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Conserved domains on  [gi|490866058|ref|WP_004728081|]
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MULTISPECIES: winged helix-turn-helix domain-containing protein [Vibrio]

Protein Classification

winged helix-turn-helix domain-containing protein( domain architecture ID 10007860)

winged helix-turn-helix (wHTH) domain-containing protein binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|8831795|15808743
SCOP:  3000034

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CadC1 COG3710
DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];
13-112 3.76e-27

DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];


:

Pssm-ID: 442924 [Multi-domain]  Cd Length: 106  Bit Score: 99.21  E-value: 3.76e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  13 RFLFDAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWveRGNKVDDSSLTQSISLLRKVLGDKATNP 92
Cdd:COG3710    7 DFRLDPARRELLRD-GEPVRLSPRAFDLLLLLLEHPGRVVSRDELLAAVW--PGRVVSDNSLTQAISRLRKALGDDGLEP 83

                         90       100
                 ....*....|....*....|
gi 490866058  93 EYIKTEARIGYRFIAPVDPV 112
Cdd:COG3710   84 RLIRTVPRRGYRLVAPVEVE 103
 
Name Accession Description Interval E-value
CadC1 COG3710
DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];
13-112 3.76e-27

DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];


Pssm-ID: 442924 [Multi-domain]  Cd Length: 106  Bit Score: 99.21  E-value: 3.76e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  13 RFLFDAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWveRGNKVDDSSLTQSISLLRKVLGDKATNP 92
Cdd:COG3710    7 DFRLDPARRELLRD-GEPVRLSPRAFDLLLLLLEHPGRVVSRDELLAAVW--PGRVVSDNSLTQAISRLRKALGDDGLEP 83

                         90       100
                 ....*....|....*....|
gi 490866058  93 EYIKTEARIGYRFIAPVDPV 112
Cdd:COG3710   84 RLIRTVPRRGYRLVAPVEVE 103
Trans_reg_C pfam00486
Transcriptional regulatory protein, C terminal;
28-105 1.95e-19

Transcriptional regulatory protein, C terminal;


Pssm-ID: 425712 [Multi-domain]  Cd Length: 77  Bit Score: 78.32  E-value: 1.95e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490866058   28 DEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDKATNPEYIKTEARIGYRF 105
Cdd:pfam00486   1 GEEVELTPKEFKLLELLAENPGRVVSREQLLEEVW-GEDYDVDDNTVDVHISRLRKKLEDDPRDPRLIKTVRGVGYRL 77
trans_reg_C cd00383
DNA-binding effector domain of two-component system response regulators; Bacteria and some ...
 14-105 3.13e-17

DNA-binding effector domain of two-component system response regulators; Bacteria and some eukaryotes use two-component signal transduction systems to detect and respond to changes in the environment. The systems consists of a sensor histidine kinase and a response regulator. The former autophosphorylates a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. This C-terminal effector domain belongs to the winged helix-turn-helix family of transcriptional regulators and contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunit of RNA polymerase.


Pssm-ID: 294013 [Multi-domain]  Cd Length: 89  Bit Score: 72.90  E-value: 3.13e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  14 FLFDAVEKSLTdAYDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDkATNPE 93
Cdd:cd00383    1 LRLDPARREVT-VDGEEVELTPKEFELLELLARNPGRVVSREELLEAVW-GYDYEVDDRTVDVHISRLRKKLED-DPEPR 77

                         90
                 ....*....|..
gi 490866058  94 YIKTEARIGYRF 105
Cdd:cd00383   78 LIKTVRGVGYRL 89
Trans_reg_C smart00862
Transcriptional regulatory protein, C terminal; This domain is almost always found associated ...
 28-105 6.90e-17

Transcriptional regulatory protein, C terminal; This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.


Pssm-ID: 214866 [Multi-domain]  Cd Length: 76  Bit Score: 71.81  E-value: 6.90e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490866058    28 DEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDkATNPEYIKTEARIGYRF 105
Cdd:smart00862   1 GEPIKLTPKEFRLLELLLRNPGRVVSREELLEAVW-GDDEDVDDNTLDVHISRLRKKLED-DGDPRLIETVRGVGYRL 76
PRK10153 PRK10153
DNA-binding transcriptional activator CadC; Provisional
 37-140 8.16e-15

DNA-binding transcriptional activator CadC; Provisional


Pssm-ID: 236658 [Multi-domain]  Cd Length: 517  Bit Score: 72.00  E-value: 8.16e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  37 ESRILTLL---TSHPNAVLSREDIYQQVWveRGNKVDDSSLTQSISLLRKVLGD-KATNPEYIKTEARIGYRFIAPVDPv 112
Cdd:PRK10153  30 EPRLIDLLvffAQHSGEVLSRDELIDHVW--DRAIVTDHVVTQSISELRKSLKDgREDNPEYIVTVPKRGYKLVAPVIW- 106

