Conserved Protein Domain Family
PBP1_aromatic_compounds_like

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cd06332: PBP1_aromatic_compounds_like 
Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes
This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Statistics
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PSSM-Id: 107327
View PSSM: cd06332
Aligned: 43 rows
Threshold Bit Score: 318.38
Threshold Setting Gi: 119715096
Created: 6-Mar-2008
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 28971615   24 KVGFISTLSGpiagFGLEIRDGFNLALknsgnkigGLPVEVVEGDDqaspDVGKQLADKMIKrdKVDFLTGIVYSnvmla 103
gi 27378498   27 KVGVTATLEGtytvLGEDGMRGHQTALnvlgkkigDKELEFIVASTdatpDSAVRAVRKLIEqdKVQILLSPLSGdegia 106
gi 33600577   45 RIGALNSYSKvfaaLGNANLNGMNMYFdqigntiaGRKVEVIREDDeinpQVGLQKLKKLVEsdRCDIVTGIQASnvama 124
gi 72384023   31 RVGLLTIKTGvaagIGQQMQDGFEYLLherggklaGRDVEVVVADTaaspAVAKAKFLQLTErdRVDVVVGPLAAfeana 110
gi 75674864   35 RLGTLASLEGplaiNGQDAYRVVELLLeeagykagGRKIEWIRESSngkpDVALARTRKLIEqdKADVVIGPLAGaegia 114
gi 84502441   26 KIGVISVLEGafagPGMDGVRGAKLAVqeaggavgGNEIEIVTMSSdaspDSAVNAARKLIEqdEVDLIVGPLSGsegla 105
gi 85707328   25 KVGLLLPFSGvyaaLGNDIEAGFTTALeqfg-setPATFEIVREDTevkpPVALAKAKKLILqdKVDVISGIVSSgvlga 103
gi 119715096  47 KIGVLLPYTGpfglYGKPMEAALTARLklddfkvgDRSIELVFEDEatdpATAVSKANKLVDqdGVSAVVCCATGaatla 126
gi 126731081  28 KFGILVATEGafaeGGADGIRNVELAIqqaggtagGLTIETVVAPTdttpDTTVRQARKLIEqdGVDIILGPLSGsegia 107
gi 149375495  33 KIGVMLPFSGiyaqLGEAGRDGLKLALkenaanlhGADIEFIELDTeakpSRAPELASSLLNqhEADFIIGPVHSgvamg 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #  ##                                              #  #          
gi 28971615  104 v--gppafaSKTFYISAAAGPAalagercnkyffGLSWQNDGQSEAVGSYLNskn-ykKVFILAPNYt-GGKENLEGFKR 179
gi 27378498  107 vk-nfakthPELTFINAASGAQettyvdpapnffRYNMDGAQWQVGLGKYAYddkkyrKIATVGEDYsfIYTQVFGLVLE 185
gi 33600577  125 a--veylrqSKAFMLCSGAGVAqlsytg-mpyffRCSISTVPIHATMGEWFYdnv-akEALLTASDFa-GGRNTLEEFKA 199
gi 72384023  111 i--rddiarAKVPVILSSAAAEdltqrkadpwmvRSSSTSAQAMHPFGEYAAttlkyrRIAVVAEDLs-FSHETVAGFQR 187
gi 75674864  115 vr-dysrtvPNKTFINGSSASQdntlrnsssnyfRFSTDGTQWTAGLGEYTKnvlnigEVTVVASDYa-FPYSQVFGFSL 192
gi 84502441  106 lr-dlsksyPDVTFLNGSSASQdttlrdasenffRFGGDGAQWMVGVGDYAFndlgyeSVAIVGEDYs-FPYTQVLGFMA 183
gi 85707328  104 v--rdmvhgAGVPLIVANAGNDeatgeacspyitRMSFSNGQVNRPMGQWMYdqg-irKVYTLAPDYa-AGRQMIDGFVQ 179
gi 119715096 127 v--gpilaeRGIPQLGPIPNPDglsef---ataaVAAPTAGHDAGKLGTYAAtdldyrSAVIVASDFa-YGHEVAENFKK 200
gi 126731081 108 mrdyaktipDKTVINGISGALEttwvdp-aenffRFNLDGAQWGAGLGSYVVnekgwtKVATVAADYs-FGYTNFLGFAV 185
gi 149375495 113 m--ikmlrgKDTVMIIPNAGAAaatgplcspnmfRTSFSSWQPSYPMGKVALekg-ykKVYAISWNYg-MGRESLDAFEE 188
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                            #           
gi 28971615  180 FFk---GEVSSEVYVklg-qldFASELAQIRSTkpdAVFFFlpsgmSINFIKQYVGAgldkdIPYFSTGhsaded---vv 252
gi 27378498  186 FCga-gGQVTNRQWVplg-tkdFASVIAALPDDv-dAIYLGlggadAVNFLNQYQQAgg--kAHLMGGSimidqtilssk 260
gi 33600577  200 GFsrkgGRIIKEIYPplg-nndFSPYLADIRSMspqATFSFyagtdAVRFVKQYDEYglkakSRLTGSGfmldsd---ti 275
gi 72384023  188 TFeeagGKIVQKLWApfn-asdFATLIAQIHPNv-dAVLINfsggnATRFLKQYRDYglkqkIPLLAGMntvdes---ll 262
gi 75674864  193 EFtragGKLNYLWTPfgt--sdYTSLIAQIPKSs-gALYVVyggsdGLAFLTQYAQAgg--sLPLLGGTlladqtlfsar 267
gi 84502441  184 EYceagGRVPEKFWTpig-nkdYSSIVYSIPQDv-dAIFVVlggadAVNFLTQYAQAgg--dKPIIGSSvtidqsvldsq 259
gi 85707328  180 TFtaagGEIVGQEFTpfqktqdFGPYMAQAKSSgaeAVFVFyaggeAISFVKQYDSFglkaeLPLYGSGfltssl---yv 256
gi 119715096 201 GFteagGSIVKEVYAplg-tsdFASYLSQLPDAd--VVFAGfagadAIRFVQQYDKFgvkakMPLIGHGplvtel---vl 274
gi 126731081 186 DFcsagGDIVERFWVplg-ssdFGGVIASLPDDv-dAIYLGvggtdAINFLNQYSQAga--dTNLIGGTimadqtvltsr 261
gi 149375495 189 SFtaggGEIVEKVLLpfp-stnFQSHVSSIADTnpdAVFTFfagggAIKFVKDYDAMglrgkIPLLGSGflteg----tl 263
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 28971615  253 tavGEQMVGLKNAAHWawdlknpqnEAFVADFKKTygri-----ptmYAFQGYDVVRLLDsavkdvkgnlsdke--alht 325
gi 27378498  261 gnaKNALIGTIAASGQadtwedpgwQKFVKAYQDAfppnkrfpspslLATNYYGSTMALIlalrevngdlsdnq-skfrt 339
gi 33600577  276 paqGRAALGALNSLHYadtldnpanLKFVADYRARfkdy-----psvYSEYGYVAARIIHlaleavdgnsedkd--klra 348
gi 72384023  263 ekmGDEAVGIISAGWYsgaistpvnERYVEGYRKQyhtt-----pgfYATGGYSAGLVLEqalqaggsatlsgr-alada 336
gi 75674864  268 gphRKVLEGTISAGPIgdhydnpvwKDFQARYVRRwskdvgqqtpgtLAFAYSTNLQATLlalnavdgdlsgnqeafrea 347
gi 84502441  260 gpfKDLLVGAPSGTPTvsnfegeewQAFVASYNEAfpdgf--sapsiFGHHYYMSTKAAMlaleevggdlsdgqeafraa 337
gi 85707328  257 naeGPAAEGVITALHYvptldnpanAQFVEAFKAKtgrv-----pseFAVHGYDAGRALIeavkagatdres-----lan 326
gi 119715096 275 nqiGPAAVGVGAAFYYsstldnaenERFISTMKAAnpdf----vpshFTAGAWASGSVLLdaieragddatdge--klaa 348
gi 126731081 262 graKEALIGTPTSGPLaddnpdpawQEYVKAYQDAfpegerfpspslFGVGYYVAALAAIeglnevdgdlsdgq-aafkn 340
gi 149375495 264 kaqGEAAEGVMTGLHYaeqldvpknREFREAFNTEyghy-----pdiYAVQGYDAGQAIAntidqlkgdisdkq--avis 336
                        330       340       350
                 ....*....|....*....|....*....|..
Feature 1                                        
gi 28971615  326 almttdfksLRGNFKFNTn-QFPMDsFYLREV 356
gi 27378498  340 alakieldaPNGKIKLDSn-RQAIGtNFVTEV 370
gi 33600577  349 amraikldaPRGPFRFNEe-TQSPIhNVYIRE 379
gi 72384023  337 mhavrlsqsPRGPLTLDRf-GNPVVtVYIRKV 367
gi 75674864  348 lrklefknyIDAHVKLDHn-RQAISdNFLTKV 378
gi 84502441  338 ltdlefvtpTGGTMRLDEn-RNGIVdNFVTEV 368
gi 85707328  327 alrqvsfdgPRGALSIDPa-TNNIVqPIYVYE 357
gi 119715096 349 airstkieaPWGPLAFDPdtGYAIApTYYYTV 380
gi 126731081 341 alstmtletPLGPVHLNEn-RQATGsVFINEV 371
gi 149375495 337 tmekltidsPRGEFTFSKa-HNPIQnVYLREV 367

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