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Conserved domains on  [gi|1396632001|gb|PXM31766|]
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AraC family transcriptional regulator [Klebsiella variicola]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 1001832)

helix-turn-helix domain-containing protein similar to DNA-binding transcriptional activator FeaR, which is a positive regulator of tynA/maoA and feaB/padA, the genes for 2-phenylethylamine catabolism

Gene Ontology:  GO:0003700|GO:0003677
PubMed:  15808743|10473770

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09685 super family cl35885
DNA-binding transcriptional activator FeaR; Provisional
 47-310 5.27e-19

DNA-binding transcriptional activator FeaR; Provisional


The actual alignment was detected with superfamily member PRK09685:

Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 85.47  E-value: 5.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  47 FDAR-LTVRGVGLVDMCSLSA-PLHSWDRTARYLRQGP-----DDDLW--LGYMQDGYGQLEQGGRKATLAADSLVLYDA 117
Cdd:PRK09685   24 FDGRpLTNRFIGELSTHDAGGlKLSTVTTNAVNLSRTWqeikhSDDAHffTVFQLSGHAIIEQDDRQVQLAAGDITLIDA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 118 AQTFRFSLGGRDNHL-VRIPRHLLSCHLPGVEHLTAMVLDDRRPGVIPLREMLRQaaampaCLNTADISGRFSQTLLDLL 196
Cdd:PRK09685  104 SRPCSIYPQGLSEQIsLLLPRELVEQYFPGQKPACAGRLSASLPMVQLSHRLLQQ------SMNGPALSETESEALLEAL 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 197 VL--SLELQDLNNV--GVERDLySRMMNYIRRQLVDPDLNIESLARAHHVSVRTVTRAFARHKKTPMAVIWQERLQASRE 272
Cdd:PRK09685  178 IAllRPALHQRESVqpRRERQF-QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCAD 256

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1396632001 273 AIE-RGRVSSVSQAALDFGFSDFSHFSHAFRKAFGISPR 310
Cdd:PRK09685  257 DLRpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPG 295
 
Name Accession Description Interval E-value
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 47-310 5.27e-19

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 85.47  E-value: 5.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  47 FDAR-LTVRGVGLVDMCSLSA-PLHSWDRTARYLRQGP-----DDDLW--LGYMQDGYGQLEQGGRKATLAADSLVLYDA 117
Cdd:PRK09685   24 FDGRpLTNRFIGELSTHDAGGlKLSTVTTNAVNLSRTWqeikhSDDAHffTVFQLSGHAIIEQDDRQVQLAAGDITLIDA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 118 AQTFRFSLGGRDNHL-VRIPRHLLSCHLPGVEHLTAMVLDDRRPGVIPLREMLRQaaampaCLNTADISGRFSQTLLDLL 196
Cdd:PRK09685  104 SRPCSIYPQGLSEQIsLLLPRELVEQYFPGQKPACAGRLSASLPMVQLSHRLLQQ------SMNGPALSETESEALLEAL 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 197 VL--SLELQDLNNV--GVERDLySRMMNYIRRQLVDPDLNIESLARAHHVSVRTVTRAFARHKKTPMAVIWQERLQASRE 272
Cdd:PRK09685  178 IAllRPALHQRESVqpRRERQF-QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCAD 256

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1396632001 273 AIE-RGRVSSVSQAALDFGFSDFSHFSHAFRKAFGISPR 310
Cdd:PRK09685  257 DLRpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPG 295
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
230-313 2.40e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 77.98  E-value: 2.40e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  230 DLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSsVSQAALDFGFSDFSHFSHAFRKAFGIS 308
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETgTTPKQYLRDRRLERARRLLRDTDLS-VTEIALRVGFSSQSYFSRAFKKLFGVT 79


                   ....*
gi 1396632001  309 PRSLL 313
Cdd:smart00342  80 PSEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
68-310 9.52e-17

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 78.67  E-value: 9.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  68 LHSWDRTARYLRQGPDDDLWLGYMQDGYGQLEQGGRKATLAADSLVLYDAAQTFRFSLGGRDNHLVRIPRHLLSCHLPGV 147
Cdd:COG2207     6 LLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 148 EHLTAMVLDDRRPGVIPLREMLRQAAAMPACLNTADISGRFSQTLLDLLVLSLELQDLNNVGVERDLYSRMMNYIRRQLV 227
Cdd:COG2207    86 LALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 228 DPDLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSsVSQAALDFGFSDFSHFSHAFRKAFG 306
Cdd:COG2207   166 LLLLTLEELARELGLSPRTLSRLFKEETgTSPKQYLRELRLERAKRLLAETDLS-ISEIAYELGFSSQSHFSRAFKKRFG 244


