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Conserved domains on  [gi|2524451297|ref|WP_286591761|]
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AraC family transcriptional regulator [Citrobacter sp. Cpo061]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09978 super family cl31382
DNA-binding transcriptional regulator GadX; Provisional
 55-253 3.45e-47

DNA-binding transcriptional regulator GadX; Provisional


The actual alignment was detected with superfamily member PRK09978:

Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 157.78  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSTSPVMTAACLTPDVFRVAAQHSVMDTVNEAERERTRSLLFTVLSRFLDSKK 134
Cdd:PRK09978   51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 135 FISLLMYMLRNCISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978  131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2524451297 215 QVSQLCGYNSTSYFISVFKEFYGMTPLHYV--SQHREPSAA 253
Cdd:PRK09978  211 RVAVSCGYHSVSYFIYVFRNYYGMTPTEYQerSAQGLPNRD 251
 
Name Accession Description Interval E-value
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 55-253 3.45e-47

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 157.78  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSTSPVMTAACLTPDVFRVAAQHSVMDTVNEAERERTRSLLFTVLSRFLDSKK 134
Cdd:PRK09978   51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 135 FISLLMYMLRNCISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978  131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2524451297 215 QVSQLCGYNSTSYFISVFKEFYGMTPLHYV--SQHREPSAA 253
Cdd:PRK09978  211 RVAVSCGYHSVSYFIYVFRNYYGMTPTEYQerSAQGLPNRD 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
162-243 5.34e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.85  E-value: 5.34e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  162 DWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 2524451297  241 LHY 243
Cdd:smart00342  81 SEY 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
164-248 2.02e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.75  E-value: 2.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 164 NLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLH 242
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                  ....*.
gi 2524451297 243 YVSQHR 248
Cdd:COG2207   250 YRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
168-243 7.75e-14

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 64.92  E-value: 7.75e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2524451297 168 VASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLL-MDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHY 243
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
 
Name Accession Description Interval E-value
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 55-253 3.45e-47

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 157.78  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSTSPVMTAACLTPDVFRVAAQHSVMDTVNEAERERTRSLLFTVLSRFLDSKK 134
Cdd:PRK09978   51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 135 FISLLMYMLRNCISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978  131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2524451297 215 QVSQLCGYNSTSYFISVFKEFYGMTPLHYV--SQHREPSAA 253
Cdd:PRK09978  211 RVAVSCGYHSVSYFIYVFRNYYGMTPTEYQerSAQGLPNRD 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
162-243 5.34e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.85  E-value: 5.34e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  162 DWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 2524451297  241 LHY 243
Cdd:smart00342  81 SEY 83
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 84-245 5.71e-23

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 94.75  E-value: 5.71e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297  84 TSPVmTAACLTPDVFRVAAQHSVMDTVNEAER---ERTRSLLFTVLSRFLDSKKFISLLMYMLRNCISDSVYHIIESDIH 160
Cdd:PRK15186  117 TKPT-TKHLLAPIETGVARVFNLLHSSNKSQKlsqDKKEYLIRFLLSEFIYEPEAFALFRELSQNTLAENIYNIIISDIS 195

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 161 KDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:PRK15186  196 RKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTP 275


                  ....*
gi 2524451297 241 LHYVS 245
Cdd:PRK15186  276 SEFLA 280
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 110-248 3.41e-21

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 89.37  E-value: 3.41e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 110 VNEAERER---TRSLLFTVLSRFLDSKKFISLLMYMLRNcISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSE 186
Cdd:PRK09940   96 LNSEERNHhnfSELLLFSCLSIFAACKGFITLLTNGVLS-VSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524451297 187 NTSYSQIITTCRMRYAVNQLLMDGkNISQVSQLCGYNSTSYFISVFKEFYGMTPLHYVSQHR 248
Cdd:PRK09940  175 QTTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYR 235
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 112-240 7.30e-21

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 89.28  E-value: 7.30e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 112 EAERERTRSLLFtVLSRFLDSKKFISLLMYMLRNCISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYS 191
Cdd:PRK15185  173 ENEELIPYFLLF-LLTAFLRLPESYEIILSSAQITLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFS 251

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2524451297 192 QIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:PRK15185  252 DIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 122-244 1.34e-19

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 85.47  E-value: 1.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 122 LFTVLSRFLDSKKFISLLMYMLRNCISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRY 201
Cdd:PRK15044  168 LMYLISAFVRKPGGFDFLERAIKITTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYLDARMNQ 247

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2524451297 202 AVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHYV 244
Cdd:PRK15044  248 AIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITPLSFM 290
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
164-248 2.02e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.75  E-value: 2.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 164 NLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLH 242
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                  ....*.
gi 2524451297 243 YVSQHR 248
Cdd:COG2207   250 YRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
168-243 7.75e-14

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 64.92  E-value: 7.75e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2524451297 168 VASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLL-MDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHY 243
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 154-243 1.65e-07

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: 51.21  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 154 IIESDIHKDWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVnQLLMDGKNISQVSQLCGYNSTSYFISVF 232
Cdd:COG2169    92 LIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHtGVTPKAYARARRLLRAR-QLLQTGLSVTDAAYAAGFGSLSRFYEAF 170

                          90
                  ....*....|.
gi 2524451297 233 KEFYGMTPLHY 243
Cdd:COG2169   171 KKLLGMTPSAY 181
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 153-253 4.16e-07

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: 49.77  E-value: 4.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524451297 153 HIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISV 231
Cdd:COG4977   217 AWMEANLEEPLSVDELARRAGMSPRTLERRFRAAtGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRA 296

                          90       100
                  ....*....|....*....|..
gi 2524451297 232 FKEFYGMTPLHYVSQHREPSAA 253
Cdd:COG4977   297 FRRRFGVSPSAYRRRFRARAAA 318
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 192-243 1.41e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 42.05  E-value: 1.41e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2524451297 192 QIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHY 243
Cdd:PRK10296  219 QIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSY 270
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 207-243 2.38e-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: 37.90  E-value: 2.38e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2524451297 207 LMDGKNISQVSQLCGYnSTSYFISVFKEFYGMTPLHY 243
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQY 40
 
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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