1UQW


Conserved Protein Domain Family
PBP2_Ylib_like

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cd08499: PBP2_Ylib_like 
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The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold.
This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 173864
View PSSM: cd08499
Aligned: 32 rows
Threshold Bit Score: 542.581
Threshold Setting Gi: 89069473
Created: 26-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
1UQW_A        26 DVVVAVgsnfttLDPYDandtlSQAVAksFYQGLFGLDk--EXKLKNVLAESYTVsddgiTYTVKLREgIKFQDGTDFNA 103 Escherichia coli
YP_551178     33 SLTYVQgteidtLDPAVsrstpSQIVIthIFNKLVSWDgpgFKKIVPDLAESWNVsadgkVWTFNLRKgVKFHDGTPLDA 112 Polaromonas sp....
ZP_02171061   64 ELTVGIeaeptsMDPQNttdgnSATVQstMFEGLLRFDe--NMNIVNVLAEDYDYsddatEITFFLREdVTFHDGTAFDA 141 Bacillus seleni...
YP_002603417  24 DIIYASestvksLDPHDtsdtySGAIEraICQGLMGFDk--NLNIVPLLAESYTFneaatQFTFKLRKgIKFHDGADFNA 101 Desulfobacteriu...
YP_076481     41 VITIAHsgdpatLDPHKsfnglVFTVTnqIYETLLYRAa--DGTLQPRLATEWAPvd-etTWEFKLREgVKFSDGTPLNA 117 Symbiobacterium...
YP_001369184  27 SLTVAVpnnltgLDPTNindtlSQTSLrlIYQGLFGFDk--DMKLIPLLAESYEAngeatEFTIKIRKgIKFHDGSDFNA 104 Ochrobactrum an...
ZP_02083261   62 TYVIGTep--ltMDTHLmsdanTGRVSvqIHENLVKRDl--EGNFQPVLATEWSPnedatEWTFKLREgVTFHDGEPFNA 137 Clostridium bol...
YP_001469836  26 RFLIGVdit-tlLGPNIpd-svSNIVAshIFEGLIDVDe--NLKIIPSLAERWEIqengtAYVFFLRKgVKFHDGEIFNA 101 Thermotoga lett...
ZP_03149356   49 DITIAVaadfttMDPHDtndtlSYSVQktMLQGLVGFDk--EMKVIPVLAENYSVndnatEFTFKLRKgIKFHDGTPFNA 126 Geobacillus sp....
ZP_03495829   20 RLVVAQgtdpttLDAPLatdspSATVVthISETLFELTp--EGKIVPHLAEGYSFadggrTLTIRLRRgITFHDGTPFNA 97  Thermus aquatic...
1UQW_A       104 AAVKANLDRASDPanhlKRHNLYKni-aKTEAID---PTTVKITLKQPFSAFINILAHpa-taXISPAALEkygk----- 173 Escherichia coli
YP_551178    113 AAVKFNLDRLRSPelgsPNRSYYA----AIETVEapsTYVVTIAAKEPSPTLLEILTEew-asISSPTAIEkrgr----- 182 Polaromonas sp....
ZP_02171061  142 EAVKENLDFVRDEenglARSSFFSfi-dDVVVED---DLTVTIVSEEPNSAMASYMAHss-asMKSVEQIEmklddpdyn 216 Bacillus seleni...
YP_002603417 102 HAVKVNIERMMTGk--yKRSSLMKpv-eSLMVLD---DYTVQFNLKEPFGAFVNAIAHpg-slILSPKALEtygd----- 169 Desulfobacteriu...
YP_076481    118 EAVKFSLERLADPetkgPGAFIVGmi-eEITVVD---DHTVHIRTSTPFTPLLAHLSHpv-taIVSPTAATsgd------ 186 Symbiobacterium...
YP_001369184 105 EAVKVNIERLANPdnklSRRSLVSmv-kEVQIVD---DATVKLILKEPFGAMIASLAHpg-amIISPAALEkygk----- 174 Ochrobactrum an...
