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Conserved domains on  [gi|486364108|ref|WP_001595134|]
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CFA/I fimbrial subunit CfaD [Escherichia coli]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 12204063)

helix-turn-helix (HTH) transcriptional regulator containing an AraC family DNA-binding HTH domain controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

CATH:  1.10.10.1310
Gene Ontology:  GO:0006355|GO:0043565|GO:0003700
PubMed:  2644244|15808743|8831795
SCOP:  4000332

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
177-258 4.15e-25

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 94.93  E-value: 4.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108   177 KWTLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTP 255
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 486364108   256 KQF 258
Cdd:smart00342  81 SEY 83
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
177-258 4.15e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 94.93  E-value: 4.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108   177 KWTLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTP 255
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 486364108   256 KQF 258
Cdd:smart00342  81 SEY 83
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 163-262 3.94e-20

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 87.43  E-value: 3.94e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 163 SDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESENTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASY 242
Cdd:PRK15186 183 AENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASY 262

                         90       100
                 ....*....|....*....|
gi 486364108 243 FIRVFNKHYGVTPKQFFTYF 262
Cdd:PRK15186 263 FTCVFKKHFKTTPSEFLAFL 282
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
179-258 1.27e-18

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 82.52  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 179 TLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTPKQ 257
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 .
gi 486364108 258 F 258
Cdd:COG2207  250 Y 250
HTH_18 pfam12833
Helix-turn-helix domain;
183-258 1.63e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 69.54  E-value: 1.63e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 486364108  183 IADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENS-YQISQISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
177-258 4.15e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 94.93  E-value: 4.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108   177 KWTLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTP 255
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 486364108   256 KQF 258
Cdd:smart00342  81 SEY 83
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 163-262 3.94e-20

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 87.43  E-value: 3.94e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 163 SDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESENTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASY 242
Cdd:PRK15186 183 AENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASY 262

                         90       100
                 ....*....|....*....|
gi 486364108 243 FIRVFNKHYGVTPKQFFTYF 262
Cdd:PRK15186 263 FTCVFKKHFKTTPSEFLAFL 282
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
179-258 1.27e-18

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 82.52  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 179 TLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTPKQ 257
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 .
gi 486364108 258 F 258
Cdd:COG2207  250 Y 250
HTH_18 pfam12833
Helix-turn-helix domain;
183-258 1.63e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 69.54  E-value: 1.63e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 486364108  183 IADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENS-YQISQISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 124-258 4.40e-15

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 73.53  E-value: 4.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 124 NINSHDNSAFisSLIYLISKIEDNEKIIESIYISSVSFFSDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESENT 203
Cdd:PRK15044 157 SIDDHDYSYF--SLMYLISAFVRKPGGFDFLERAIKITTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEV 234

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 486364108 204 NFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:PRK15044 235 SFSKIYLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITPLSF 289
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 165-258 4.44e-15

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 73.04  E-value: 4.44e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 165 KVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESENTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFI 244
Cdd:PRK09978 146 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFI 225

                         90
                 ....*....|....
gi 486364108 245 RVFNKHYGVTPKQF 258
Cdd:PRK09978 226 YVFRNYYGMTPTEY 239
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 119-258 9.32e-15

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 72.72  E-value: 9.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 119 LDELKNINSHDNSAFISS-------LIYLISKIEDNEKIIESIYISSVSFFSDKVRNVIEKDLSRKWTLGIIADAFNVSE 191
Cdd:PRK15185 157 KDTSKGCSNCNNKSCIENeelipyfLLFLLTAFLRLPESYEIILSSAQITLKERVYNIISSSPSRQWKLTDVADHIFMST 236

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 486364108 192 ITIRKRLESENTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:PRK15185 237 STLKRKLAEEGTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTF 303
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 163-257 4.27e-14

