Conserved Protein Domain Family
PBP1_Amide_Urea_BP_like

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cd06356: PBP1_Amide_Urea_BP_like 
Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF)
This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Statistics
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PSSM-Id: 107351
View PSSM: cd06356
Aligned: 13 rows
Threshold Bit Score: 523.827
Threshold Setting Gi: 109645894
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 77975943   10 KIGLLEDASGnFALPVIPKIHATELAVEEINAkGGILGRPIELVKYDTQSdnTRFQQMARRLIKndKVDVIFGAFsSASR 89
gi 76801647   37 TVGILEDRSGnFQLNGTSKWQATRLAIEEINEdGGILGEEVEIVDPDPQSdnERYQELTERLILqdQVDALWAGYsSATR 116
gi 76803424   43 TLAVLENRSGkFAELGTSKWQASRLAVEELNEsGGALGRKIELIDPDPASdvKRYRQLTTEILEerDVDAIWAGYaSSER 122
gi 13507186   45 KMGSILDLSGgLDIYGKPMQMVMQMAVDEINAsGGLNGSELEIVSYDTQSnmQLYAQYAQQAALqdRVDFVNGGItSASR 124
gi 91978751   32 KVGLLEDISGdLAFMGMPKLHGSQLAVEEINKsGGILGRQIELIHLDPQGdnARYQEFARRLLNrdKVDVLIGGItSAAR 111
gi 86136422   18 KLGSILDTSGiFDAYGKPMDMAMRLAVKEINAaGGLLGKEVEVVAYDTQSdmALYSQYGQQLTRqdRVDVVHGGIlSASR 97
gi 114763546  35 KVGGLHDLSGaLDAVGVPMNQVFQMAIKEINEaGGLLGREVEAVIYDPQSnmSLYSQYATQMALrdQVDVVMGGItSASR 114
gi 146341005  38 TVGSLHDQSGpIGTSGTPMVYALQLAVDEINAaGGLLGRPLKVIHYDTQSniQLYSQYAQQLAVkdKVDVVHGGItSASR 117
gi 118035579  31 KIGLLEDASGnFALATIPKIHATELAVDEINAkGGILGRPVQLIAYDTQSdnTKFQELARRLVQtdKPDVIFGAFsSASR 110
gi 121607350  32 KFGSLLDTSGnFDAYGKPMNMATDLAIDEINRsGGLIGRQIKKSAYDTQSnmAMYTKFAQQLARqdKVDVVIGGIlSASR 111
gi 39935477   33 KLGVLEDQSGdFAVATIGKVHAIQLAADEINKaGGIMGRPLELVVYDTQSdnTRYQEFMRRVLQrdKADAVFAGFsSASR 112
gi 110669470  44 KIGVLEDRSGnFSLVGTPKWRASKLAIDEINAdGGIMGKQIELFDPDPQSdnERYQQLTSRLIRqeNVDALWAGYsSATR 123
gi 109645894 271 KVGIIGDFTGiCSELERGKVAAYKLAADEINRmGGINEKKVELLFRDDRSlsELTREAVKELTEeeRVDVLMGSTlSPSR 350
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #  ##                                         #                  
gi 77975943   90 EAIRPIMDREKQLYWYNNQYEGGVCDsnvfVTGAVPEQQFSTLIPWMMekYGKKVYTIAADYNFGQISAEWVRKIVeenG 169
gi 76801647  117 EAIRPIINDEDQLYFYTTQYEGGVCDdtifAVGSTARQQLGAVTPYLAdqYGEDIYIIAADYNFGQLSGDWVNVIAeenG 196
gi 76803424  123 EVVRPITNAHRQLYFYTNQYEGGVCDrytfPVGATARQQLGAVLPYLVseYGPKIFTIAADYNFGHLSSDWVEILAaenD 202
