Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_14

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cd08497: PBP2_NikA_DppA_OppA_like_14 
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.
This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. 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: 173862
View PSSM: cd08497
Aligned: 116 rows
Threshold Bit Score: 369.543
Threshold Setting Gi: 94502169
Created: 11-May-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
YP_423752     53 GFKHFDYVNPEAPKGGeirl----aeiGGWDSLNPFIVkgdPPAGAdl-----pFETLMVNSADEa--FSEYGLIAESVE 121 Magnetospirillu...
YP_002604113  62 NDHDPVFASPLAVKGGtfh-----talLSFPRTFRLVGp--DSNGSfagplranNLSLINIHPNT---GHIIPELATHWA 131 Desulfobacteriu...
ZP_01875277   62 GSEQKTFSDPQATKGGtwe-----aymQSFPPNFRQVGp-eSNSGFrglm-ddnDIDLVEIHPVT---NKLMPGIAKRWA 131 Lentisphaera ar...
ZP_01076305   38 GPDAPLFADKNAKQGGvynlr-lstfpLTFRTIGPDSNg-sFRPFLld-----gQPGLLQMHPNT---REYLPSLATEWA 107 Marinomonas sp....
YP_857919     34 NDTDPVFASPKALPGGsitmf-vdsfpLTFRTVGPDSNg-aFRSFImd-----nQLRLISFHPNT---GNPIPSLATHWA 103 Aeromonas hydro...
YP_857363     45 NNADPAFADPAAKRGGtfr-----gfmTSFPLTLRVYGp-dSNGGFagym-retNLPLLSTHPVT---GNPMPMLANEWA 114 Aeromonas hydro...
YP_001878284  88 GMEEPDVGDPRAVKGGkvrlwintpfpGTLRAFGPGSEn--FFNYSaid---nvWLPLVGLHPET---FRPIPGLADRWA 159 Akkermansia muc...
YP_001878448 122 GLDNPEIGDPNAKKGGvlrq---wapgSYPDTFRPNGPn--SNSGFrgplydeiIIGLVSIHPVT---GKIIPGIAHKWA 193 Akkermansia muc...
YP_001528829  58 NDTDPVFASPDAVTGGtlrls-llsfpLTFRVVGPDSNs-sFRSAIlg-----nQLSLISIHPNT---ERIVPEIATHWA 127 Desulfococcus o...
ZP_03727261   39 GGPLPEIGSPARKRGGtwngr-iqdfpRTLRVIGPDSNs--AFRGYlqd---dfALSFAGLHPDVpgpHQYFPALATQWA 112 Opitutaceae bac...
YP_423752    122 VpadrSWVIFNLRPKARWHDGKPITADDVVFSFEVLKAkg-----hPRYRFYYAAVdkVEKLAERRVRFAFkp-gdNREL 195 Magnetospirillu...
YP_002604113 132 FdpdkKTMYFKLNPLARWSDNVPVTAADYVYTLEFMRSphi--iapFYNDYYTREIesVVVYDDYTIAVKStk--aMPEL 207 Desulfobacteriu...
ZP_01875277  132 VtkdrTKIFFEIDPDATWDDGVPITVDDFIFRLKAMRSpgv--vapWYNQYYSTMLvdILKFSDHRMAVVLps--aMADT 207 Lentisphaera ar...
ZP_01076305  108 FdddqKTVYFKLDKTARWSDGADISSADFEFLFDYMRSdna--kapWYKDYYTNSItgITVYDEDTFALHSadrlpQDDL 185 Marinomonas sp....
YP_857919    104 IapdnQTVYFKLDPRAKWSDGKPVVADDYTFGYEMMRSkdi--qgpWFNNYYTTEVvaVEKVDDHTILVKAgtrkaKLDL 181 Aeromonas hydro...
YP_857363    115 FgpdhKTLYLRINPKARWSDGQPVTADDWLFTLKLLRSkei--ndpWYNNYYSTQIseVTKFDDHTLAISSgtaksRQDL 192 Aeromonas hydro...
YP_001878284 160 LsadgKTVFYHLDPEAAYSDGRIVKAQDFLLNICLRTSgfa--rdpFWTTLFRSMYdqITVYGDSVIALTLps--rGPLL 235 Akkermansia muc...
YP_001878448 194 EspdrRTVYFELDPDARYTDGAKVKAIDLLVNMYIRTSeys--rdvFYNNFFYQNAsnITIYDDSRFSITLpf--aKPLL 269 Akkermansia muc...
YP_001528829 128 FgkdkKTMYFRLNPDARWSDGMPVTAHDFAYTLAFMRSphi--vapWYNDYYTKEIekVVVYDDHTLAVVAsk--pDPDL 203 Desulfococcus o...
ZP_03727261  113 IdlpnRTVYVKIDPAARWSDGPPVNTDDVFFTFWFHQSpyiqapwyNNYYGIGENYtrITRYDTHTFSVTLke--aRPDL 190 Opitutaceae bac...
