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Conserved domains on  [gi|488866843|ref|WP_002779082|]
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MULTISPECIES: AraC family transcriptional regulator [Campylobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11454391)

helix-turn-helix (HTH) domain-containing protein with an AraC family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.60
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  10473770|15808743|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
152-287 3.64e-21

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 3.64e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 152 ILDPIVSLKFEEIFLHLLLNKNTYFIGFLAGILKEFRLDLSQLFEYcgrEFVSVSEMADFAKLDFATFSREFKKCFGQSP 231
Cdd:COG2207  121 LLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL---LLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488866843 232 KKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKR 253
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
152-287 3.64e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 3.64e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 152 ILDPIVSLKFEEIFLHLLLNKNTYFIGFLAGILKEFRLDLSQLFEYcgrEFVSVSEMADFAKLDFATFSREFKKCFGQSP 231
Cdd:COG2207  121 LLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL---LLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488866843 232 KKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKR 253
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
203-284 7.75e-20

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.83  E-value: 7.75e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843   203 VSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPK 282
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 488866843   283 QY 284
Cdd:smart00342  82 EY 83
HTH_18 pfam12833
Helix-turn-helix domain;
218-287 4.30e-16

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 71.85  E-value: 4.30e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488866843  218 TFSREFKKCFGQSPKKWLDEKRLQKAKVLL-EFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:pfam12833  11 TLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 190-287 5.01e-12

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 65.37  E-value: 5.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 190 DLSQLFEYC----GREFvSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSS 265
Cdd:PRK09393 219 RLGPLIDWMrahlAEPH-TVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGS 297

                         90       100
                 ....*....|....*....|..
gi 488866843 266 VAWFIERFKEKYNQTPKQYQKS 287
Cdd:PRK09393 298 EESLRHHFRRRAATSPAAYRKR 319
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 202-285 1.40e-04

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 42.74  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843  202 FVSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEfSKKNVNEIANECAFSSVAWFIERFKEKYNQTP 281
Cdd:TIGR04094 301 PLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLR-SQIPVSEVSNELGFYDLSHFSRTFKKHTGVSP 379


                  ....
gi 488866843  282 KQYQ 285
Cdd:TIGR04094 380 KQYQ 383
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
152-287 3.64e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 3.64e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 152 ILDPIVSLKFEEIFLHLLLNKNTYFIGFLAGILKEFRLDLSQLFEYcgrEFVSVSEMADFAKLDFATFSREFKKCFGQSP 231
Cdd:COG2207  121 LLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL---LLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488866843 232 KKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKR 253
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
203-284 7.75e-20

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.83  E-value: 7.75e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843   203 VSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPK 282
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 488866843   283 QY 284
Cdd:smart00342  82 EY 83
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 203-286 1.32e-16

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: 78.28  E-value: 1.32e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 203 VSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPK 282
Cdd:COG4977  227 LSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPS 306


                 ....
gi 488866843 283 QYQK 286
Cdd:COG4977  307 AYRR 310
HTH_18 pfam12833
Helix-turn-helix domain;
218-287 4.30e-16

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 71.85  E-value: 4.30e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488866843  218 TFSREFKKCFGQSPKKWLDEKRLQKAKVLL-EFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:pfam12833  11 TLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 190-287 5.01e-12

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 65.37  E-value: 5.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 190 DLSQLFEYC----GREFvSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSS 265
Cdd:PRK09393 219 RLGPLIDWMrahlAEPH-TVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGS 297

                         90       100
                 ....*....|....*....|..
gi 488866843 266 VAWFIERFKEKYNQTPKQYQKS 287
Cdd:PRK09393 298 EESLRHHFRRRAATSPAAYRKR 319
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 201-286 3.07e-10

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: 60.07  E-value: 3.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 201 EFVSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEfSKKNVNEIANECAFSSVAWFIERFKEKYNQT 280
Cdd:COG2169   99 DRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSLSRFYEAFKKLLGMT 177


                 ....*.
gi 488866843 281 PKQYQK 286
Cdd:COG2169  178 PSAYRR 183
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
201-282 6.61e-08

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 52.76  E-value: 6.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 201 EFVSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQT 280
Cdd:PRK13503 186 EEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWS 265


                 ..
gi 488866843 281 PK 282
Cdd:PRK13503 266 PR 267
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 239-289 1.71e-05

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 45.37  E-value: 1.71e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488866843 239 RLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKSKN 289
Cdd:PRK15185 258 RMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTFIKMAN 308
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 202-285 1.40e-04

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 42.74  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843  202 FVSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEfSKKNVNEIANECAFSSVAWFIERFKEKYNQTP 281
Cdd:TIGR04094 301 PLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLR-SQIPVSEVSNELGFYDLSHFSRTFKKHTGVSP 379


                  ....
gi 488866843  282 KQYQ 285
Cdd:TIGR04094 380 KQYQ 383
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
188-286 1.52e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 42.58  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 188 RLDL--SQLFEYCGREFvsvsEMADFA---KLDFATFSREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECA 262
Cdd:PRK13501 177 QLDLimSALQQSLGAYF----DMADFChknQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCG 252

                         90       100
                 ....*....|....*....|....
gi 488866843 263 FSSVAWFIERFKEKYNQTPKQYQK 286
Cdd:PRK13501 253 FEDSNYFSAVFTREAGMTPRDYRQ 276
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 220-287 3.55e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 41.28  E-value: 3.55e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488866843 220 SREFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKS 287
Cdd:PRK10296 206 TRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKK 273
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 228-285 5.36e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 40.68  E-value: 5.36e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488866843 228 GQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQ 285
Cdd:PRK09978 183 ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQ 240
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
166-285 7.85e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 40.47  E-value: 7.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488866843 166 LHLLLNKNTYFIGFLAGILKEFRLD--LSQLFEYCGREFvSVSEMADFAKLDFATFSREFKKCFGQSPKKWLDEKRLQKA 243
Cdd:PRK13500 185 LVMLLNRHRYTSDSLPPTSSETLLDklITRLAASLKSPF-ALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHA 263

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 488866843 244 KVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQ 285
Cdd:PRK13500 264 QYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 305
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 250-286 1.22e-03

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: 35.98  E-value: 1.22e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 488866843  250 SKKNVNEIANECAFSSvAWFIERFKEKYNQTPKQYQK 286
Cdd:pfam00165   7 TNLTIADIADELGFSR-SYFSRLFKKYTGVTPSQYRH 42
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
221-289 3.35e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.50  E-value: 3.35e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488866843 221 REFKKCFGQSPKKWLDEKRLQKAKVLLEFSKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQKSKN 289
Cdd:PRK13502 211 QQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLSN 279
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 235-286 5.38e-03

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 37.76  E-value: 5.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488866843 235 LDEKRLQKAKVLLEFsKKNVNEIANECAFSSVAWFIERFKEKYNQTPKQYQK 286
Cdd:PRK09940 182 LLDARMQHAKNLIRV-EGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSK 232
 
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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