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Conserved domains on  [gi|991839754|gb|AMG08034|]
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transcriptional repressor [Vibrio parahaemolyticus]

Protein Classification

transcriptional repressor( domain architecture ID 10793271)

transcriptional repressor such as ferric uptake regulators, iron-dependent, DNA-binding repressors and activators involved in iron metabolism, other metalloregulatory proteins, or the peroxide-responsive repressor PerR

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
fur PRK09462
ferric uptake regulator; Provisional
 1-147 8.23e-109

ferric uptake regulator; Provisional


:

Pssm-ID: 236527  Cd Length: 148  Bit Score: 305.50  E-value: 8.23e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   1 MSDNNQALKDAGLKVTLPRLKILEVLQQPDCQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 80
Cdd:PRK09462   1 MTDNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 991839754  81 ELSTQHHHDHLVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSDGGCKENPDAHKP 147
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEHAHEG 147
 
Name Accession Description Interval E-value
fur PRK09462
ferric uptake regulator; Provisional
 1-147 8.23e-109

ferric uptake regulator; Provisional


Pssm-ID: 236527  Cd Length: 148  Bit Score: 305.50  E-value: 8.23e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   1 MSDNNQALKDAGLKVTLPRLKILEVLQQPDCQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 80
Cdd:PRK09462   1 MTDNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 991839754  81 ELSTQHHHDHLVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSDGGCKENPDAHKP 147
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEHAHEG 147
FUR pfam01475
Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that ...
 11-130 5.23e-58

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: 176.28  E-value: 5.23e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   11 AGLKVTLPRLKILEVLQQPDCQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFELSTQHHHDH 90
Cdd:pfam01475   2 AGLKLTPQRLKILEVLQKSDKEHLSAEEIYKELREEDPNISLATVYRTLNLLEEAGLVKRLEFDGGESRFELNTGHHHDH 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 991839754   91 LVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLY 130
Cdd:pfam01475  82 LICEDCGKVIEFKDDEIEKRQEEIAKKHGFKLVSHRLELY 121
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
1-140 1.13e-53

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


Pssm-ID: 440498  Cd Length: 140  Bit Score: 165.90  E-value: 1.13e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   1 MSDNNQALKDAGLKVTLPRLKILEVLQQPDcQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 80
Cdd:COG0735    4 LEEAEELLREAGLRLTPQRLAILELLLESD-RHLSAEEIYEALRKKGPSISLATVYRTLDLLVEAGLVHRIEFGGGKARY 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754  81 ELSTQHHHDHLVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSDggCKE 140
Cdd:COG0735   83 ELNEGDHHHHLICTKCGKVIELDDDEIEELLEELAEPHGFEIESHELEIYGLCPD--CQK 140
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 18-133 9.20e-46

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: 145.03  E-value: 9.20e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754  18 PRLKILEVLQQPDcQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFELSTQHHHDHLVCLDCG 97
Cdd:cd07153    2 QRLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNTDEHHHHLICTKCG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991839754  98 EVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKC 133
Cdd:cd07153   81 KVIDFEDCPLEELLEELAAKTGFKITSHRLELYGIC 116
 
Name Accession Description Interval E-value
fur PRK09462
ferric uptake regulator; Provisional
 1-147 8.23e-109

ferric uptake regulator; Provisional


Pssm-ID: 236527  Cd Length: 148  Bit Score: 305.50  E-value: 8.23e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   1 MSDNNQALKDAGLKVTLPRLKILEVLQQPDCQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 80
Cdd:PRK09462   1 MTDNNTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 991839754  81 ELSTQHHHDHLVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSDGGCKENPDAHKP 147
Cdd:PRK09462  81 ELTQQHHHDHLICLDCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYGHCAEGDCREDEHAHEG 147
FUR pfam01475
Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that ...
 11-130 5.23e-58

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: 176.28  E-value: 5.23e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   11 AGLKVTLPRLKILEVLQQPDCQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFELSTQHHHDH 90
Cdd:pfam01475   2 AGLKLTPQRLKILEVLQKSDKEHLSAEEIYKELREEDPNISLATVYRTLNLLEEAGLVKRLEFDGGESRFELNTGHHHDH 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 991839754   91 LVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLY 130
Cdd:pfam01475  82 LICEDCGKVIEFKDDEIEKRQEEIAKKHGFKLVSHRLELY 121
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
1-140 1.13e-53

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


Pssm-ID: 440498  Cd Length: 140  Bit Score: 165.90  E-value: 1.13e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754   1 MSDNNQALKDAGLKVTLPRLKILEVLQQPDcQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 80
Cdd:COG0735    4 LEEAEELLREAGLRLTPQRLAILELLLESD-RHLSAEEIYEALRKKGPSISLATVYRTLDLLVEAGLVHRIEFGGGKARY 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754  81 ELSTQHHHDHLVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSDggCKE 140
Cdd:COG0735   83 ELNEGDHHHHLICTKCGKVIELDDDEIEELLEELAEPHGFEIESHELEIYGLCPD--CQK 140
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 18-133 9.20e-46

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: 145.03  E-value: 9.20e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754  18 PRLKILEVLQQPDcQHISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFELSTQHHHDHLVCLDCG 97
Cdd:cd07153    2 QRLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNTDEHHHHLICTKCG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991839754  98 EVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKC 133
Cdd:cd07153   81 KVIDFEDCPLEELLEELAAKTGFKITSHRLELYGIC 116
PRK11639 PRK11639
zinc uptake transcriptional repressor Zur;
12-140 9.82e-04

zinc uptake transcriptional repressor Zur;


Pssm-ID: 183251  Cd Length: 169  Bit Score: 37.43  E-value: 9.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991839754  12 GLKVTLPRLKILEVL-QQPDCqhISAEDLYKKLIDLGEEIGLATVYRVLNQFDDAGIVTR----------HHFEggksvf 80
Cdd:PRK11639  21 NVRLTPQRLEVLRLMsLQPGA--ISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKvestnsyvlcHLFD------ 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 991839754  81 elstQHHHDH--LVCLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKCSdgGCKE 140
Cdd:PRK11639  93 ----QPTHTSamFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCA--ACVE 148
 
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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