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The query sequence YP_669403.1 may be preliminary or obsolete. For more information, check Entrez.
Conserved domains on  [gi|110641673|ref|YP_669403.1|]
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transcriptional regulator YdeO [Escherichia coli 536]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 11484528)

AraC family transcriptional regulator controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 1-253 7.33e-180

transcriptional regulator YdeO; Provisional


:

Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 493.83  E-value: 7.33e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80
Cdd:PRK09940   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160
Cdd:PRK09940  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240
Cdd:PRK09940 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240

                        250
                 ....*....|...
gi 110641673 241 GMNTDNTMNALAI 253
Cdd:PRK09940 241 GMNTGNTMSALAI 253
 
Name Accession Description Interval E-value
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 1-253 7.33e-180

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 493.83  E-value: 7.33e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80
Cdd:PRK09940   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160
Cdd:PRK09940  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240
Cdd:PRK09940 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240

                        250
                 ....*....|...
gi 110641673 241 GMNTDNTMNALAI 253
Cdd:PRK09940 241 GMNTGNTMSALAI 253
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
150-235 1.82e-27

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 100.71  E-value: 1.82e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673   150 PWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRV-EGSVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDtDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....*...
gi 110641673   228 krvsKEYR 235
Cdd:smart00342  81 ----SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
152-235 2.33e-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: 2.33e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 152 KLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKR 229
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 110641673 230 VSKEYR 235
Cdd:COG2207  250 YRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
156-235 3.06e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 68.77  E-value: 3.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673  156 ICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEG--SVNKIAEQCGYASTSYFIYAFRKHFGNSPkrvsK 232
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEDTglSVAEIALALGFSDASHFSRAFRRLFGLTP----S 76


                  ...
gi 110641673  233 EYR 235
Cdd:pfam12833  77 EYR 79
 
Name Accession Description Interval E-value
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 1-253 7.33e-180

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 493.83  E-value: 7.33e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80
Cdd:PRK09940   1 MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFNENTIKKYLQCTNIQTVTVPVPAKFLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160
Cdd:PRK09940  81 ASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240
Cdd:PRK09940 161 YISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQRHT 240

                        250
                 ....*....|...
gi 110641673 241 GMNTDNTMNALAI 253
Cdd:PRK09940 241 GMNTGNTMSALAI 253
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 110-250 1.87e-29

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 111.56  E-value: 1.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 110 LLFSCLSIFAACKGFITLLTNgVL--SVSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARM 187
Cdd:PRK09978 117 LIFALLSVFLEDEHFIPLLLN-VLqpNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRM 195

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 110641673 188 QHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVsKEYRCQRHTGMNTDNTMNA 250
Cdd:PRK09978 196 QRALQLIVIHGfSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEY-QERSAQGLPNRDSAASIVA 258
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
150-235 1.82e-27

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 100.71  E-value: 1.82e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673   150 PWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRV-EGSVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDtDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....*...
gi 110641673   228 krvsKEYR 235
Cdd:smart00342  81 ----SEYR 84
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 134-243 4.81e-22

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 92.44  E-value: 4.81e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 134 SVSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIR-VEGSVNKIAEQCGYAST 212
Cdd:PRK15186 181 TLAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRnSEYNITRVAYMCGYDSA 260

                         90       100       110
                 ....*....|....*....|....*....|.
gi 110641673 213 SYFIYAFRKHFGNSPKRVSKEYRCQRHTGMN 243
Cdd:PRK15186 261 SYFTCVFKKHFKTTPSEFLAFLSSSRHQYVN 291
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 127-227 5.32e-22

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 92.37  E-value: 5.32e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 127 LLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRV-EGSVNKIAE 205
Cdd:PRK15185 199 ILSSAQITLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSDIYLSARMNQAAKLLRIgNHNVNAVAL 278

                         90       100
                 ....*....|....*....|..
gi 110641673 206 QCGYASTSYFIYAFRKHFGNSP 227
Cdd:PRK15185 279 KCGYDSTSYFIQCFKKYFKTTP 300
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
152-235 2.33e-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: 2.33e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 152 KLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKR 229
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 110641673 230 VSKEYR 235
Cdd:COG2207  250 YRKRLR 255
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 102-227 9.15e-17

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 77.77  E-value: 9.15e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 102 NHHNFSELLLFSCLSIFAACKGFITLLTNGV-LSVSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQ 180
Cdd:PRK15044 159 DDHDYSYFSLMYLISAFVRKPGGFDFLERAIkITTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSK 238

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 110641673 181 ILLDARMQHAKNLIRV-EGSVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
Cdd:PRK15044 239 IYLDARMNQAIKLLRMgAGNISQVATMCGYDTPSYFIAIFKRHFKITP 286
HTH_18 pfam12833
Helix-turn-helix domain;
156-235 3.06e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 68.77  E-value: 3.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673  156 ICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEG--SVNKIAEQCGYASTSYFIYAFRKHFGNSPkrvsK 232
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEDTglSVAEIALALGFSDASHFSRAFRRLFGLTP----S 76


