NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|493444972|ref|WP_006400349|]
View 

MULTISPECIES: ferric iron uptake transcriptional regulator [Burkholderia]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 229396)

helix-turn-helix domain-containing protein may bind DNA and be involved in the regulation of gene expression

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 1-142 5.57e-62

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member PRK09462:

Pssm-ID: 481199  Cd Length: 148  Bit Score: 186.86  E-value: 5.57e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972   1 MT-NPTDLKNIGLKATLPRLKILEIFQQSPVRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVF 79
Cdd:PRK09462   1 MTdNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493444972  80 ELNEGSHHDHLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSCTTENCPHRKH 142
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEH 143
 
Name Accession Description Interval E-value
fur PRK09462
ferric uptake regulator; Provisional
 1-142 5.57e-62

ferric uptake regulator; Provisional


Pssm-ID: 236527  Cd Length: 148  Bit Score: 186.86  E-value: 5.57e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972   1 MT-NPTDLKNIGLKATLPRLKILEIFQQSPVRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVF 79
Cdd:PRK09462   1 MTdNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493444972  80 ELNEGSHHDHLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSCTTENCPHRKH 142
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEH 143
FUR pfam01475
Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that ...
 9-129 4.23e-55

Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.


Pssm-ID: 426280  Cd Length: 121  Bit Score: 168.58  E-value: 4.23e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972    9 NIGLKATLPRLKILEIFQQSPVRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSHHD 88
Cdd:pfam01475   1 EAGLKLTPQRLKILEVLQKSDKEHLSAEEIYKELREEDPNISLATVYRTLNLLEEAGLVKRLEFDGGESRFELNTGHHHD 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 493444972   89 HLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMY 129
Cdd:pfam01475  81 HLICEDCGKVIEFKDDEIEKRQEEIAKKHGFKLVSHRLELY 121
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
7-132 1.93e-49

Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];


Pssm-ID: 440498  Cd Length: 140  Bit Score: 154.73  E-value: 1.93e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972   7 LKNIGLKATLPRLKILEIFQQSPvRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSH 86
Cdd:COG0735   11 LREAGLRLTPQRLAILELLLESD-RHLSAEEIYEALRKKGPSISLATVYRTLDLLVEAGLVHRIEFGGGKARYELNEGDH 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 493444972  87 HDHLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSC 132
Cdd:COG0735   90 HHHLICTKCGKVIELDDDEIEELLEELAEPHGFEIESHELEIYGLC 135
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 17-132 4.21e-43

Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.


Pssm-ID: 133478 [Multi-domain]  Cd Length: 116  Bit Score: 138.10  E-value: 4.21e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972  17 PRLKILEIFQQSPvRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSHHDHLVCLDCG 96
Cdd:cd07153    2 QRLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNTDEHHHHLICTKCG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 493444972  97 RVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSC 132
Cdd:cd07153   81 KVIDFEDCPLEELLEELAAKTGFKITSHRLELYGIC 116
HTH_ICLR smart00346
helix_turn_helix isocitrate lyase regulation;
19-69 5.31e-03

helix_turn_helix isocitrate lyase regulation;


Pssm-ID: 214629 [Multi-domain]  Cd Length: 91  Bit Score: 34.10  E-value: 5.31e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 493444972    19 LKILEIFQQSPvRHLTAEDvyrnlLNEQLDIGLATVYRVLTQFEQAGLLSR 69
Cdd:smart00346   8 LAVLRALAEEP-GGLTLAE-----LAERLGLSKSTAHRLLNTLQELGYVEQ 52
 
Name Accession Description Interval E-value
fur PRK09462
ferric uptake regulator; Provisional
 1-142 5.57e-62

ferric uptake regulator; Provisional


Pssm-ID: 236527  Cd Length: 148  Bit Score: 186.86  E-value: 5.57e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972   1 MT-NPTDLKNIGLKATLPRLKILEIFQQSPVRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVF 79
Cdd:PRK09462   1 MTdNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493444972  80 ELNEGSHHDHLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSCTTENCPHRKH 142
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEH 143
FUR pfam01475
Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that ...
 9-129 4.23e-55

Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.


Pssm-ID: 426280  Cd Length: 121  Bit Score: 168.58  E-value: 4.23e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972    9 NIGLKATLPRLKILEIFQQSPVRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSHHD 88
Cdd:pfam01475   1 EAGLKLTPQRLKILEVLQKSDKEHLSAEEIYKELREEDPNISLATVYRTLNLLEEAGLVKRLEFDGGESRFELNTGHHHD 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 493444972   89 HLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMY 129
Cdd:pfam01475  81 HLICEDCGKVIEFKDDEIEKRQEEIAKKHGFKLVSHRLELY 121
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
7-132 1.93e-49

Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];


Pssm-ID: 440498  Cd Length: 140  Bit Score: 154.73  E-value: 1.93e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972   7 LKNIGLKATLPRLKILEIFQQSPvRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSH 86
Cdd:COG0735   11 LREAGLRLTPQRLAILELLLESD-RHLSAEEIYEALRKKGPSISLATVYRTLDLLVEAGLVHRIEFGGGKARYELNEGDH 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 493444972  87 HDHLVCLDCGRVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSC 132
Cdd:COG0735   90 HHHLICTKCGKVIELDDDEIEELLEELAEPHGFEIESHELEIYGLC 135
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 17-132 4.21e-43

Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.


Pssm-ID: 133478 [Multi-domain]  Cd Length: 116  Bit Score: 138.10  E-value: 4.21e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493444972  17 PRLKILEIFQQSPvRHLTAEDVYRNLLNEQLDIGLATVYRVLTQFEQAGLLSRSNFESGKAVFELNEGSHHDHLVCLDCG 96
Cdd:cd07153    2 QRLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNTDEHHHHLICTKCG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 493444972  97 RVEEFFDAEIESRQQAIAKERGFRLQEHSLAMYGSC 132
Cdd:cd07153   81 KVIDFEDCPLEELLEELAAKTGFKITSHRLELYGIC 116
HTH_ICLR smart00346
helix_turn_helix isocitrate lyase regulation;
19-69 5.31e-03

helix_turn_helix isocitrate lyase regulation;


Pssm-ID: 214629 [Multi-domain]  Cd Length: 91  Bit Score: 34.10  E-value: 5.31e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 493444972    19 LKILEIFQQSPvRHLTAEDvyrnlLNEQLDIGLATVYRVLTQFEQAGLLSR 69
Cdd:smart00346   8 LAVLRALAEEP-GGLTLAE-----LAERLGLSKSTAHRLLNTLQELGYVEQ 52
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH