Conserved Protein Domain Family
PBP1_FmdD_like

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cd06355: PBP1_FmdD_like 
Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF)
This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Statistics
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PSSM-Id: 107350
View PSSM: cd06355
Aligned: 23 rows
Threshold Bit Score: 494.502
Threshold Setting Gi: 144899619
Created: 2-Jul-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative ligand
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on sequence similarity to the Pseudomonas aeruginosa AmiC complexed with butyramide.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       #
gi 2661835    51 KVGILHSATGTMAiSETGSIQAEKLAIEQINAmGGILGRKIEIIQEDGa-----sDWPTFAEKAKKLLEKdKVAAVMGCW 125
gi 144899619 360 RIGILHSLSGGSAvGERPLKDVLLMEVAALNArGGLLGRPVEALLYNPr-----sDAKRTAELADQALGQdRVQALFGAW 434
gi 54310856   32 KVGILHSLSGTMAiSETVLKDTALMAIAEINAkGGVLGRKLEPVVVDPa-----sNWPLFAEKTKQLLTQdKVAVIFGCW 106
gi 13470931   35 KVGILHSLSGTMAiSETTLKDAMLMLIDEQNAkGGLLGKKLEAVVVDPa-----sNWPLFAEKARELISKdKVAAVFGCW 109
gi 157737050  27 KVGVLHSLSGTMAiSETTLKDTVLMLIEEQNKkGGVLGKKLEPVVVDPa-----sNWPLFAEKMRGLLTKdKVDVTFGCW 101
gi 15600051   32 KVGILHSLSGTMAiSETSLKDMALMTIDEINAkGGVNGRKLEAVVVDPa-----sNWPLFAEKARQLLTQdKVAVVFGCW 106
gi 27381164   30 KVGILHSLSGTMAnSESALKDTVLMMIADQNKkGGLLGRKLEPVVADPa-----sDWDAFTDKARELLANeKVAVVFGCW 104
gi 82702686   36 RIGVLHSLSGVLAaSEKPLIDAIQLAVEEANAaGGIHGHEIEAVVADCr-----sDAGHCAREAERLILEeRVEALFGCW 110
gi 53804248   32 RIGILHSLTGAMAiSEKSAVDAELMAIDEINAgGGLLGRRVEAVVADGa-----sDWGTFARQAGRLITEeKVSAIIGCW 106
gi 88809243   41 RVGILHSRTGTMAlSEATVAEAERLAIEEINA-AGGLKLNGRLVLVEPieedgmsDPAVFARKAQRMLNDdKAVAIFGGW 119
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                            #  ##                                                  #    
gi 2661835   126 TSASRKAALPVFEKDNGLLFYPTFYEGleqsKNVFYTGQEATQQILAGLDWIAkek--------kakTFYLIGSDYiwPR 197
gi 144899619 435 SSTARKETLPVLGRRNGLLFYPSQYEGaetdANVVYCGAPPNQQLLPAIQYLMsaeg------ggysRFYLIGNDTlyPR 508
gi 54310856  107 TSVSRKSVLPVVEELNGLLFYPVQYEGeelsRNVFYTGAAPNQQAIPAVEYLMskdg------ggakRFVLLGTDYvyPR 180
gi 13470931  110 TSVSRKSVLPVFSELDNILFYPVQYEGeeseRNVFYTGAAPNQQAIPAVDYLMskdg------gsvkRWVLEGTDYvyPR 183
gi 157737050 102 TSVSRKSVLPVVEELNGLLFYPVQYEGeessKNVFYTGAAPNQQAIPAVDYLInem--------gvkRFVLAGTDYvyPR 173
gi 15600051  107 TSVSRKSVLPVFEELNGLLFYPVQYEGeelsPNVFYTGAAPNQQAIPAVEYLMsedg------ggarRFFLLGTDYvyPR 180
gi 27381164  105 TSTSRKAVIPVFERLNGLLFYPVQHEGeessRNVFYTGAAPSQQAIPAVRYLMskeg------ggirRWVLLGTESdyPR 178
gi 82702686  111 TSTCRNAVKSVVERHDHLLFYALRYEGmeqsPNIIYGGAVPNQLVMPAVYWALenlgnrkharhsgkRVYLAGSENvfSR 190
gi 53804248  107 TSACRKNVKPVVEKHDHLLIYPMAYEGleisKNIIYTGLAPNQQIVPALKWSLdkl---------grRVFLVGSDYvwPH 177
gi 88809243  120 TSASRKAMVPVMEASNRLLFYPVQYEGqecsPAVVYGGSVPNQQSEPALGWMLnnh---------skRLLLIGSDYvyPR 190
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 2661835   198 TSMKIARKHIeqh-lhGTVVGEEYIALDdtqFGSVINKIKLKkp-----dVIYAAVVGGSNVAWFKQLNAAgln-sskQT 270
