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Conserved domains on  [gi|15595361|ref|NP_248853|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 18598964)

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

CATH:  2.60.120.10
Gene Ontology:  GO:0003677|GO:0003700|GO:0006355|GO:0043565
PubMed:  11264412|11282467|33837749|9409145|12270809|19478949|14697267|9573603
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 24-118 4.37e-36

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


:

Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 123.84  E-value: 4.37e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  24 VYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEVVTSTRAEMRSLYIRGDACAWA 103
Cdd:cd06124   1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                        90
                ....*....|....*
gi 15595361 104 PTRCRVLEVTPLARE 118
Cdd:cd06124  81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
3-265 5.87e-19

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 83.68  E-value: 5.87e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361   3 MNGQPAELHRPIPTLARLPRPVYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEV 82
Cdd:COG2207   2 RLLILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  83 VTSTRAEMRSLYIRGDACAWAPTRCRVLEVTPLARELIKSFCELPVDYPEGDSAESRLVQVLLDQLRLLPEVAFSLPMPR 162
Cdd:COG2207  82 LLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLL 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361 163 EPRLLRLcqalideptqsLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SVTGAALDSGYD 241
Cdd:COG2207 162 LLLLLLL-----------LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFS 230

                       250       260
                ....*....|....*....|....
gi 15595361 242 STSAYIAAFKGLFGFTPGELFRQR 265
Cdd:COG2207 231 SQSHFSRAFKKRFGVTPSEYRKRL 254
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 24-118 4.37e-36

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 123.84  E-value: 4.37e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  24 VYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEVVTSTRAEMRSLYIRGDACAWA 103
Cdd:cd06124   1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                        90
                ....*....|....*
gi 15595361 104 PTRCRVLEVTPLARE 118
Cdd:cd06124  81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
3-265 5.87e-19

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 83.68  E-value: 5.87e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361   3 MNGQPAELHRPIPTLARLPRPVYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEV 82
Cdd:COG2207   2 RLLILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  83 VTSTRAEMRSLYIRGDACAWAPTRCRVLEVTPLARELIKSFCELPVDYPEGDSAESRLVQVLLDQLRLLPEVAFSLPMPR 162
Cdd:COG2207  82 LLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLL 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361 163 EPRLLRLcqalideptqsLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SVTGAALDSGYD 241
Cdd:COG2207 162 LLLLLLL-----------LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFS 230

                       250       260
                ....*....|....*....|....
gi 15595361 242 STSAYIAAFKGLFGFTPGELFRQR 265
Cdd:COG2207 231 SQSHFSRAFKKRFGVTPSEYRKRL 254
HTH_18 pfam12833
Helix-turn-helix domain;
186-264 1.11e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.02  E-value: 1.11e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361   186 WAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNAL--EAGDSVTGAALDSGYDSTSAYIAAFKGLFGFTPGELFR 263
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLleDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 15595361   264 Q 264
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
181-261 3.04e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 3.04e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361    181 LTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SVTGAALDSGYDSTSAYIAAFKGLFGFTPG 259
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 15595361    260 EL 261
Cdd:smart00342  82 EY 83
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
16-95 1.68e-08

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.00  E-value: 1.68e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  16 TLARLPRPVYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEVVTSTRAEMRSLYI 95
Cdd:COG1917  15 VLADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVV 94
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 161-265 1.42e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 51.57  E-value: 1.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  161 PREPRLLRLCQALIDEPTQS--LTMGDWAQRLGTSEKTLSRLFQREtGMNYRLWRQRQRL---LASLNALEAGDSVTGAA 235
Cdd:PRK09685 193 PRRERQFQKVVALIDQSIQEeiLRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLdrcADDLRPAADDEKITSIA 271

                         90       100       110
                 ....*....|....*....|....*....|
gi 15595361  236 LDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:PRK09685 272 YKWGFSDSSHFSTAFKQRFGVSPGE-YRRK 300
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 37-169 6.11e-04

