Conserved Protein Domain Family
PBP1_AraR

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cd01541: PBP1_AraR 
Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators
Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Statistics
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PSSM-Id: 107254
View PSSM: cd01541
Aligned: 26 rows
Threshold Bit Score: 338.386
Threshold Setting Gi: 160901785
Created: 1-Jul-2004
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative ligandputative
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on sequence similarity to other members of the LacI family.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    ##  #                                             #                 
gi 28379868   82 IIGVIATHVADYIFPQIIYGIDQVIsegGYSLLLGNTHNNHQRERk-NLINMLNSKVAGLIIEPTQSaldNPNMDLYqei 160
gi 160901785  77 NIGILTQSLTDYIFPFIVMGAEEVLkntKCKSFIGNAKNDPVVERe-TLERWMDLGLKGMIVDPVVSatkQANVTLLkei 155
gi 148543720  82 IIGVISTHMADYIFPPIISGIDSVVteqGYSMIVGNTLNDHKRERq-TILNMLDLQIAGLIIEPTESampNPNLDLYrqv 160
gi 160941628  84 NIAVISTYVDSYIFPPVVRGIERVLskkGYTTQIAFTGNRVSREQdiLNNLIDKDIIDGLIVEPAKSalpNPNLHYYqel 163
gi 146295761  91 CIAVLTTFISDYIFPLIIRGIEKVIaheGYGLLLFSTDNSYEFERyhLESIINNPNIDAVIIEPTKSalpSKNQDLYrkl 170
gi 118586701  85 TIAVITTHIADYIFPNIINAIDNVVskaGYSLILANTHNDPKRERd-SLLRLLKLKPAAWIIEPTQSavnHENINLYrqi 163
gi 116617961  82 VIGILSTHVASYIFPAIIDGADQVLsenGFSLILANTHNDPKRERt-ALTNLMSQNLGGLIIEPTQSaidTPNIDLYqki 160
gi 116491971  82 MIGVISTHIADYIFPNIITGIDRYVsaeGYSILISNTQNDPQKERk-GIKKMMEIGLSGLIIEPTQSalgNPNRDLYdkl 160
gi 124520632 131 TIGLITTYISDYIFPNIITGIDNYVsnyGYSILITNTQNNPEKERk-SLSNLLSNKISGLIIEPTKSalsNTNKSIYdni 209
gi 118726261  84 NIGVITTYISEYIFPKVIQGIDSVLssnGYSIMLKNTNNNTNKEAv-CLEDVLQKNVEGLIIEPTKSalySENMEFYeal 162
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  #             #                                  #                    
gi 28379868  161 kdnGIPVLFINASYpnl-dfqAVTTSDQEAEQRMIEYLFemGHESILGIFQvddaQGVHRMNGFVKAyqeqpeisyksni 239
gi 160901785 156 -seQIPTVIINSDLnip-yagTLVLNDYDCGSFAAKKFIelGHKRVAVIYKavhkAANERANGFIDTikehkq--illye 231
gi 148543720 161 qkyKIPTILFHSTYpgf-dfpSLLTKDREAEEELVKYLFslGHTNILGVFQiddqQGVDRMAGMIKAyqdnnipttksnv 239
gi 160941628 164 kerGIPILFFNSRYpel-elpCVSMNDEQVGKKAVEYLIknGHRNIGGVFKsddgQGHLRYKGFLSGmleagikvkdanv 242
gi 146295761 171 iqkEIPVIFINTILqdi-aqnYIITKDQSAVYKLTQSLIksGCKKLLGIFKgddlQGIKRYSGFEKAckeaq---aefda 246
