: 69  Bit Score: 35.33  E-value: 3.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1148323821  34 IQDDGFIknsvLAIKIDNRYLIIDGTHRTSALKTLGCRRIPIQVVD 79
Cdd:cd16404    24 IRKNGII----VPIIVDQDGVIIDGHHRYRIAKELGIKEVPVIVYD 65
 
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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