                         90       100
                 ....*....|....*....|....*...
gi 490866058 113 YSVIPLEELVEVTEQNVQPAANTRQTPA 140
Cdd:PRK10153 107 YSEEEGEEILASSPPPIPEAVPATAEPS 134
 
Name Accession Description Interval E-value
CadC1 COG3710
DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];
13-112 3.76e-27

DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];


Pssm-ID: 442924 [Multi-domain]  Cd Length: 106  Bit Score: 99.21  E-value: 3.76e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  13 RFLFDAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWveRGNKVDDSSLTQSISLLRKVLGDKATNP 92
Cdd:COG3710    7 DFRLDPARRELLRD-GEPVRLSPRAFDLLLLLLEHPGRVVSRDELLAAVW--PGRVVSDNSLTQAISRLRKALGDDGLEP 83

                         90       100
                 ....*....|....*....|
gi 490866058  93 EYIKTEARIGYRFIAPVDPV 112
Cdd:COG3710   84 RLIRTVPRRGYRLVAPVEVE 103
Trans_reg_C pfam00486
Transcriptional regulatory protein, C terminal;
28-105 1.95e-19

Transcriptional regulatory protein, C terminal;


Pssm-ID: 425712 [Multi-domain]  Cd Length: 77  Bit Score: 78.32  E-value: 1.95e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490866058   28 DEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDKATNPEYIKTEARIGYRF 105
Cdd:pfam00486   1 GEEVELTPKEFKLLELLAENPGRVVSREQLLEEVW-GEDYDVDDNTVDVHISRLRKKLEDDPRDPRLIKTVRGVGYRL 77
trans_reg_C cd00383
DNA-binding effector domain of two-component system response regulators; Bacteria and some ...
 14-105 3.13e-17

DNA-binding effector domain of two-component system response regulators; Bacteria and some eukaryotes use two-component signal transduction systems to detect and respond to changes in the environment. The systems consists of a sensor histidine kinase and a response regulator. The former autophosphorylates a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. This C-terminal effector domain belongs to the winged helix-turn-helix family of transcriptional regulators and contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunit of RNA polymerase.


Pssm-ID: 294013 [Multi-domain]  Cd Length: 89  Bit Score: 72.90  E-value: 3.13e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  14 FLFDAVEKSLTdAYDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDkATNPE 93
Cdd:cd00383    1 LRLDPARREVT-VDGEEVELTPKEFELLELLARNPGRVVSREELLEAVW-GYDYEVDDRTVDVHISRLRKKLED-DPEPR 77

                         90
                 ....*....|..
gi 490866058  94 YIKTEARIGYRF 105
Cdd:cd00383   78 LIKTVRGVGYRL 89
Trans_reg_C smart00862
Transcriptional regulatory protein, C terminal; This domain is almost always found associated ...
 28-105 6.90e-17

Transcriptional regulatory protein, C terminal; This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.


Pssm-ID: 214866 [Multi-domain]  Cd Length: 76  Bit Score: 71.81  E-value: 6.90e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490866058    28 DEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLGDkATNPEYIKTEARIGYRF 105
Cdd:smart00862   1 GEPIKLTPKEFRLLELLLRNPGRVVSREELLEAVW-GDDEDVDDNTLDVHISRLRKKLED-DGDPRLIETVRGVGYRL 76
PRK10153 PRK10153
DNA-binding transcriptional activator CadC; Provisional
 37-140 8.16e-15

DNA-binding transcriptional activator CadC; Provisional


Pssm-ID: 236658 [Multi-domain]  Cd Length: 517  Bit Score: 72.00  E-value: 8.16e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  37 ESRILTLL---TSHPNAVLSREDIYQQVWveRGNKVDDSSLTQSISLLRKVLGD-KATNPEYIKTEARIGYRFIAPVDPv 112
Cdd:PRK10153  30 EPRLIDLLvffAQHSGEVLSRDELIDHVW--DRAIVTDHVVTQSISELRKSLKDgREDNPEYIVTVPKRGYKLVAPVIW- 106

                         90       100
                 ....*....|....*....|....*...
gi 490866058 113 YSVIPLEELVEVTEQNVQPAANTRQTPA 140
Cdd:PRK10153 107 YSEEEGEEILASSPPPIPEAVPATAEPS 134
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 9-97 7.37e-07

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 47.64  E-value: 7.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058   9 VINSRFLFDAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWVErgNKVDDSSLTQSISLLRKVLGDk 88
Cdd:COG0745  124 VLRVGDLLDLAAREVTRD-GEPVELTPKEFRLLELLMRNPGRVVSREQLLEEVWGY--DYGDDRTVDVHISRLRKKLED- 199


                 ....*....
gi 490866058  89 atnpEYIKT 97
Cdd:COG0745  200 ----DLIET 204
orf27 CHL00148
Ycf27; Reviewed
 29-105 1.57e-06