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 70.11  E-value: 4.27e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 163 SDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESENTNFNQILMQLRMSKAA-LLLLENSyqISQISNMIGISSAS 241
Cdd:PRK09940 136 SGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKnLIRVEGS--VNKIAEQCGYASTS 213

                         90
                 ....*....|....*.
gi 486364108 242 YFIRVFNKHYGVTPKQ 257
Cdd:PRK09940 214 YFIYAFRKHFGNSPKR 229
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 165-258 1.69e-09

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 57.09  E-value: 1.69e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 165 KVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMSKAALLLLENSYQISQISNMIGISSASYF 243
Cdd:COG4977  214 RAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAAtGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*
gi 486364108 244 IRVFNKHYGVTPKQF 258
Cdd:COG4977  294 RRAFRRRFGVSPSAY 308
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
156-258 5.50e-07

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 49.67  E-value: 5.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 156 ISSVSFFSDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESEN-TNFNQILMQLRMSKAALLLLENSYQISQISNM 234
Cdd:PRK13502 171 ATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTgMTINQYLRQVRICHAQYLLQHSPLMISEISMQ 250

                         90       100
                 ....*....|....*....|....
gi 486364108 235 IGISSASYFIRVFNKHYGVTPKQF 258
Cdd:PRK13502 251 CGFEDSNYFSVVFTRETGMTPSQW 274
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
152-258 3.64e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 47.40  E-value: 3.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 152 ESIYISSVSFFSDKVRNVIEKDLSRKWTLGIIADAFNVSEITIRKRLESEN-TNFNQILMQLRMSKAALLLLENSYQISQ 230
Cdd:PRK13500 197 DSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTgMTINQYLRQVRVCHAQYLLQHSRLLISD 276

                         90       100
                 ....*....|....*....|....*...
gi 486364108 231 ISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:PRK13500 277 ISTECGFEDSNYFSVVFTRETGMTPSQW 304
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 170-258 1.25e-05

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 45.81  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 170 IEKDLSRKWTLGIIADAFNVSEITIRKRLESE-NTNFNQILMQLRMsKAALLLLENSYQISQISNMIGISSASYFIRVFN 248
Cdd:COG2169   93 IEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHtGVTPKAYARARRL-LRARQLLQTGLSVTDAAYAAGFGSLSRFYEAFK 171

                         90
                 ....*....|
gi 486364108 249 KHYGVTPKQF 258
Cdd:COG2169  172 KLLGMTPSAY 181
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
213-258 1.73e-05

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 44.96  E-value: 1.73e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 486364108 213 RMSKAALLLLENSYQISQISNMIGISSASYFIRVFNKHYGVTPKQF 258
Cdd:PRK10572 236 RISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 228-260 4.85e-04

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 37.13  E-value: 4.85e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 486364108  228 ISQISNMIGISSaSYFIRVFNKHYGVTPKQFFT 260
Cdd:pfam00165  11 IADIADELGFSR-SYFSRLFKKYTGVTPSQYRH 42
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
164-262 7.38e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 40.27  E-value: 7.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486364108 164 DKVRNVIEKDLSRKWTLGIIADAFNVSEITIrKRLESENTNFN--QILMQLRMSKAALLLLENSYQISQISNMIGISSAS 241
Cdd:PRK13501 179 DLIMSALQQSLGAYFDMADFCHKNQLVERSL-KQLFRQQTGMSisHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSN 257

                         90       100
                 ....*....|....*....|.
gi 486364108 242 YFIRVFNKHYGVTPKQFFTYF 262
Cdd:PRK13501 258 YFSAVFTREAGMTPRDYRQRF 278
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
209-260 1.75e-03

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 38.99  E-value: 1.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 486364108 209 LMQLRMSKAALLLLENSYQISQISNMIGISsASYFIRVFNKHYGVTPKQFFT 260
Cdd:COG2207  152 LLLLLLLLLLLLLLLLLLTLEELARELGLS-PRTLSRLFKEETGTSPKQYLR 202
 
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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