                  ...
gi 110641673  233 EYR 235
Cdd:pfam12833  77 EYR 79
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 149-235 6.84e-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: 58.53  E-value: 6.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 149 HPWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
Cdd:COG2169   99 DRPSLEDLAARLGLSPRHLRRLFKAHtGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAGFGSLSRFYEAFKKLLGMTP 178


                 ....*...
gi 110641673 228 krvsKEYR 235
Cdd:COG2169  179 ----SAYR 182
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 147-235 3.51e-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: 56.32  E-value: 3.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 147 LAHPWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFG 224
Cdd:COG4977  223 LEEPLSVDELARRAGMSPRTLERRFRAAtGTTPARYLQRLRLERARRLLETTDlSIEEIAAACGFGSASHFRRAFRRRFG 302

                         90
                 ....*....|.
gi 110641673 225 NSPkrvsKEYR 235
Cdd:COG4977  303 VSP----SAYR 309
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
147-243 8.06e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 46.05  E-value: 8.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 147 LAHPWKLKDICDCLYISESLLKKKLKQeQT--TFSQILLDARMQHAKNLIRV-EGSVNKIAEQCGYASTSYFIYAFRKHF 223
Cdd:PRK13501 189 LGAYFDMADFCHKNQLVERSLKQLFRQ-QTgmSISHYLRQIRLCHAKCLLRGsEHRISDIAARCGFEDSNYFSAVFTREA 267

                         90       100
                 ....*....|....*....|.
gi 110641673 224 GNSPKRVSKEY-RCQRHTGMN 243
Cdd:PRK13501 268 GMTPRDYRQRFiRSPVLPAKN 288
ftrA PRK09393
transcriptional activator FtrA; Provisional
 182-227 9.10e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 46.11  E-value: 9.10e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 110641673 182 LLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
Cdd:PRK09393 267 LLRERLARARDLLESSAlSIDQIAERAGFGSEESLRHHFRRRAATSP 313
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
147-229 3.48e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 44.32  E-value: 3.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 147 LAHPWKLKDICDCLYISESLLKKKLKQEQ-TTFSQILLDARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFG 224
Cdd:PRK13500 219 LKSPFALDKFCDEASCSERVLRQQFRQQTgMTINQYLRQVRVCHAQYLLQhSRLLISDISTECGFEDSNYFSVVFTRETG 298


                 ....*
gi 110641673 225 NSPKR 229
Cdd:PRK13500 299 MTPSQ 303
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
138-229 3.59e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 43.89  E-value: 3.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQ-TTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYF 215
Cdd:PRK13502 180 KLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTgMTINQYLRQVRICHAQYLLQHSPlMISEISMQCGFEDSNYF 259

                         90
                 ....*....|....
gi 110641673 216 IYAFRKHFGNSPKR 229
Cdd:PRK13502 260 SVVFTRETGMTPSQ 273
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
167-228 5.50e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 40.43  E-value: 5.50e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110641673 167 LKKKLKQeQT--TFSQILLDARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPK 228
Cdd:PRK13503 204 LHRQLKQ-QTglTPQRYLNRLRLLKARHLLRhSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPR 267
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 199-235 5.79e-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: 36.75  E-value: 5.79e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 110641673  199 SVNKIAEQCGYaSTSYFIYAFRKHFGNSPkrvsKEYR 235
Cdd:pfam00165  10 TIADIADELGF-SRSYFSRLFKKYTGVTP----SQYR 41
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
164-238 5.80e-04

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 40.15  E-value: 5.80e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110641673 164 ESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYaSTSYFIYAFRKHFGNSPKRVSKEYRCQR 238
Cdd:COG2207  135 ELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGL-SPRTLSRLFKEETGTSPKQYLRELRLER 208
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
141-235 8.77e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 39.96  E-value: 8.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110641673 141 NIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEqtTFSQILL---DARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFI 216
Cdd:PRK10572 190 QYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQ--LGISVLRwreDQRISRAKLLLQTTRmPIATIGRNVGYDDQLYFS 267

                         90
                 ....*....|....*....
gi 110641673 217 YAFRKHFGNSPkrvsKEYR 235
Cdd:PRK10572 268 RVFKKCTGASP----SEFR 282
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 147-182 2.92e-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: 34.82  E-value: 2.92e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 110641673  147 LAHPWKLKDICDCLYISESLLKKKLKQE-QTTFSQIL 182
Cdd:pfam00165   5 LSTNLTIADIADELGFSRSYFSRLFKKYtGVTPSQYR 41
 
Blast search parameters
Data Source: Live blast search RID = PWKP8PJ3016
User Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01   Maximum number of hits: 500

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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