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Conserved domains on  [gi|507084667|ref|WP_016155411|]
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MULTISPECIES: AraC family transcriptional regulator [Citrobacter]

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 6.50e-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: 157.01  E-value: 6.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSANPVMTAVCLTPDVFRVAAQYSVMDTMDEGESVRTRSLLFTVLSRFLGSKK 134
Cdd:PRK09978  51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 135 FISLLMHILRSRISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978 131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 507084667 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 6.50e-47

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 157.01  E-value: 6.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSANPVMTAVCLTPDVFRVAAQYSVMDTMDEGESVRTRSLLFTVLSRFLGSKK 134
Cdd:PRK09978  51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 135 FISLLMHILRSRISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978 131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 507084667 215 QVSQLCGYNSTSYFISVFKEFYGMTPLHYV--SQHREPSAA 253
Cdd:PRK09978 211 RVAVSCGYHSVSYFIYVFRNYYGMTPTEYQerSAQGLPNRD 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
162-243 7.05e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.85  E-value: 7.05e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667   162 DWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 507084667   241 LHY 243
Cdd:smart00342  81 SEY 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
164-248 3.26e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.36  E-value: 3.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 164 NLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLH 242
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 507084667 243 YVSQHR 248
Cdd:COG2207  250 YRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
168-243 1.00e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 64.53  E-value: 1.00e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507084667  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 6.50e-47

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 157.01  E-value: 6.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667  55 VVHISRDIIKDYLRFLNKDLSQIPLWQRSANPVMTAVCLTPDVFRVAAQYSVMDTMDEGESVRTRSLLFTVLSRFLGSKK 134
Cdd:PRK09978  51 FVLVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEH 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 135 FISLLMHILRSRISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNIS 214
Cdd:PRK09978 131 FIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIK 210

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 507084667 215 QVSQLCGYNSTSYFISVFKEFYGMTPLHYV--SQHREPSAA 253
Cdd:PRK09978 211 RVAVSCGYHSVSYFIYVFRNYYGMTPTEYQerSAQGLPNRD 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
162-243 7.05e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.85  E-value: 7.05e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667   162 DWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 507084667   241 LHY 243
Cdd:smart00342  81 SEY 83
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 121-248 2.19e-22

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 92.46  E-value: 2.19e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 121 LLFTVLSRFLGSKKFISLLMHILRSrISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMR 200
Cdd:PRK09940 110 LLFSCLSIFAACKGFITLLTNGVLS-VSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQ 188

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 507084667 201 YAVNQLLMDGkNISQVSQLCGYNSTSYFISVFKEFYGMTPLHYVSQHR 248
Cdd:PRK09940 189 HAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYR 235
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 112-240 5.43e-22

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 92.37  E-value: 5.43e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 112 EGESVRTRSLLFtVLSRFLGSKKFISLLMHILRSRISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYS 191
Cdd:PRK15185 173 ENEELIPYFLLF-LLTAFLRLPESYEIILSSAQITLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFS 251

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 507084667 192 QIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTP 240
Cdd:PRK15185 252 DIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 93-245 5.72e-22

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 92.05  E-value: 5.72e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667  93 LTPDVFRVAAQYSVMDTMDEGESV---RTRSLLFTVLSRFLGSKKFISLLMHILRSRISDSVYHIIESDIHKDWNLSMVA 169
Cdd:PRK15186 125 LAPIETGVARVFNLLHSSNKSQKLsqdKKEYLIRFLLSEFIYEPEAFALFRELSQNTLAENIYNIIISDISRKWALKDIS 204

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507084667 170 SCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHYVS 245
Cdd:PRK15186 205 DSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSEFLA 280
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 122-244 7.02e-20

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 86.24  E-value: 7.02e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 122 LFTVLSRFLGSKKFISLLMHILRSRISDSVYHIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRY 201
Cdd:PRK15044 168 LMYLISAFVRKPGGFDFLERAIKITTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYLDARMNQ 247

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 507084667 202 AVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLHYV 244
Cdd:PRK15044 248 AIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITPLSFM 290
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
164-248 3.26e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.36  E-value: 3.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507084667 164 NLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISVFKEFYGMTPLH 242
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 507084667 243 YVSQHR 248
Cdd:COG2207  250 YRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
168-243 1.00e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 64.53  E-value: 1.00e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507084667  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 507084667 154 IIESDIHKDWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVnQLLMDGKNISQVSQLCGYNSTSYFISVF 232
Cdd:COG2169   92 LIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHtGVTPKAYARARRLLRAR-QLLQTGLSVTDAAYAAGFGSLSRFYEAF 170

                         90
                 ....*....|.
gi 507084667 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 507084667 153 HIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSE-NTSYSQIITTCRMRYAVNQLLMDGKNISQVSQLCGYNSTSYFISV 231
Cdd:COG4977  217 AWMEANLEEPLSVDELARRAGMSPRTLERRFRAAtGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRA 296

                         90       100
                 ....*....|....*....|..
gi 507084667 232 FKEFYGMTPLHYVSQHREPSAA 253
Cdd:COG4977  297 FRRRFGVSPSAYRRRFRARAAA 318
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 192-243 1.35e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 42.44  E-value: 1.35e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 507084667 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 507084667  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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