Conserved Protein Domain Family
PBP1_Qymf_like

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cd06291: PBP1_Qymf_like 
Click on image for an interactive view with Cn3D
Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs
This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that 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 sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. 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: 107286
View PSSM: cd06291
Aligned: 44 rows
Threshold Bit Score: 292.159
Threshold Setting Gi: 24378626
Created: 24-Jan-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:3CTP_A; Alkaliphilus metalliredigens transcriptional regulator binds D-Xylulofuranose, contacts calculated at 3.5 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  # #                                                 #                 
3CTP_A        62 TIGLMVPNIsNPFFNQMASVIEEYAknkGYTLFLCNtdddkekektYLEVLQSHRVAGIIASRsqced--eyaniDIPVV 139
gi 1710834    61 LIGLVFPTIkNIFYAELIEKIEQALfirGYKAMLATtehdeqkerdYLALLLSNQVDGIIYGShnlkah-dyiaiEAPIV 139
gi 1173387    62 LIGVIFSDIsNPFFGELVSRIEKILfakNYKVILCNsaddpqkerdYLQMLMANQVDGIIAGAhnlgie-eyqqyGLPII 140
gi 29376164   62 LIGLVFPSVsHPFFGELIETLERKLfvqGYKVILCDsekdpekeraYLRMLAANKVDGVITGShnlain-eyenvSLPIV 140
gi 92089348   62 FVGLIFPNLiNPFFAELANELEHELfkkGYKTIIASsaqnpeieheYLNMLMANQVDGIISGShnlgie-eyhqlTAPIV 140
gi 116514639  26 MIGVIMPSItNPFFAELVAAIEDKLeadGYKMLLCDagqdsdkerrYLRMLEANQVDGIIAGShnlgie-eyqryGLPIV 104
gi 81429406   62 MIGLIFPSVsNPFFGELIERLEKKLfdkGYKSILCDsnrepekekaYLGMLAANQVDGIIAGGhntelq-eyekmSAPVI 140
gi 71854139   62 LIGLIFPNIsNIFYAELIEHLEIELfkqGYKTIICNsehnpvkereYLEMLAANQVDGIISSShnlgie-dyervEAPIV 140
gi 33149355   62 LVGLIFPEItNPFFAELVQEIESALfkqNYKVILCNagrdrqkereYLRMLQANQVDGIIAGAhnlgie-eykqlGLPIV 140
gi 47132630   61 TIGVIMPTIaHPFFSTLTAHLQREFaarDLKTLLCStadtdkgeseYIDMLQRHMMDGIIMAAhtehpadywtsiHRPIV 140
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #                                                    #                        
3CTP_A       140 AFEnhildniiTISSDNYNGGRMAFDHLYekGCRKILHIKGpev-----feaTELRYKGFLDGara-kdLEIDFIEFQHD 213
gi 1710834   140 AFDrlltpettVVSSDNFEGGILATKALInsGSKKIAIFTGndnt----nspTYLRRDGYLLEler-nqLKTHIIKIPSQ 214
gi 1173387   141 SFDrylsdnipIVSSDNYQGGWLATQTLHqaGATNVAIFTGksha----gspTNGRREGYEAYlta-qqLTPHVHELPFE 215
gi 29376164  141 SFDrflapgipIVSSQNFQGGQKATEALFasGAQKIAIITGannt----gapSDYRLAGYKQTmek-ygAEKTILQIDNG 215
gi 92089348  141 SFDryladnipIVAADSYHGGELAAKYLVehDVKHLAVIVDedts----vspTINRIQGALDF------LNKQKRDFEPL 210
gi 116514639 105 SFDrdlsdqvpIVTSDNYQGGCLATQALVdaGCGHVYFVGNpvkt----gnpTSRRFDGYADTva---aAGLTVHTARSA 177
gi 81429406  141 SFDrllsthipIISSDNFAGGQIATNTLInlGAKRIGIITGsnet----nspTLLRLNGYLDAlqk-ngLDPFVFQIKST 215
gi 71854139  141 AFDrnlapnipVISSDNFEGGKLAAQTLQkhGCQNIVMITGndns----dspTGLRQLGFNYQl----kRSAEIIKLPNN 212
gi 33149355  141 SFDrklsdnvpIVSCDNYQGIKMATHELIqtGCKHIYFLGNnqrk----gnpTDERLEAYLDEtkk-ydFTPHIRSVAFS 215
gi 47132630  141 AFDrtlgegvpVVRSDHEQGGRLIARQLIdsGARHVVLVGGprsqfaegttfPTIRYHLTVERllaeagIACDYVEAGTV 220
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                      #                           #                #    
3CTP_A       214 FQvk---mlEEDINSMKDIVNy--DGIFVfNDIAAATVMRALKKRgvsiPQEVQIIGFDNSfigellyPSLTTINQPiEA 288
gi 1710834   215 WTllr--kkVEIKKILENNDF---DGVFCtDDLTAILVKDLASNL----KKSLNVVGFDGTefienyyPNLTTIKQPiND 285
gi 1173387   216 LTpal--kmMEIKTIMTQHQY---DGIFCsDDLAALLVLNVAQQLsltvPEQLRVVGYDGTalirdyhSELTTVEQPlAD 290
gi 29376164  216 TSttl--knLEIERLLQNKTV---DGIFCtDDLTAITVMNIAQKLkisiPEELKVIGYDGTklikriaPQLSTIVQPiDE 290
gi 92089348  211 AI-------QHLDLEATFPGNy--DGVLAsNDVQALTISNLYYQAgkqiNKDFFITGYDGSrlirkvaPYLPTVIQPiSL 281
gi 116514639 178 FYespaakaRELRELLTSGRKi--DGVFCsDDLTAILLLKEARKLgikvPEDLKIVGFDGTqlvqnyvPELATVVQPvPD 255
gi 81429406  216 TSn-----sLKKIEIARILREehlDGLFCtDDLTAISVMNEAQNQnikiPQDLKLIGYDGTeliqkyfPQLTTIIQPiDE 290
gi 71854139  213 LSpvr--reMEIKSILATRKP---DGLFVsDDLTAILIMKVAKQLhitiPEDMKVIGYDGTtfiqqyvPQLATIRQPiDE 287
gi 33149355  216 DSsni--knMQIHNMLVDDKP---DGVVCtDDLTAILVLQEAQKLgikvPQELKVIGFDGTqlvqtyhSELSTIAQPiDD 290
gi 47132630  221 ADiaa--heATACAIFEQYPDv--DAIVG-SDVVASVALQEASRRgievPADLQVIAYDGTlmaetagKRLTAIRQDfPA 295
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
Feature 1                                                           
3CTP_A       289 LAYTIIELLikiing----------------egvliEDYIMEVKLIERETT 323
gi 1710834   286 LAELLVDLIir-----------------------kiDGDNIDITYQLPVQL 313
gi 1173387   291 ISTLLVSLLlqried---------------anctleSKYTLPVKLIKGFTA 326
gi 29376164  291 MCDVMIDLLlrrmkd---------------pdvaleENYPIPIQLSLSESC 326
gi 92089348  282 LAHELIETLm--------------------------KRIETPHEKIETKLV 306
gi 116514639 256 LAGTLVKLLyeriadp--------------ekklaqNSYLLPVKLLRNQTV 292
gi 81429406  291 IASLLAELItlried---------------psapleMRYTLPVKLLQSNSI 326
gi 71854139  288 IAKLSVEILikkik-----------------kektsKDYILPITLLPGASI 321
gi 33149355  291 IATLLVDLLlkritnp--------------kqkfesKNYVLPVKLIKRETT 327
gi 47132630  296 IAAALAVRMdsqiaadggpaspskndsasdvdtqptPEEVIPVALIPGETT 346

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