Conserved Protein Domain Family
PBP1_BmpA_Med_like

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cd06353: PBP1_BmpA_Med_like 
Click on image for an interactive view with Cn3D
Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea
Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Statistics
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PSSM-Id: 107348
View PSSM: cd06353
Aligned: 71 rows
Threshold Bit Score: 200.108
Threshold Setting Gi: 14026430
Created: 11-Jul-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
putative ligand
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on structural similarity to purine nucleoside receptor (PnrA)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1              ##       #                                                                
2HQB_A         7 XVGLLVEDtiddqGWNRKAYEGLLNIHsn--lDVDVVLEEgvnseQKAHRRIKELVDg-GVNLIFGHghafaeYFSTIHN 83
gi 160940451  89 KVALCLSGaandmGWCQSAYDGLKLLEad--yGCEVTYTEnl-tpDDIEAAFADYAAs-GYDVVIGHgyefgdPAVDVAE 164
gi 119718367  50 PLVYGVFAtpleePWDGAIHAALESAAad--gLIEYKHVDdlstsDAMERSLRDIATneKPDAIIGDafaaeeAVRKVAA 127
gi 115424451  38 KVAAIYTVpv-eqQWVSRIHKALTAAKek--gDIDYVYSEsv-gnADYERVLRQYAEq-GNNLIVGEafavesAARKVAK 112
gi 83594116   30 KVAAVYTVpi-eqQWVSRIHKALTAAKer--gEIDYAYSEsv-anADYERVMREYAEk-GNALVIGEvfgveqAARRVAK 104
gi 86606247   41 KVAGVYTVpi-eqQWVSRIHKALMTAQer--gDIDYTWSEsv-snTDYPRVLRQYAEs-GVQLLVGEvfgverEAREVAK 115
gi 163797248  77 KVAGIYTQpi-qqKWDARLHQALDKAAka--gEIEYVFSEkv-anTDYVRVLREYAEg-GAKLIVGEafgisrEARKVAD 151
gi 13473538   45 KVAAIFATpi-eePWDNQIHVALQKAEke--lGIEYKWSEkv-qtADFSRVMREYAQg-GYQLVLGDafaaerESRRTAK 119
gi 134300602  41 KVALILPGkiddvSWNQAMYEGVKALEkeyagKIEVTYTEqvyevSNIEPTLRDFASq-GYDLIIGHgfqfmePIIKVAQ 119
gi 16263875   31 KMGLLVPGsvseeGWNRIGFNALKGVEae--lGAEVSYVElqqnpASFEKAFRDFASq-GYNVILGHgfefqdAALEVAP 107
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  #                                                #                    
2HQB_A        84 QYPDVHFVSFNGevkg---enitSLHFEGYAXGYFGGXVAAsxsetHKVGVIAAf---pWQPEVEGFVDGakyx-neseA 156
gi 160940451 165 QYPDTKFIVTEGevsa---dnvaSYVSKCEEGGYIMGMLAAgmsesGKVGFIGPiqgasLVKIMNGFEDGakevnpdiqV 241
gi 119718367 128 EFPDIPFAFGSGgepve--pnmsVFDNWLQDPAYLAGMLAGgltesGTIGVVGAmpipeVNRIVNAFVLGvketnpdatV 205
gi 115424451 113 DYPKTGFLMGSSgkpqq--pnfsVFDNYIQEPAYLTGMIAAgmsksGQIGLVGGypipeVNRLMQAFMAGaqeinpqarF 190
gi 83594116  105 DYPDTAFLMGSSfkpqa--pnfsVFDNYIHEPSYLTGMIAGgmtktAKIGLVGGypipeVNRLMNAFIAGarevnpqasF 182
