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 1 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: 380578
Aligned: 43 rows
Threshold Bit Score: 446.252
Created: 2-Jul-2007
Updated: 2-Oct-2020
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:
Feature 1                                                                               #     
CAA75186   51 KVGILHSATGTMaiSETGSIQAEKLAIEQINAmGGILGRKIEIIQEDGasDWPTFAEKAKKLLEKdKVAAVMGCWTSASR 130 Methylophilus meth...
CUI16532   35 KVGLVFSTTGFRaqAEKPALEAALMAIEEINQkGGIHERKIEPIIIDAqsDWEKAKPAIERLISKdHVDVFFGGWTKASR 114 Protochlamydia nae...
OIO60311   44 RVGVLYSMSGRMesEEKPVVDAILFAIDEINQsGGLLGRRIEPVVVDGasRRSVFKEQAINLIEKdKVAVIFGGWMLLSR 123 Verrucomicrobia ba...
OGT46102   39 KVGVLFSQSGTMelTEKTIINATLLAIDEVNKsGILPGVRLEPVVYDGasNWERFAFLARKMILKdKVKVIVGCWSSSCR 118 Gammaproteobacteri...
AGC71433  441 RVGVLNSLSGTMaiSTRPIVEATLLAIDEINAqGGLLGRRIDAVRVDGrsDNNTFAVETERLIKQeKVVTIFGGWTPSNR 520 uncultured bacteri...
OYY25368   45 LVGVVHSQTGTMasAEGGVLQMTLAAINYLNQqGGVLGRPVKPVVMDGasDAQQFAKAVDSLIVDhGVVAIFGGWTSASR 124 Thiotrichales bact...
OHE17260   30 KIGLLYSASGTMstNEKPLSDMLRAAVWQINReGGIFGREVEIVEFDGksDSKEFKKGAKELIDK-GVVSIFGCWTSASR 108 Sulfurimonas sp. R...
AFS81355   48 KVGILHSLTGTMasSELPVLNATLFAIEEINSkGGLLDKKIVPIIYDGesNGQTFASRATDLLKDdNVSVIFGGWTSASR 127 Candidatus Nitroso...
AHF00719   32 KVGVLHALTGTMatSEQPLVQMVELAVEQINQqGGLLGRQLELVIADTesDADIAAYQAQKLIVDdQVSVVFGCWTSACR 111 Thiomicrospira aer...
EON92513   39 RIGALHSLTGTMasSESQEVDTLRALVAATNRqGGLLGRPLELVIADGasDPSTFARHAESLIKEqAVSVIFGCWLSSAR 118 Marinobacter lipol...
Feature 1                    #  ##                                          #                 
CAA75186  131 KAALPVFEKDNGLLFYPTFYEGleqsKNVFYTGQEATQQILAGLDWIAkekkakTFYLIGSDYi-wPRTSMKIARKHIeq 209 Methylophilus meth...
CUI16532  115 YTTKELFEKYNSLLINPFQFEGtltsPNIIWVGATLNQQVLPTVAYILknv-gkRIYLVGSKDyilSHLISTMVKDQLsa 193 Protochlamydia nae...
OIO60311  124 DIVRPVFEDRESLLFYPYQSKGmassTHVVNTGALLNQQVVPGISWAYrnl-gqRFFLVGSKEv-fPYAANTVIKDHIya 201 Verrucomicrobia ba...
OGT46102  119 KAVKSVVEKYNNLLIYPTQFEGteesHNIVYLGAAPNQQVIPGISWMFdhy-gkKVYLIGSDYi-yPHVANEIILADVks 196 Gammaproteobacteri...
AGC71433  521 RAMKPLLEKYDHLLIFPARDEGmedsHNIIYLGSTPYQQVIPAARWALdklgakRLFFIGLDGl-wGHISHELVRDTIkg 599 uncultured bacteri...