gi 118586701 164 eklNVPALFINSSYpgi-nfpYLRTDDETGVFKLTNYLFsiGHRRIIGAFQiddlQGVDRMKGFTKAylnhpyfsdqlst 242
gi 116617961 161 aqlNIPMVFINASYnnf-egtTLVSDDKNAIYQVTEYLIkrGHKRITGVFQvsdvQGIHRLNGFLQSyqnhpnilpesss 239
gi 116491971 161 ketGLPTVFINAHYpel-dfpYLEVNDYEAERQVTNKLIgmGHEKILGIFKiddtQGVHRMKGYISAyqehrdlvmlsem 239
gi 124520632 210 kslGIPMLFINAVYddm-nipYLVMDDLKTGEMVTDYLIslGHKKIVGIFKvddkQGIHRMNGYIKAfqkhpeisnmgei 288
gi 118726261 163 dnhRIPYIFIHGFYqqlenksHIILDDAKGMYSAVEYLTklGHKKIVGIFKaddvQGVERHNGYAKAiadagmsynpddv 242
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1              #                                                       #                #
gi 28379868  240 LMYQSGDPfEKLAHRLDTYLQnn--erPTAIACYNDQLAIRVMDYLKGKGLNIPTDISIVGFDDYhmsrymsPGITTMNH 317
gi 160901785 232 LPFHGQETsDEVFNLIMSLLSlpknniPTAIFCSNDLVAMQVIMAAKKLNLDIPNDISLIGFDDAdfa--qaLEISTFRH 309
gi 148543720 240 IMYQSSEDyEDIIKKVDMMLNsn--ndITAIACYNDRLATRVISHLQKQGKQVPTDISVIGFDNYemaqiisPSLTTANH 317
gi 160941628 243 VWLDTEDF-LDLDQWADYLFRrl--esCTGVVCYNDEVAYVLSGLCEKRGIAIPDQLSVVSIDNSdlatlagVKLTSFPH 319
gi 146295761 247 IFFTSEEY-NFVHNRAAEIISre---rFDAAVCYNDKIALPLCVKLKEMGFRIPQDISVTGYDNSllstlteIKLTTVEH 322
gi 118586701 243 IMYKSTDGyEMVFDRIMNFYNnqninkPDAIICYNDQFAISLIDTFKEQGWRIPEDISIIGFDDFkmssyitPTLTTLSH 322
gi 116617961 240 IMYKSDEVnEALQNMRELLVKnpd-qrPTAVIAYNDQLAIRIVDLIHEVGLKVPQDISVIGFDDFqlsqylsPRLTTVSH 318
gi 116491971 240 VMYQSSDNmHNVFTRIESILArp--drPTAIICYHDQIAIRVIDLVRSMGLKIPEDISIFGFDNYklakyisPKLSTVEH 317
gi 124520632 289 MMYQTEENkINLFKKLHTILSrpe-faPTAIVCYNDQLAIQVMNFVKEIGLNVPKDLSVIGVDDYqfskfinPALTTVRH 367
gi 118726261 243 IWFHTEDRvVKPYNMVKRFLEen--reVDAIACYNDQIAFRVYELLTGLGVKVPEDISLVGFDDSyfsancpVKITTVRH 320
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
Feature 1                                                
gi 28379868  318 EKTTMGEDTGRQmlrll----hkqpvESIVYTPKLIVRTS 353
gi 160901785 310 PKQQFGEKAAQMllkmive-nnngkpEKIVEKAEFIGRNS 348
gi 148543720 318 PKRQLGEDAGKMilkmi----ageevTSKVYPPTIIKGQS 353
gi 160941628 320 PMEALGRKAAENmismie---npyfdGNYLFDSDIIERDS 356
gi 146295761 323 PKEKLGEMAAKAalsmik---ksrtgVKEEVECEIIFRNS 359
gi 118586701 323 PKSQMGRDAGKMilqli----nnqkvESITYEPELILRKS 358
gi 116617961 319 AKEKMGQDAARLllqki----khhkvESIVYHSQLIERES 354
gi 116491971 318 PKETMGRDAAKTifdiie---grpyeKNKVYDPELIIRES 354
gi 124520632 368 PQEKMGLDAGKMiidml----nkqpvTSKIYEPELVKRDS 403
gi 118726261 321 PKEKLGEEAAEIllemikdndylknpVQKVVIPELIIKES 360

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