gi 86606247  116 DYPKVSFLMGSSlkpdpalsnfaVFDNYIHEPSYLTGMVAGgltrsKIIGMVGGypipeVNRLMNAFMAGarelqpevkF 195
gi 163797248 152 DYPKVAFLMGDPfkphg--snfaVFDNYIHEPCYLMGMIAGsmtksNKIGMVGGypigeVNRLFHAFMAGarsvnpkveF 229
gi 13473538  120 QFPKTAWLFGSGagpae--pnfgVFDNWIHEPAYLAGMIAGkmsksGTVGAVAAmgipeVNRLVNAFFAGakevnpnvkK 197
gi 134300602 120 EYPETKFALGTGfktl---pntcVYDVKLEDGGYLMGTLAGlmtktNKIGVVGGadvaeIYRGHEAFKHAakqvnpdiqI 196
gi 16263875  108 EYPDTVFLISSSyife---gnviGLNTDTSQPFYLMGVIAAkt--gKKAGLVGGmeippIKEAFEGFTNGvrsvapdfpV 182
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               #                                                #                  #    
2HQB_A       157 FVRYVGEWtDADKALELFQELQKEQVDVFYPagdgyHVPVVEAIKDQg--DFAIGYVGDQADLGg--sTILTSTVQHVDD 232
gi 160940451 242 QTAWTGSFtDTALGKEAAQAMIDNGADVIGHcanesGTGAINAAKEAk--VYATGDSYDQNDLAp--dTILSSSVYHIPH 317
gi 119718367 206 KVSFINSFfDPAAAKQAAQAHISAGADVLFAe----RDGVIAAAEEAd--IPVIGMMVDQKAESp--eHVVTSLIWDVRP 277
gi 115424451 191 TVTFIGSWfDPPKAKEAAFAMIDKGADVLYAe----RFGVSDAAKERg--KLAIGNVVNTQAQYp--eTVVATALWNMEP 262
gi 83594116  183 TVSFIGSWfDPPKAKEAAFAMIERGVDVLYAe----RFGVSDAAKEKg--VLAIGNVIDTQADYp--qTVVASALWSMEP 254
gi 86606247  196 LVTFIGSWfDPPKAKEAAFAQIDAGADILYAe----RFGVSDAAKERg--VLAIGNVIDTQPDYp--eTVVVSALWHMEP 267
gi 163797248 230 KVNFIGSWyDPPKAKEAAFAQVEAGVDVLYAe----RAGVVSAAREKg--IIAFGNVNDMNKEEngtgVVVTSALWDMTS 303
gi 13473538  198 KVAFIGSFfDPPKAKEAAVAQIDAGVDVIYAe----RFGVIEAAVEKk--ILAISNMSDQSSLGp--dTVITGPVWDMYP 269
gi 134300602 197 QELYTGDWrDAAKAKEGAISMYDAGADVIWHsgdgiGLGVVDAGKEKn--KTVLGNVADQNVLAp--nNVLSGIAYNWTP 272
gi 16263875  183 SEVYIGNFtDATATKEASLSLISQGADFVLPnasgaTVGGFQAAAESgadVKTFSIFSDYTSVAp--kNILGLYVADYAR 260
                        250       260       270
                 ....*....|....*....|....*....|...
Feature 1                                         
2HQB_A       233 LYVLVAKRFQegk---lesGNLYYDFqDGVVSL 262
gi 160940451 318 VIEVAFKTVAdgt---fegGIYQLGMaDGAVSV 347
gi 119718367 278 TVDAVVDQIEngp----egVDLGKYSfMAAGGS 306
gi 115424451 263 TIAHALTAVKagn----fkAEDYGQYsLMKHQG 291
gi 83594116  255 TIAKALEMVKakt----fkAEDYSVYsYMKHQG 283
gi 86606247  268 TIDRAIAAVKage----fkAEDYGIYsMMKYGG 296
gi 163797248 304 AINYAIAQTKagt----fkAEDYKEWtMMAKGG 332
gi 13473538  270 TVEQAIKLVKagv----ytAQDYGDFsRMAKGG 298
gi 134300602 273 VVKEMVDDILnnnftnrdkKFYWLTAaNGGVTV 305
gi 16263875  261 GVIRIVGDIRngkk--pttNVEFGLKdADVMKF 291

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