gi 13507186  125 EVIRPILRRYNALYFYSTQYEGGVCDrnafCTGITPAMQEKNAIEWAVkkWGAKMYSIGADYNAPRIMSDWARKYGeavG 204
gi 91978751  112 EALRPIVGRTSTPYFYTNQYEGGVCDasmiSMGAVPEQQFSTLVPWMVekFGKKVYVVAADYNFGQISAEWNRKIIkdlG 191
gi 86136422   98 EAIRQTMRKTKTLYFYNVLYEGGVCDgnifINGVTPAQQVEALVPYAMgkSGPKVYILAADYNYGQITARWIQKFVaenG 177
gi 114763546 115 ETIRPIFHRYDTFYFYNTQYEGGVCDrneiTLGTTPAQTVARLIPYGMnlYGKKVYTIAADYNYGHITAAWVKRYVeenG 194
gi 146341005 118 EAIRPTFDRFKVLYFYNTLYEGGVCDrntfCTGTTPAQTVEKLVPSAMkkSGKKAYIIAADYNYGQITAKWMTKYCkdnG 197
gi 118035579 111 EAIRPIMDRAHQLYWYDNQYEGGVCDtntfVTGAVPEQQFSTLIPWMMqkYGKKVYTIAADYNFGQISAEWVRNIVkenG 190
gi 121607350 112 EAIRPLLNREKILYVYTPLYEGGVCDgntfLTGTTPAQQAEVLVPYAVkkWGRKAYILAADYNYGQYMAKWFQKFLaesG 191
gi 39935477  113 EAYRPIVDQLNGLAFYNNQYEGGVCDghmiVTGAVPEQQFSTLIPWMMekYGKKVYTLAADYNFGQISAEWVRNIVkqhG 192
gi 110669470 124 EAIRPTIDRNEQLYFYTTQYEGGVADeytfCMGPTARQQLGSVVPYMIenFGSDIYTIAADYNFGQLSADWVKVIAdenD 203
gi 109645894 351 EIMQHYADQTKTLYLDTQQTEGGVSShytfCLSAMPEQQMTQMLAYLLqkYGRKCYVVAADYNYGILSAEWVKYLVhqlG 430
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 77975943  170 GTMVGEEFIPLsvsqFGQTIQNIQKAkpdFVMTLLVGanQSSYYEQQAAAkl--nLPMGSSVNVgqayehkrFKAPALKD 247
gi 76801647  197 YNIVGEEYIPLdesdFSSVINRIQAEdpdFIMSMLVGanHENFYDQRDSNdl--mIPIGTSTTMaqghehirYEPNAVTD 274
gi 76803424  203 AEVIGTEFVPLsetsFEWLVDRIEAAdpdFVMSMLVGdnHAEFFREKATRdl--sMPIGTSTAMaqafehkrYEPPAFAD 280
gi 13507186  205 GAQVANEFFPLdvteFGPLITKIQAAkpdFVCSTLVGaaHLGFYRQWAAAgmvgkIPILSFTFGagne-htmLPASESEG 283
gi 91978751  192 GQVVGEEFIPLgvsqFAQTIQNIQKAkpdWLLTINVGaaQDSFFEQAAAAnl--nLPMGSSIKVmlgfehkrFKPPALNN 269
gi 86136422  178 GETVGVDFFPLdvsdFGSTIAKIQAVgpdLVIAPLVGgaHLSFFRQWAAAgmkdrIPLASTTLGvgne-hkvLTPAEGDG 256
gi 114763546 195 GEVIETEFFPLdvaqFGSTISKIQGAapdFVLSALVGtsHLGFYRQWAAAgmkseIPVMSTVLGaggsdqliLTAEEGNG 274
gi 146341005 198 GEILSTDFFPLdvtnFGSTISKIQAAkpdLILSALVGgnHTAFYRQWTAAgmkskIPIASTTFGlvne-pstLDAAESDA 276
gi 118035579 191 GTMVGEEFIPLsvsqFGQTIQNIQKAkpdFVVTLLVGanQSSYYEQQASAhl--nLPMASSVNVgqayehkrFKPPALKD 268
gi 121607350 192 AADVGLEFFPLdvsdFNSTIAKIQAAkpdFVISALVGgaHLSFYRQWAAAgmkgkIPLVSTTLGvgne-hqvLTAAEGDG 270
gi 39935477  193 GEMAGVEFIPLgvsqFSQSIQNIQKAkpdFVVTLLVGtaQASYYEQAASAnv--nLPMASSVNVgqgyehkrFKPPSLKD 270
gi 110669470 204 AEVIGEEFIPLsvqnFGSTISNIQDAdpdFVMAILVGanHSSFWNQRTSAgl--eIPMGTSTVMaqgyqhkrLEAPALKD 281