                  ....
gi 1396632001 307 ISPR 310
Cdd:COG2207   245 VTPS 248
HTH_18 pfam12833
Helix-turn-helix domain;
236-310 4.00e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 69.16  E-value: 4.00e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1396632001 236 LARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSSVSQAALDFGFSDFSHFSHAFRKAFGISPR 310
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELgLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPS 76
 
Name Accession Description Interval E-value
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 47-310 5.27e-19

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 85.47  E-value: 5.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  47 FDAR-LTVRGVGLVDMCSLSA-PLHSWDRTARYLRQGP-----DDDLW--LGYMQDGYGQLEQGGRKATLAADSLVLYDA 117
Cdd:PRK09685   24 FDGRpLTNRFIGELSTHDAGGlKLSTVTTNAVNLSRTWqeikhSDDAHffTVFQLSGHAIIEQDDRQVQLAAGDITLIDA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 118 AQTFRFSLGGRDNHL-VRIPRHLLSCHLPGVEHLTAMVLDDRRPGVIPLREMLRQaaampaCLNTADISGRFSQTLLDLL 196
Cdd:PRK09685  104 SRPCSIYPQGLSEQIsLLLPRELVEQYFPGQKPACAGRLSASLPMVQLSHRLLQQ------SMNGPALSETESEALLEAL 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 197 VL--SLELQDLNNV--GVERDLySRMMNYIRRQLVDPDLNIESLARAHHVSVRTVTRAFARHKKTPMAVIWQERLQASRE 272
Cdd:PRK09685  178 IAllRPALHQRESVqpRRERQF-QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCAD 256

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1396632001 273 AIE-RGRVSSVSQAALDFGFSDFSHFSHAFRKAFGISPR 310
Cdd:PRK09685  257 DLRpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPG 295
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
230-313 2.40e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 77.98  E-value: 2.40e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  230 DLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSsVSQAALDFGFSDFSHFSHAFRKAFGIS 308
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETgTTPKQYLRDRRLERARRLLRDTDLS-VTEIALRVGFSSQSYFSRAFKKLFGVT 79


                   ....*
gi 1396632001  309 PRSLL 313
Cdd:smart00342  80 PSEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
68-310 9.52e-17

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 78.67  E-value: 9.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  68 LHSWDRTARYLRQGPDDDLWLGYMQDGYGQLEQGGRKATLAADSLVLYDAAQTFRFSLGGRDNHLVRIPRHLLSCHLPGV 147
Cdd:COG2207     6 LLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 148 EHLTAMVLDDRRPGVIPLREMLRQAAAMPACLNTADISGRFSQTLLDLLVLSLELQDLNNVGVERDLYSRMMNYIRRQLV 227
Cdd:COG2207    86 LALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 228 DPDLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSsVSQAALDFGFSDFSHFSHAFRKAFG 306
Cdd:COG2207   166 LLLLTLEELARELGLSPRTLSRLFKEETgTSPKQYLRELRLERAKRLLAETDLS-ISEIAYELGFSSQSHFSRAFKKRFG 244


                  ....
gi 1396632001 307 ISPR 310
Cdd:COG2207   245 VTPS 248
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 209-310 1.28e-15

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: 75.96  E-value: 1.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 209 GVERDLYSRMMNYIRRQLVDPdLNIESLARAHHVSVRTVTRAFARH-KKTPMAVIWQERLQASREAIERGRvSSVSQAAL 287
Cdd:COG4977   206 GHRDPRLARAQAWMEANLEEP-LSVDELARRAGMSPRTLERRFRAAtGTTPARYLQRLRLERARRLLETTD-LSIEEIAA 283

                          90       100
                  ....*....|....*....|...
gi 1396632001 288 DFGFSDFSHFSHAFRKAFGISPR 310
Cdd:COG4977   284 ACGFGSASHFRRAFRRRFGVSPS 306
HTH_18 pfam12833
Helix-turn-helix domain;
236-310 4.00e-15

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 69.16  E-value: 4.00e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1396632001 236 LARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRVSSVSQAALDFGFSDFSHFSHAFRKAFGISPR 310
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELgLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPS 76
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 213-312 2.26e-11