ZP_02083261  138 EAVKYNIERLKDPatgsPKSSLVTmi-sDFDIVN---DYEIKFILDQPCAVIPAMVSTys-tgMMSPKALEeygk----- 207 Clostridium bol...
YP_001469836 102 YAVKKHFDYVLGSs--lRNVGMFKgiikEVQVVD---DYTVKIILFRPYPPILYRLATssaawIISPKAIDefgsdp--a 174 Thermotoga lett...
ZP_03149356  127 EAVKANLDRLTDPnstlIRSSLFKvv-kETIVID---EYTVKVILSEPFGAMINTFAHpa-amMISPQALKqygd----- 196 Geobacillus sp....
ZP_03495829   98 EAVKFNLERLVSRelasPFAFLLSel-eRVEVVD---SHTVRLRLKNPFAPLLAHLTHss-taMQSPTAIArlga----- 167 Thermus aquatic...
1UQW_A       174 eigfYPVGTGPYELDTWNQtDFVKVKKFAGYWqp-gLPKLDSITWRPVADNnTRAAXLQTGeAQFAFPIPyeQATLLEKn 252 Escherichia coli
YP_551178    183 aygrNPVGTGPYVFKSWIPnERAEIVRNPDYFg--tPGKTDRLVFRPVPENaARVIELKTGnADVAANIApeLTGDFKGs 260 Polaromonas sp....
ZP_02171061  217 ldreGAVGTGPFTFVEWRDgEHVIVERNPDYWnqdeLANVEQITFRPVQEAaTRVNMLRTGeVDLIFPIPtlNAQELEQe 296 Bacillus seleni...
YP_002603417 170 evskHPVGTGPFIFDQWVSgNFVTIKKNPDYWr--gDVKVDTITFRPIPESgSRLAMLRAGqAHYIYPMPa-ELLKIAEr 246 Desulfobacteriu...
YP_076481    187 -lskQPAGTGPFLLEDWKAgDSVTLKANPDYWg--gKPKLDRVVLRIIPEAgTQLTELKAGtVDLISGVQpeRFNEIDSd 263 Symbiobacterium...
YP_001369184 175 eigrNPVGTGPFKFKNWSA-DTLEVVKNDNYWke-gLPKIDGVTVRSVPESgARFAMLQTGeAQFIPSFPp-ELMQVAEk 251 Ochrobactrum an...
ZP_02083261  208 dystHAAGTGPLKLKEWIPgTSMSLEKNESYWg--kAATAETIDIKIIAEDsARAMMLKTGdADVAANIPsvLVDELQSd 285 Clostridium bol...
YP_001469836 175 lfgkNPIGTGPFMFKSWKAgEKVELVKNPNYWre-gLPYLDSLVFSIVSEDiSRVTQVRAGdADVMYNPPpaLVPALEKd 253 Thermotoga lett...
ZP_03149356  197 evskHPVGTGPYMFEEWQPgDHLTVKKNPDYWna-tGNEVDSIIFKPTPENgTRIAMLQAGdADIIYPVPteSVKSIDGk 275 Geobacillus sp....
ZP_03495829  168 qyrdNPVGTGPYRFQAWQKgQFVDLVRNENYWg--pKPAIPQVRFIPVPEGtTRVALVETGqAHVAVRIPpqDIARLQAn 245 Thermus aquatic...
1UQW_A       253 kniELX--ASPSixQRYISXNvtqkPFDNPKVREALNYAINRPALVKVAFaGYATPAtgv-vpPSIAYAQSYKpw---pY 326 Escherichia coli
YP_551178    261 --dKMVlqQAPSafQVFFELNvtkpPFDDVRVRKAVNVAIDRQAIVDKILlGYGRVPv----sPFPEGTQARRifpaykY 334 Polaromonas sp....
ZP_02171061  297 egiDLY--TGPTtdLFYIGMNfeqeKYQDLAVRQAMNHAVDKDGLIAQVLdGYGIVAdsa-iaPNVYGYAEQPiy---eY 370 Bacillus seleni...