gi 109645894 431 GEIVGVEYLDDritdFNPLIDRILQLeadILFSICVFpnHDAFYLQWHQRgl-nhIPNASTMVAaeayqnvrFAPPVLEN 509
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 77975943  248 MYITANYIEEVd-sPASNDFKQRFHAKFpn--epYINQEAANAYDAVYLYKaavekaGSTDMDAVRKSLESGdic--tdg 322
gi 76801647  275 VYAGVSYMEELgdlREGENFVEDFYDRWpd--anYLNQEAQNNYFSVYMWKeaveeaGTFDQDAVIDVLEEGvem---na 349
gi 76803424  281 VYAGVNYMEELs-tQENTTFVERFYEMFpd--adYINQEAQNNYVSIHLYAkaveaaGTTDQDAVIEQLESGlsf---da 354
gi 13507186  284 IVASYSYLEEId-nPANKAFLTSYREKYgan-avYQNNISIGAYEATWLWAtavrtaGTAEREKVIEALEAGttw---vg 358
gi 91978751  270 MHATANWFEEIa-tPEAEAFKKRWRAKFpd--etYINDMGYNAYNALYMYKtlaekaKSTKLEDLRKVIATGeac--ida 344
gi 86136422  257 IMVAYNYSQELd-tAANIAFKDKWSAAYgd--sgMIHELAVSNYQGMLTWAeavrqaGSIERAAVIAALETGlsi---eg 330
gi 114763546 275 ITASFGYFEEId-nPTNKAFLERVAQEYpdk-dwVMSEISEVTYEGMMIWAdavreaGTTERDPLLEVLTSGkay---dl 349
gi 146341005 277 VIGAYGYFEELt-tPASKSFVEKIKKAHpd--spYISELASCTYEGVMLWAegvkkaGSIDRMKVIEALESGlvf---dg 350
gi 118035579 269 MYVTANYVEEVd-tPASNDFKKRFHAKFpn--epYINQEAANAYDAIYLYKaavekaKSTNQDQVRKALESGdic--ttg 343
gi 121607350 271 ILVAYNYSPELq-tPANKVFLQAWGKMHggn-tkAINELAVLHYQGIKLWAegvrkaGSLERAKVIGAMASGisi---dg 345
gi 39935477  271 MYVTTNYIEEId-sPQSKAFLAKFKAKFpn--epYVNQEAENSYLAVYLYKqmveraKSTNRDEIRKVIAQGdvc--mda 345
gi 110669470 282 VYGGFNYMEEIp-tSRNEDYVSRYYDKFpd--agYANEESINNYFSIYMYKqaveeaGTTDQEAVRDVLESGmeitgdrs 358
gi 109645894 510 MYVMASFIEELn-tPAAQRFVKKFRAAYdhrevpYMSMDTETVYTAMYVYKravelaGTTDTEEVITALESGavy--vdg 586
                        330       340
                 ....*....|....*....|.
Feature 1                             
gi 77975943  323 PSGKVCIDPKSHHLSHTIYLA 343
gi 76801647  350 PSGRIELDGATHHITHQMRVA 370
gi 76803424  355 PEGRVAIDGATHHINHTMRIA 375
gi 13507186  359 PAGALKMDGATHHCARDIRLA 379
gi 91978751  345 PEGKVCIDPKSQHTSHRMRLI 365
gi 86136422  331 PAGRVTVDPKTHHAVLDVHLM 351
gi 114763546 350 PAGKVKIDPKTQHAIRDVYIA 370
gi 146341005 351 PSGKVSLDKQTHHTVRNAFLA 371
gi 118035579 344 EQGKVCIDPKSHHASHTIFLV 364
gi 121607350 346 PSGKVSIDGPTHHVTLDVHVM 366
gi 39935477  346 PEGKVCIDPKSQHMSHTIYLA 366
gi 110669470 359 PEGDISFQGPVHHMTHNMRVM 379
gi 109645894 587 PGGRVTVRGEDHHTSRSLSCF 607

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