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: 63.92  E-value: 2.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 213 DLYSRMMNYIRRQLVDPdLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIERGRvsSVSQAALDFGF 291
Cdd:COG2169    84 DLVARACRLIEAGAEDR-PSLEDLAARLGLSPRHLRRLFKAHTgVTPKAYARARRLLRARQLLQTGL--SVTDAAYAAGF 160

                          90       100
                  ....*....|....*....|.
gi 1396632001 292 SDFSHFSHAFRKAFGISPRSL 312
Cdd:COG2169   161 GSLSRFYEAFKKLLGMTPSAY 181
AraC_binding_2 pfam14525
AraC-binding-like domain; This domain is related to the AraC ligand binding domain pfam02311.
 26-174 2.49e-11

AraC-binding-like domain; This domain is related to the AraC ligand binding domain pfam02311.


Pssm-ID: 434015  Cd Length: 173  Bit Score: 61.17  E-value: 2.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001  26 WNDVVLRHCIPAASAPLAGVDFDARLTVRGVGLVDMCSLSAPlhswdrTARYLRQGPDDDLWLGYMQ-DGYGQLEQGGRK 104
Cdd:pfam14525   1 WREAVSRAFGPHRLRPLGPDRFDARLRGVRLGGLSLGRLRYG------AAVHIRPPELDDFYLLQLPlSGSAEIEQGGRE 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1396632001 105 ATLAADSLVLYDAAQTFRFSLGGRDNHL-VRIPRHLLSCHLPGVEHLTAMVLDDRRPGVIPLREMLRQAAA 174
Cdd:pfam14525  75 VVLGPGDAVLLDPGRPYRLRWSEDCEQLvLRIPLRALLGRPLRRPLRFAPRLDLDSGLGALWLRLLRLLAA 145
ftrA PRK09393
transcriptional activator FtrA; Provisional
 211-309 1.35e-07

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 52.27  E-value: 1.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 211 ERDLYSRMMNYIRRQLVDPdLNIESLARAHHVSVRTVTRAF-ARHKKTPMAVIWQERLQASREAIERGRVSsVSQAALDF 289
Cdd:PRK09393  216 ESDRLGPLIDWMRAHLAEP-HTVASLAARAAMSPRTFLRRFeAATGMTPAEWLLRERLARARDLLESSALS-IDQIAERA 293

                          90       100
                  ....*....|....*....|
gi 1396632001 290 GFSDFSHFSHAFRKAFGISP 309
Cdd:PRK09393  294 GFGSEESLRHHFRRRAATSP 313
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
230-312 3.53e-07

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 50.83  E-value: 3.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 230 DLNIESLARAHHVSVRTVTRAFARHK-KTPMAVIWQERLQASREAIeRGRVSSVSQAALDFGFSDFSHFSHAFRKAFGIS 308
Cdd:PRK13503  187 EVNWEALADQFSLSLRTLHRQLKQQTgLTPQRYLNRLRLLKARHLL-RHSDASVTDIAYRCGFGDSNHFSTLFRREFSWS 265


                  ....
gi 1396632001 309 PRSL 312
Cdd:PRK13503  266 PRDI 269
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 281-313 1.90e-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: 35.59  E-value: 1.90e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1396632001 281 SVSQAALDFGFSDfSHFSHAFRKAFGISPRSLL 313
Cdd:pfam00165  10 TIADIADELGFSR-SYFSRLFKKYTGVTPSQYR 41
PRK10130 PRK10130
HTH-type transcriptional regulator EutR;
212-313 3.05e-03

HTH-type transcriptional regulator EutR;


Pssm-ID: 182258 [Multi-domain]  Cd Length: 350  Bit Score: 38.75  E-value: 3.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396632001 212 RDLYSRMMNYIRRQLVDPdLNIESLARAHHVSVRTVTRAF-ARHKKTPMAVIWQERLQA-SREAIER-GRVSSVSQAALD 288
Cdd:PRK10130  239 RRLLSRAREYVLENMSEP-VTVLDLCNQLHVSRRTLQNAFhAILGIGPNAWLKRIRLNAvRRELISPwSQSTTVKDAAMQ 317

                          90       100
                  ....*....|....*....|....*
gi 1396632001 289 FGFSDFSHFSHAFRKAFGISPRSLL 313
Cdd:PRK10130  318 WGFWHLGQFATDYQQLFAEKPSLTL 342
 
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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