YP_002603417 247 d-aNIDiiKQPSiiARYLIMNtqfkPFADIRVRQAVNYALDKEAIIKIAWgGAASEAdsi-ipPNLQFYKKQAvw---pH 321 Desulfobacteriu...
YP_076481    264 pqlSAT--RFLGwgSMFLGFNmkagPLAQPEVRQAIAMAIDRQGIVDTLRqGMAQFGnsl-vpPTVFGSVPDLtg--peY 338 Symbiobacterium...
YP_001369184 252 n-pNVEvdKDPSivEWYVSLNnlkkPFDDVRVRHALNYAVDKKAYCKIVYnDLCEPAds--iiPKNLAFHVPVgn--yeY 326 Ochrobactrum an...
ZP_02083261  286 --pNVEieMVPGyrTIYLGLNfqdeKLANLKVREAIDYAIDRDAIINGILgGYVTYPstgvisSSIQNAKQGIgdd-ykY 362 Clostridium bol...
YP_001469836 254 pklNVI--TIPTvrVIYIGLNslvpPLNDVRVRQALNYAVDKEKLCSIIMrGMARPSdsp-lsSITYGYTSTGgy---pY 327 Thermotoga lett...
ZP_03149356  276 --nGIIveTNPSivVQYLSMNtlkkPFDDPRVRQAINYAINKEAFTQVVFnGFASPLksv-iaPNTQFYSEQKgy---dF 349 Geobacillus sp....
ZP_03495829  246 ravQVV--RTPSlrTIYIYFNtqrpPFNDVRVRQALNHAVNREEILQFVLgGIGRISdap-iaPGIFGYTPVGry---eY 319 Thermus aquatic...
1UQW_A       327 DPVKARELLKEAGYp-nGFSTTLWSShnh-staQKVLQFTQQQLAQVGIKAQVTaxDAGQRAAEVEGkgqk------esg 398 Escherichia coli
YP_551178    335 NPDEARRLLKAAFPggyPGVVTMWTPsgrytkdRAAAEAVQGYLNAVGLKTEFKvwEWASYQKELYRaepgkgtgkgsng 414 Polaromonas sp....
ZP_02171061  371 DVALAEELLEGSDQa-gGFEATLWTRnnt--efITVAEYVAIQLEEIGISVNVEpfEAGTLFDMLDAge----------g 437 Bacillus seleni...
YP_002603417 322 DLEKAKALMKEAGYe-nGFEVVFLTPnas--nrLRATEMAQQQLKKIGITGSLQsmDVASFYNKLEGyrvdd----akpl 394 Desulfobacteriu...
YP_076481    339 DPEGARALLAQAGVt-tPLKLTLNTYega--enQQIAQAIQAQLSQIGIDLEVVitDYGAFTEAIAKdd----------- 404 Symbiobacterium...
YP_001369184 327 NLDKAKELMTEAGLe-nGFETEIWANsnt--esIRAVQFIQQQLAQINVKVNVMplETGVAAQKIWSiekpe-----daa 398 Ochrobactrum an...
ZP_02083261  363 DPEKAKQLLAEAGYp-dGFTTKINTPegryamdRQVAEAIQAMLSQVGITAEVNvlDWGAYTEAAAAgd----------- 430 Clostridium bol...
YP_001469836 328 NPQKARQLLKEAGYe--NLKLELITPkgrylndYETAVAIQGMLSEVGIDLDVKpmEWGTYVAKILSnkpe------dwd 399 Thermotoga lett...
ZP_03149356  350 DLEKAKKLMAEAGYa-nGFTATLWGNnns--tsMKAMEFIQQQLAQINIKVTIEsmESGTLSDKIWNvktpe-----eae 421 Geobacillus sp....
ZP_03495829  320 NPQRAQELLRQAGVs-tPLRVTLHCPtgryfqdIQVCEAIQGQLRRVGVEASIQtmEWGAYLQETQRplke-------nr 391 Thermus aquatic...