Ycf27; Reviewed


Pssm-ID: 214376 [Multi-domain]  Cd Length: 240  Bit Score: 47.02  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  29 EKIIIGDNESRILTLLTSHPNAVLSREDIYQQVW---VERgnKVDDSSLTQSISLLRKVLGDKATNPEYIKTEARIGYRF 105
Cdd:CHL00148 158 ERIRLTGMEFSLLELLISKSGEIFSRATILKEVWgytPER--HIDTRVVDVHISRLRAKLEDDPSNPDLILTARGTGYLF 235
PRK12370 PRK12370
HilA/EilA family virulence transcriptional regulator;
1-109 7.41e-06

HilA/EilA family virulence transcriptional regulator;


Pssm-ID: 237080 [Multi-domain]  Cd Length: 553  Bit Score: 45.61  E-value: 7.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058   1 METPNDKVvINSRFLFD----AVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWVErgNKVDDSSLTQ 76
Cdd:PRK12370   2 MHFNPVPV-SNKKFVFDdfilNMDGSLLRS-EKKVNIPPKEYAVLVILLEAAGEIVSKNTLLDQVWGD--AEVNEESLTR 77

                         90       100       110
                 ....*....|....*....|....*....|...
gi 490866058  77 SISLLRKVLGDKATNpEYIKTEARIGYRFIAPV 109
Cdd:PRK12370  78 CIYALRRILSEDKEH-RYIETLYGQGYRFNRPV 109
PRK10701 PRK10701
DNA-binding transcriptional regulator RstA; Provisional
 17-108 1.02e-05

DNA-binding transcriptional regulator RstA; Provisional


Pssm-ID: 236738 [Multi-domain]  Cd Length: 240  Bit Score: 44.63  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  17 DAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVwveRGNKVD--DSSLTQSISLLRKVLGDKATNPEY 94
Cdd:PRK10701 147 DPVNRQVTLA-GEEISLSTADFDLLWELATHAGQIMDRDALLKNL---RGVSYDglDRSVDVAISRLRKKLLDNAAEPYR 222

                         90
                 ....*....|....
gi 490866058  95 IKTEARIGYRFiAP 108
Cdd:PRK10701 223 IKTVRNKGYLF-AP 235
ompR PRK09468
osmolarity response regulator; Provisional
 3-106 2.26e-05

osmolarity response regulator; Provisional


Pssm-ID: 181883 [Multi-domain]  Cd Length: 239  Bit Score: 43.81  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058   3 TPNDKVVINSRFLFDAVEKSLTDAyDEKIIIGDNESRILTLLTSHPNAVLSREDIYQqvwVERGNKVD--DSSLTQSISL 80
Cdd:PRK09468 133 SQEEEVIAFGKFKLNLGTRELFRG-DEPMPLTTGEFAVLKALVSHPREPLSRDKLMN---LARGREYSamERSIDVQISR 208

                         90       100
                 ....*....|....*....|....*.
gi 490866058  81 LRKVLGDKATNPEYIKTEARIGYRFI 106
Cdd:PRK09468 209 LRRLIEEDPAHPRYIQTVWGLGYVFV 234
PRK10529 PRK10529
DNA-binding transcriptional activator KdpE; Provisional
 28-106 5.10e-04

DNA-binding transcriptional activator KdpE; Provisional


Pssm-ID: 182522 [Multi-domain]  Cd Length: 225  Bit Score: 39.79  E-value: 5.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490866058  28 DEKIIIGDNESRILTLLTSHPNAVLSREDIYQQVWVErgNKVDDSS-LTQSISLLRKVLGDKATNPEYIKTEARIGYRFI 106
Cdd:PRK10529 147 EEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGP--NAVEHSHyLRIYMGHLRQKLEQDPARPRHFITETGIGYRFM 224
PRK13856 PRK13856
two-component response regulator VirG; Provisional
 37-113 2.37e-03

two-component response regulator VirG; Provisional


Pssm-ID: 172377 [Multi-domain]  Cd Length: 241  Bit Score: 37.87  E-value: 2.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490866058  37 ESRILTLLTSHPNAVLSREDIYQQVWVeRGNKVDDSSLTQSISLLRKVLGDKATNPEYIKTEARIGYRFIAPVDPVY 113
Cdd:PRK13856 160 EFNLLVAFLEKPRDVLSREQLLIASRV-REEEVYDRSIDVLILRLRRKLEQDPANPQLIKTARGAGYFFDADVDVSY 235
PRK10161 PRK10161
phosphate response regulator transcription factor PhoB;
33-105 4.90e-03

phosphate response regulator transcription factor PhoB;


Pssm-ID: 182277 [Multi-domain]  Cd Length: 229  Bit Score: 36.62  E-value: 4.90e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490866058  33 IGDNESRILTLLTSHPNAVLSREDIYQQVWvERGNKVDDSSLTQSISLLRKVLgDKATNPEYIKTEARIGYRF 105
Cdd:PRK10161 155 MGPTEFKLLHFFMTHPERVYSREQLLNHVW-GTNVYVEDRTVDVHIRRLRKAL-EPGGHDRMVQTVRGTGYRF 225
 
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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