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 38.96  E-value: 6.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361    37 TSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEH--EVVTSTRAEMRSLYIRGDAcawaptrcrvLEVTP 114
Cdd:pfam02311  16 FPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHdyEPESEDGWRYRWLYFEPEL----------LERIL 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595361   115 LARELIKSFCELPVDYPEgdsaesrlVQVLLDQL-RLLPEVAFSLPMPREPRLLRL 169
Cdd:pfam02311  86 ADISILAGGPLPLLRDPE--------LAALLRALfRLLEEAGRSDDLLAEALLYQL 133
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 24-118 4.37e-36

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 123.84  E-value: 4.37e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  24 VYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEVVTSTRAEMRSLYIRGDACAWA 103
Cdd:cd06124   1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                        90
                ....*....|....*
gi 15595361 104 PTRCRVLEVTPLARE 118
Cdd:cd06124  81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
3-265 5.87e-19

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 83.68  E-value: 5.87e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361   3 MNGQPAELHRPIPTLARLPRPVYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEV 82
Cdd:COG2207   2 RLLILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  83 VTSTRAEMRSLYIRGDACAWAPTRCRVLEVTPLARELIKSFCELPVDYPEGDSAESRLVQVLLDQLRLLPEVAFSLPMPR 162
Cdd:COG2207  82 LLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLL 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361 163 EPRLLRLcqalideptqsLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SVTGAALDSGYD 241
Cdd:COG2207 162 LLLLLLL-----------LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFS 230

                       250       260
                ....*....|....*....|....
gi 15595361 242 STSAYIAAFKGLFGFTPGELFRQR 265
Cdd:COG2207 231 SQSHFSRAFKKRFGVTPSEYRKRL 254
HTH_18 pfam12833
Helix-turn-helix domain;
186-264 1.11e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.02  E-value: 1.11e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361   186 WAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNAL--EAGDSVTGAALDSGYDSTSAYIAAFKGLFGFTPGELFR 263
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLleDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 15595361   264 Q 264
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
181-261 3.04e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 3.04e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361    181 LTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SVTGAALDSGYDSTSAYIAAFKGLFGFTPG 259
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 15595361    260 EL 261
Cdd:smart00342  82 EY 83
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 148-261 3.22e-18

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: 82.79  E-value: 3.22e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361 148 LRLLPEvAFSLPMPREPRLLRLCQALIDEPTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEA 227
Cdd:COG2169  69 KRCRPD-LAPGSPPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQT 147

                        90       100       110
                ....*....|....*....|....*....|....
gi 15595361 228 GDSVTGAALDSGYDSTSAYIAAFKGLFGFTPGEL 261
Cdd:COG2169 148 GLSVTDAAYAAGFGSLSRFYEAFKKLLGMTPSAY 181
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 154-265 1.07e-14

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: 72.50  E-value: 1.07e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361 154 VAFSLPMPREPRLLRLCQALIDE-PTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGD-SV 231
Cdd:COG4977 199 SPLLVPLGHRDPRLARAQAWMEAnLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDlSI 278

                        90       100       110
                ....*....|....*....|....*....|....
gi 15595361 232 TGAALDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:COG4977 279 EEIAAACGFGSASHFRRAFRRRFGVSPSA-YRRR 311
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
16-95 1.68e-08

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.00  E-value: 1.68e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  16 TLARLPRPVYARAESLRAGSWTSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEHEVVTSTRAEMRSLYI 95
Cdd:COG1917  15 VLADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVV 94
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 161-265 1.42e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 51.57  E-value: 1.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  161 PREPRLLRLCQALIDEPTQS--LTMGDWAQRLGTSEKTLSRLFQREtGMNYRLWRQRQRL---LASLNALEAGDSVTGAA 235
Cdd:PRK09685 193 PRRERQFQKVVALIDQSIQEeiLRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLdrcADDLRPAADDEKITSIA 271

                         90       100       110
                 ....*....|....*....|....*....|
gi 15595361  236 LDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:PRK09685 272 YKWGFSDSSHFSTAFKQRFGVSPGE-YRRK 300
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
161-246 5.11e-07

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 50.18  E-value: 5.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  161 PREPRLLRLCQAL-IDEPTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGDSVTGAALDSG 239
Cdd:PRK15435  79 PQQHRLDKITHACrLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTSILNAG 158


                 ....*..
gi 15595361  240 YDSTSAY 246
Cdd:PRK15435 159 FPDSSSY 165
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 173-214 1.46e-06

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: 44.07  E-value: 1.46e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 15595361   173 LIDEPTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQ 214
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
ftrA PRK09393
transcriptional activator FtrA; Provisional
 159-259 1.68e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 48.42  E-value: 1.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  159 PMPREP--RLLRLCQALIDEPTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEA-GDSVTGAA 235
Cdd:PRK09393 211 PVASREsdRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESsALSIDQIA 290

                         90       100
                 ....*....|....*....|....
gi 15595361  236 LDSGYDSTSAYIAAFKGLFGFTPG 259
Cdd:PRK09393 291 ERAGFGSEESLRHHFRRRAATSPA 314
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
140-265 5.05e-05

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 43.81  E-value: 5.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  140 LVQVLLDQLRLLPEvafSLPMPREPRLLRLCQALIDEPTQSLTMGDWAQRLGTSEKTLSRLFQRETGMNYRLWRQRQRLL 219
Cdd:PRK10572 162 LERLLLRCMEAIPE---SLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRIS 238

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15595361  220 -ASLNALEAGDSVTGAALDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:PRK10572 239 rAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSE-FRAR 284
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 168-258 3.52e-04

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 41.13  E-value: 3.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  168 RLCQALIDEPTQSLTMGDWAQRLGTSEKTLSRLFQRE-TGMNYRLWRQRQRLLASLnaLEAGD-SVTGAALDSGYDSTSA 245
Cdd:PRK15185 210 RVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEgTSFSDIYLSARMNQAAKL--LRIGNhNVNAVALKCGYDSTSY 287

                         90
                 ....*....|...
gi 15595361  246 YIAAFKGLFGFTP 258
Cdd:PRK15185 288 FIQCFKKYFKTTP 300
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 37-169 6.11e-04

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 38.96  E-value: 6.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361    37 TSRHRHAWVQLSYAISGVLGVHTAEGSFFAPPQRAIWIPAQLEH--EVVTSTRAEMRSLYIRGDAcawaptrcrvLEVTP 114
Cdd:pfam02311  16 FPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHdyEPESEDGWRYRWLYFEPEL----------LERIL 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595361   115 LARELIKSFCELPVDYPEgdsaesrlVQVLLDQL-RLLPEVAFSLPMPREPRLLRL 169
Cdd:pfam02311  86 ADISILAGGPLPLLRDPE--------LAALLRALfRLLEEAGRSDDLLAEALLYQL 133
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
115-265 1.52e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 39.12  E-value: 1.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595361  115 LARELIKsfcELPVDYPEGDSAESRLVQVLLDQLRLL-------PEVAFSLPMPREPRLLRlcQALIDEPTQSLTMGDWA 187
Cdd:PRK13501 125 QARPIIQ---QLAQESRKTDSWSIQLTEVLLLQLAIVlkrhryrAEQAHLLPDGEQLDLIM--SALQQSLGAYFDMADFC 199

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15595361  188 QRLGTSEKTLSRLFQRETGMNYRLWRQRQRLLASLNALEAGDSVTG-AALDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:PRK13501 200 HKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISdIAARCGFEDSNYFSAVFTREAGMTPRD-YRQR 277
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 230-265 4.12e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 37.81  E-value: 4.12e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 15595361  230 SVTGAALDSGYDSTSAYIAAFKGLFGFTPGElFRQR 265
Cdd:PRK10296 239 SVTDIAFEAGYSSPSLFIKTFKKLTSFTPGS-YRKK 273
 
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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