1UQW_A       399 vRXFYTGWSAstgEADWALSPLFASqnwp-----ptlfNTAFYSNKQVDDFLAQAlktnDPAEKTRLYKAAQDIIWQe-S 472 Escherichia coli
YP_551178    415 aNMWLLGTGIp--NADIRLRRKLSTgd---------psNLTGYSNPMVDGLLAKAagemNYDKRMATYGDVQRVVWEleP 483 Polaromonas sp....
ZP_02171061  438 tDLWIGRWSPgtgEADYGLRPNFASdrvp-----pnfnNSGFYINEELDAMFDEAistpDEEEALSIYADIQEKIYQd-A 511 Bacillus seleni...
YP_002603417 395 pFIAFGGWSAstgDADWGTRPLISTeafp-----pamsNFGFFSDKKVDGFITAGlasaNPDIRKKAYADLQDYVWDk-A 468 Desulfobacteriu...
YP_076481    405 hGLWLTSWGTvtmDADYTLWALLHSgqh-------gadNKAFYANPQVDEWLTEArrtaDDAQRQALYRQIQEQVMKd-L 476 Symbiobacterium...
YP_001369184 399 vQMYYGGWSAstgDADWGIRPLLYGqsfp-----pamfNVAYFKDAKVDAAIEGAistaDPARRAEFYADAQKAAWEg-A 472 Ochrobactrum an...
ZP_02083261  431 tEIFLLGKGCatgDLAQDLMYNYRTge---------lqNYTFYSNPEYDKVCEEQqrtaDENARKELLYKMQDIIHEdrA 501 Clostridium bol...
YP_001469836 400 yQMFLLGWAPgtaEGHWVLFPLFHSvnqmgnpegtaryNNFFYRNPEVDDLIDKIgkelNEEKLMEYYAEAQKIILQd-A 478 Thermotoga lett...
ZP_03149356  422 iQLYYGGWSPstgDADWGIRPLLGGkesyp----pfsyNTAYYNNEKVNKLISDAlktaDPNVRKNVYAEIQTEIWNd-A 496 Geobacillus sp....
ZP_03495829  392 iQMAMLGWGTvtgDADYGLYPLFHSsqwa------pgfNRAFYKNPEVDKLLAQAristLPQGRLSLYKEAMTRIWQd-A 464 Thermus aquatic...
1UQW_A       473 PWIPLVVEklVSAHSK-NLTGFWIXPd-tGFSFED 505 Escherichia coli
YP_551178    484 NTIPLFDQvqLIGQRK-GVKGLTVYSd-eIVEFNN 516 Polaromonas sp. JS666
ZP_02171061  512 PWVFLHIPdaIIAKSE-DLHGIYILPs-gAVQMNL 544 Bacillus selenitireducens MLS10
YP_002603417 469 PWGYLFVDtmVAAKSK-KLKGIYPMPd-gAFSVEE 501 Desulfobacterium autotrophicum HRM2
YP_076481    477 PYLNLYYPlsSYAKND-RLQGEVYPFaaiNLDLRK 510 Symbiobacterium thermophilum IAM 14863
YP_001369184 473 PWIFLGVNqnLSAKTK-SLSGVYMLPd-rGFLLEE 505 Ochrobactrum anthropi ATCC 49188
ZP_02083261  502 SIILYYENq-TFGTRA-DVSGLVIYPn-eTIELAY 533 Clostridium bolteae ATCC BAA-613
YP_001469836 479 PWLFLYEMk-IATVSRkEIRGLKIYPt-eRFNMTY 511 Thermotoga lettingae TMO
ZP_03149356  497 PWAFLAVTdtICGYKN-YVKGAYLLPd-gSLSVDH 529 Geobacillus sp. G11MC16
ZP_03495829  465 PWIFLHSEvqVTAIRQ-EVQGFLVHPt--ERYLAY 496 Thermus aquaticus Y51MC23
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