OYY25368  125 RAMLPVIEQHKGLLVYPVQYEGleesQNIIYTGTTPTQQLNLAITWMLehf-gsRVLLVGSDYi-fPRVENTIAQLVLkr 202 Thiotrichales bact...
OHE17260  109 KEVKEVVEAANNVLFYPLQYEGfessPNIVYLGLSANQQINPTIDFIRtnf-gnNVYLVGSDYi-yPKAANFYINELSkl 186 Sulfurimonas sp. R...
AFS81355  128 KSMIPVLDEYDAVLFYPVQYEGlesrPNILYLGAAPNQQVIPGIIWAQenl-gtKFFLVGSDYv-fPYSANTIIKDYSkt 205 Candidatus Nitroso...
AHF00719  112 KMVKPVFEEHHHLLFYPVQYEGleasNHIFYTGSSPNQQIVPGARWAMqqf-gpRVLLLGSDYv-fPRIANMILADMIsa 189 Thiomicrospira aer...
EON92513  119 KAVKPVIERYDSLLMYPAQHEGlersEHIIYAGTTPNQQLFPSLIWAQntf-gnKLFLVGSDYv-yPKSLNVITRILApk 196 Marinobacter lipol...
Feature 1                                                                                     
CAA75186  210 hlhGTVVGEEYIALDdt-qFGSVINKIKLKkpdVIYAAVVGGSNVAWFKQLNAAgln---sskQTMLTISVtedev---- 281 Methylophilus meth...
CUI16532  194 -leGEIVGETYIPIHeq-eMDDLMLDIEAKkpdAILSSLISESNNAFYTNLVKAgvt---alpPPVFSLSTdeii----- 263 Protochlamydia nae...
OIO60311  202 -lgGSIVGEEYISIEse-dIDSIVSIIKNVkpeVIVCTTLGKTTIALYQSLRKAgis---pddIPSIGFTIdevllq--q 274 Verrucomicrobia ba...
OGT46102  197 -lgGEIVGVKYLPLGsn-dVGDVINDIIKKrpdFIVNTINGSTNIAFFTQLNALttg---ikrIPVISFSVsdaev---- 267 Gammaproteobacteri...
AGC71433  600 -tsAKIVGKEFVLLSet-dFSGIVKKIQSSradVVLNFVQGDSNLPLFRELRNAgls---ptkLPVISFGIgenei---- 670 uncultured bacteri...
OYY25368  203 -lgAQVCGEYYIKLGsa-sVDGLANMVAECkpdFIINTVNGSDNLALFRLLRQEga------nLPLMSLSMdelqlqqli 274 Thiotrichales bact...
OHE17260  187 -tdLNVLGERYFVLDsk-dFKDLFKDIKSKkpdAIINTLNGDSNIEFFKRLKEHgis---ssdIPVISLSLdeaslf-ki 260 Sulfurimonas sp. R...
AFS81355  206 -ygFDIVGEEYALLGak-nFVDIVANIKKTnpdVIINTINGDSNEYFFKELRKQgit---sdlIPTMSFSLsqsq----- 275 Candidatus Nitroso...
AHF00719  190 -nqGEILAELYKPLGdl-dFDAVIKQIEQLkpdVILNTLNGDSNLAFFNSLVTSgl-----qdIPTMSFSVaepel---- 258 Thiomicrospira aer...
EON92513  197 -igLEVIGERYLDLVdhdaAKALADEIALSganFVLNSINGDGNEAFFQALDNIyrkkpdkplPAVISLSLdena----- 270 Marinobacter lipol...
Feature 1                                                                                     
CAA75186  282 lgigGENLAGFYSAMKYFQSqd--nPENKKFVEAFKKRWgkda----vigdVTQAAYLGPWLYKAAVERAGSFDVDKVQA 355 Methylophilus meth...
CUI16532  264 lqqaPEEIVGTYATWNYFQSid--tPRNHAFVKNFQTFSdlka-----idnATEATYLGVHLWAKAVAEAGTTNPRALSY 336 Protochlamydia nae...
OIO60311  275 lmqaNIDMAGDYGVWNYFQSiq--sQQNHAFLNEFKKKYgqnr----avsdTMVSAYIGVKLWAEAVKSGKSFREADVLD 348 Verrucomicrobia ba...
OGT46102  268 nkigIDKYKGNYQVWSYFTLld--tPENKAFLKAYQKKYgnvn----nisdPAITAYAGLKLWTQGLAQAITQSVDLNPN 341 Gammaproteobacteri...
AGC71433  671 sqldGVDLSGDYLAWSYFESvd--rPQNKQFVESFKKKFgdhr----gisdPMEAAYAGVYLWAQAVRAAGTDDVQAIRR 744 uncultured bacteri...
OYY25368  275 valgERVAKEHYVATGYLSSle--tPENREFKARVANVTnhhqldvryisaAMKSAWDGVFLWAQAVNAASELSAEQVLH 352 Thiotrichales bact...
OHE17260  261 sandKNVMYGHYATWGYFDIm---nKSRNEFSTLLKDRFkqdv----vvtdAMFSIYLGAQLFKQAILKSKKTTPEEILK 333 Sulfurimonas sp. R...
AFS81355  276 isnyAVSVEDDYLVWNYFENip--sYENRQFVSNIKKTLgsky----fisdSMEAAYVGIYLYAKAVEKANSFENDDVLD 349 Candidatus Nitroso...
AHF00719  259 qawgGERLTQHYGVWGFFQSlt--dPLTRELVSAYQQRFganl----pvsdPMIASYLGVQLWASAVVYEQSANPRQVNN 332 Thiomicrospira aer...
EON92513  271 arslPNLQGHSYLSWSYFYDpehweQPNDPVISDALNHElsgy----pisaTMAATIISYTLWRSTVEHIGTPQPRAVNA 346 Marinobacter lipol...
Feature 1                                                     
CAA75186  356 ALPgy---tfKDAPEGPVTVEA-NHHLTTKLRIGQWGKDGQAKVVYTS 399 Methylophilus methylotrophus
CUI16532  337 ILAsm----rIEAPEGTVIMDIeGRRAWKFVRIGQVQPNGQFRIVWQS 380 Protochlamydia naegleriophila
OIO60311  349 HVGgk----sMESPGGLVYVDPqTNHLYKTVYIGEALSNGQYKLVWES 392 Verrucomicrobia bacterium CG1_02_43_26
OGT46102  342 IIRgfmlrqsIASPAGVIYIDPfNAMAWRTVLISKVNDQGKMDIVWSS 389 Gammaproteobacteria bacterium RIFCSPHIGHO2_12_FULL...
AGC71433  745 ALQgq----sIEGPGATLRLDPgNNHAWKMFRMGKIVDATRIELVYSS 788 uncultured bacterium A1Q1_fos_1070
OYY25368  353 AIEgm----sYASATGPVTVDPfNRHLWQPVFIGKAQANGQFALEWQT 396 Thiotrichales bacterium 35-46-9
OHE17260  334 NIKra----sLNISDNIYYVDSiNKHLHRNVFIGKVSTQNQFDIVWQS 377 Sulfurimonas sp. RIFOXYD2_FULL_37_8
AFS81355  350 KLKqi----tFSAPSGITGIDP-TNHVYKTMRIGKILSDGQVEIIFSS 392 Candidatus Nitrosopumilus koreensis AR1
AHF00719  333 VYLqs---lsMPAPGSMVVFERtNRHLWRPMRIGHVQPDGQYQQVYVT 377 Thiomicrospira aerophila AL3
EON92513  347 SIRnr----gIRLLGGHIFADPeTGHLYQFSKIAAHQNQVPLPIVWQS 390 Marinobacter lipolyticus SM19

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