gi 144899619 509 LTHKVLTDYLrgrgisGQSLRETLLPVGaddWARAVADIRAFaragggkaLVVSTVGGDSNFHFFRQLGGAe------VP 582
gi 54310856  181 TTNKILRAFLkskgvaEADIMEEYTPFGhsdYQTIIGKIKKFsgeg-kktAVISTINGDSNVPFYKELGNAglk-atdVP 258
gi 13470931  184 TTNKILEAYLkskgvaAEDIMTNYTPFGfsdWQTEVSAIKKFgsag-kktAVVSTVNGDANVPFYKELGNQgik-aedIP 261
gi 157737050 174 TTNKILEAYLmskgvkKENIMINYTPFGhsdWQSIVSDIKKFgstg-vktAVVSTINGDANVPFYKELGNQgik-aedIP 251
gi 15600051  181 TTNKILRAFLhskgvdDKDIQEVYTPFGhsdYQTIVADIKKFaag--gktAVVSTVNGDSNVPFYKELANQgle-ateVP 257
gi 27381164  179 MTNRILGAYLaaegvnAEDVTTIYAPLGhsdWREIVEKIKVLgsqg-kktAVISTISGDANGHLYNELAAQqve-arkIP 256
gi 82702686  191 VVNILIKDVLav--ngGIVAGEYYLPLGsqnMESLVEDIVDQqp-----dLILSTIAGAYNAGFFQTLNRRgit-aesTP 262
gi 53804248  178 SVNAVLRDWIkg--ldGEIVGEEYVFFGssdVGSVVEKIVALrp-----sVVISTIAGESNLAFYRVLRESgiq-akdVP 249
gi 88809243  191 TANRIIRAQAer--eqARVLKEHYLPLGseaVQPLIADIQAAlna--gpvAVVNTLNGDSNIAFFQALQRQglnqrsaLK 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 2661835   271 MLTISVtedevlgigGENLAGFYSAMKYFQSqdnPENKKFVEAFKKRWgkda--------vigdVTQAAYLGPWLYKAAV 342
gi 144899619 583 VLTVSIgeaeaalldPRLLAGHMVAWNYLMSidtPENQAFLRQWRQHCddpea-------vvndAMEASVMALRLWAAAV 655
gi 54310856  259 VVAFSVgeeelrgvdTKPLVGHLAAWNYFMSvknPTNTEFTKKWSAYAktkgiaghkdkaltndPMEATYIGVYMWKQAV 338
gi 13470931  262 VMAFSVgeeelagldTKPLVGHLAAWNYFESvntPENKKFIANWHKFIknnkr-------ttndPMEAHYIGFNMWVKAV 334
gi 157737050 252 VVAFSVgeeelsgidTKPLVGHLAAWNYFESvktPENDKFIANWKKFIkddkr-------vtndPMEATYIGFNLWVKAV 324
gi 15600051  258 VVAFSVgeeelrgidTKPLVGNLAAWNYFESvsnPVNEKFVADWKAYAkaknlpny-gtavtndPMEATYVGIHMWAQAV 336
gi 27381164  257 VMGLSVtarelrgvdVSRLVGHMAARSYFQSvttPENDAFVKMWTDFNeqrdn-------itndPMEATFIGFRMWAQAV 329
gi 82702686  263 VLSFSVtevvlsgqdKIPMTGHFAVRNYFQTipsPENQAFVKRFHDRYgeqa--------vvdsPAEASYVNVRMWIQAA 334
gi 53804248  250 VVSLSVgeeelrdipPGDAVGHYSAWGYFQAvarEENTSFVRRFRERYgqdr--------vtadFPETAYFSVLLWAEAV 321
gi 88809243  267 VLSLSVseeeavaigRRNIAGTYASWSYFQSlqtPESAAFAQRFRQRYgfhr--------vindPAEAGYSLVHLWAQAV 338
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
Feature 1                                                                   
gi 2661835   343 ERAGSFDVDKVQAALPgytfKDAPEGPVTVEA--NHHLTTKLRIGQWGKDGQAKVVYTS 399
gi 144899619 656 EACGSTEPDKVRAALPgqktRSLTGFDVSVDDt-NNHLHKPCLLGRMQADGTIAIVWRS 713
gi 54310856  339 EKAQSTDVDKVIAAMGgq-tFKAPSGFTAKMDekNHHLHKPVFIGEIKADGQFNVVWKT 396
gi 13470931  335 EKAGTTDPDKVIDAMIgv-sVPNLTGGYSTMMp-NHHITKPVLIGEIQANGQFETVSKT 391
gi 157737050 325 EKAGTTDVNAVSKAIIgl-eVPNLTGGTAKMLk-NHHLTKPVFIGEIQEDGQFETVFST 381
gi 15600051  337 EKAGSTEVDKVREAMAgq-sFKAPSGYTLVMDksNHHLHKPVMIGEIQDDGQFEVVWKT 394
gi 27381164  330 TQAGTSDANAVRQAMYgq-rIKAPSGFEVVMNt-NHHLSKPAMIGKLNPDGRFDVVWRS 386
gi 82702686  335 AEAGSGNLAKVQRLILrq-sLPAPEGIVALDPv-TRHAWKVARVGKVREDGQFDIVWDS 391
gi 53804248  322 REAGSPEAALVNEYMLgq-sIDAPEGVVTIDPa-TRHTWRSFNIGRILDNGQVEIVWST 378
gi 88809243  339 ETSGSVETDAVRQALIgs-rFTAPQGDLQVSSs-LHLKKRSLLAKADPKGGFRVLEDFG 395

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