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Conserved domains on  [gi|913734932|ref|WP_050480118|]
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Dps family protein [Herbaspirillum rhizosphaerae]

Protein Classification

Dps family protein( domain architecture ID 10002504)

Dps family protein similar to DNA starvation/stationary phase protection protein that binds and protects DNA from cleavage caused by reactive oxygen species

CATH:  1.20.1260.10
Gene Ontology:  GO:0016491|GO:0008199
SCOP:  4000839

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 8-162 1.64e-77

DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms];


:

Pssm-ID: 440546 [Multi-domain]  Cd Length: 156  Bit Score: 227.41  E-value: 1.64e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932   8 AINIGINDKDRKKIADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSY 87
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 913734932  88 KDFARLSSIPE-ADGVPAADEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLEG 162
Cdd:COG0783   81 AEFAKLSTIKEePEGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLED 156
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 8-162 1.64e-77

DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms];


Pssm-ID: 440546 [Multi-domain]  Cd Length: 156  Bit Score: 227.41  E-value: 1.64e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932   8 AINIGINDKDRKKIADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSY 87
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 913734932  88 KDFARLSSIPE-ADGVPAADEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLEG 162
Cdd:COG0783   81 AEFAKLSTIKEePEGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLED 156
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 23-160 1.07e-61

DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) display an N-terminal extension of variable length that contains two or three positively charged lysine residues that extends into the solvent and is thought to play an important role in the stabilization of the complex with DNA. DPS Listeria Flp, Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter pylori HP-NAP which lack the N-terminal extension, do not bind DNA. DPS proteins from Helicobacter pylori, Treponema pallidum, and Borrelia burgdorferi are highly immunogenic.


Pssm-ID: 153102  Cd Length: 139  Bit Score: 186.60  E-value: 1.07e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  23 DGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDFARLSSIPEAD-G 101
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 913734932 102 VPAADEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLL 160
Cdd:cd01043   81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 22-161 1.91e-25

Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.


Pssm-ID: 459712  Cd Length: 141  Bit Score: 94.66  E-value: 1.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932   22 ADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDFARLSSIPEADG 101
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  102 VPaadEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLE 161
Cdd:pfam00210  81 VL---EVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLE 137
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 11-162 4.17e-18

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 76.18  E-value: 4.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  11 IGINDKDRKKIADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDF 90
Cdd:PRK09448  13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 913734932  91 ARLSSIPEAD-GVPAADEMIRQLVAGQEAVTRTARSlfpAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLEG 162
Cdd:PRK09448  93 ASKTPLKSYPlDIHNVQDHLKALADRYAIVANDVRK---AIDEAGDEDTADIFTAASRDLDKFLWFIEAHIEE 162
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
15-102 2.30e-14

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 66.51  E-value: 2.30e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  15 DKDR-KKIADGLSKLLADTYTLY--LKTHnfHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALG-YPAPGSyKDF 90
Cdd:NF041388  17 DAEKaEQIVDALNTDLAATYVLYhqLKKH--HWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGgVPVSGP-AAL 93

                         90
                 ....*....|...
gi 913734932  91 ARLSSI-PEADGV 102
Cdd:NF041388  94 EEHAPVePEGEDV 106
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 8-162 1.64e-77

DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms];


Pssm-ID: 440546 [Multi-domain]  Cd Length: 156  Bit Score: 227.41  E-value: 1.64e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932   8 AINIGINDKDRKKIADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSY 87
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 913734932  88 KDFARLSSIPE-ADGVPAADEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLEG 162
Cdd:COG0783   81 AEFAKLSTIKEePEGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLED 156
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 23-160 1.07e-61

DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) display an N-terminal extension of variable length that contains two or three positively charged lysine residues that extends into the solvent and is thought to play an important role in the stabilization of the complex with DNA. DPS Listeria Flp, Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter pylori HP-NAP which lack the N-terminal extension, do not bind DNA. DPS proteins from Helicobacter pylori, Treponema pallidum, and Borrelia burgdorferi are highly immunogenic.


Pssm-ID: 153102  Cd Length: 139  Bit Score: 186.60  E-value: 1.07e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  23 DGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDFARLSSIPEAD-G 101
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 913734932 102 VPAADEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLL 160
Cdd:cd01043   81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 22-161 1.91e-25

Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.


Pssm-ID: 459712  Cd Length: 141  Bit Score: 94.66  E-value: 1.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932   22 ADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDFARLSSIPEADG 101
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  102 VPaadEMIRQLVAGQEAVTRTARSLFPAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLE 161
Cdd:pfam00210  81 VL---EVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLE 137
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 11-162 4.17e-18

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 76.18  E-value: 4.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  11 IGINDKDRKKIADGLSKLLADTYTLYLKTHNFHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALGYPAPGSYKDF 90
Cdd:PRK09448  13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 913734932  91 ARLSSIPEAD-GVPAADEMIRQLVAGQEAVTRTARSlfpAVDAAADEPTADLLTQRMQLHEKNAWMLRSLLEG 162
Cdd:PRK09448  93 ASKTPLKSYPlDIHNVQDHLKALADRYAIVANDVRK---AIDEAGDEDTADIFTAASRDLDKFLWFIEAHIEE 162
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
15-102 2.30e-14

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 66.51  E-value: 2.30e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 913734932  15 DKDR-KKIADGLSKLLADTYTLY--LKTHnfHWNVTGPMFNTLHLMFEGQYNELALAVDLIAERIRALG-YPAPGSyKDF 90
Cdd:NF041388  17 DAEKaEQIVDALNTDLAATYVLYhqLKKH--HWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGgVPVSGP-AAL 93

                         90
                 ....*....|...
gi 913734932  91 ARLSSI-PEADGV 102
Cdd:NF041388  94 EEHAPVePEGEDV 106
 
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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