YP_423752    196 PLIvGQLPILPRHYWQgrdfav---------------------------------------------------------- 217 Magnetospirillu...
YP_002604113 208 YLR-LGISPTPRHFFGtlddtfv--------------------------------------------------------- 229 Desulfobacteriu...
ZP_01875277  208 VLK-GTIPPLPYHFYGelreirktypanralsylkrdgkevpteltqlleehnkaletlakdekppkeptyeitvedvqp 286 Lentisphaera ar...
ZP_01076305  186 IAR-LGVTPRPKHFYPdglpenfi-------------------------------------------------------- 208 Marinomonas sp....
YP_857919    182 LNT-TELWPQPKHYYKltpnwvk--------------------------------------------------------- 203 Aeromonas hydro...
YP_857363    193 LES-LPFSPAPSHVIKisadwvk--------------------------------------------------------- 214 Aeromonas hydro...
YP_001878284 236 PYM-ACADFHPAHPGFyhdfnalf-------------------------------------------------------- 258 Akkermansia muc...
YP_001878448 270 PYYcTLFIPSPPHFYCefgpnyv--------------------------------------------------------- 292 Akkermansia muc...
YP_001528829 204 YLK-VGISPTPSHFYGdldenfv--------------------------------------------------------- 225 Desulfococcus o...
ZP_03727261  191 PSRvLGLAPTPRHFYKetgpdfv--------------------------------------------------------- 213 Opitutaceae bac...
YP_423752    218 -----ttlepPLGSGPYK--VAGFDT------QHTITYERVKDYWGaDLAVRKGEYNFDRIRYDSYRDttVALEAFKAGe 284 Magnetospirillu...
YP_002604113 230 ---egfnwriIPNTGPYQ--ISEFKK------GKRVRFERKKQWWAkDLRYFKNRFNLDAVVFNVIRDynMIWEYFKKGe 298 Desulfobacteriu...
ZP_01875277  287 dwvntynwkiQPRTGPYN--IYSYIK------GKEVVFKRNENWWAkDKKFYKHRYNVDYIRYTVIRDnnLAFEKFKLGe 358 Lentisphaera ar...
ZP_01076305  209 ---krynwkaEPVTGPYI--LGKVKK------GKSIEFVKVKDWWGyNNPYYQNRYNVDRVRLKIIRDqdVAMKHFEKGs 277 Marinomonas sp....
YP_857919    204 ----qynwavVPNTGPYV--MSDVKK------GKSITFSKQKEWWAkDDRYNQHRFNLDTIKVQVIRDhnIAFRHFLKGe 271 Aeromonas hydro...
YP_857363    215 ----aynwklLPVTGPYQ--LGEVKK------GKSVTFERVKDWWGnDERYFQHRFNPDRIELKVLRDqnIAWQHFLRGe 282 Aeromonas hydro...
YP_001878284 259 --leryqwkvPPNTGGYMvvPSKIRI------GESITLARVKNWWAkERKYYRHSCNADQVEHVFVNMenKAVEMFRRGe 330 Akkermansia muc...
YP_001878448 293 ---eryqwriPPTTGAYV--VKPDGIi----rGRQVTLQRVPDWWAkDKKFTKYMYNVDQIVYNFIAEpsKAIELFRIGe 363 Akkermansia muc...
YP_001528829 226 ---rdynwkiAPNTGPYQ--VSGFEK------GKFVEFSRKPDWWAsDLRFFKNRFNVDKVVYTVVKDfnMSWEYFKQAe 294 Desulfococcus o...
ZP_03727261  214 ---trynwrfAPTTGAYV--ITDAELrrtttnRNHITLERLADWWAsEKPYFRYRYNPAKIRLRVIREttTAWEAFLTGe 288 Opitutaceae bac...
YP_423752    285 yDWRSeneaKKWATAYe-dWTGLKDGrgrkNAFan-qRPAGMQGYAFNLRRalFADIRVRRALGLAFDF-EWTNKTLFYs 361 Magnetospirillu...
YP_002604113 299 iDVFDltmpKYWYDRAd--TRVFNRGyakkIWFfn-dTPVSAMGMWLNQDKeiFADPRVRMAFAHAMNV-DKVIKEVLRg 374 Desulfobacteriu...
ZP_01875277  359 lDQFGlilpNYWHSKAk-yMDPVDMGymqkIWFyt-qQPQGSSQINFNLDKakLKDINLRLGIIYSLNI-QNMIDTVLYg 435 Lentisphaera ar...
ZP_01076305  278 iDAFSmilpGVWHNQG---KGPLYDKgfieKSWlfndTPQGATGVWLNLENplMQDANVRKGIAYSINVdKMIETALFG- 353 Marinomonas sp....
YP_857919    272 lDTFEmilpNWWHEKAv--TPEYKQGyvqkVMAmt-dTKQGGQGVHLNVANpkLADLNVRLGIQHAFNI-DKMIKTVLRg 347 Aeromonas hydro...
YP_857363    283 lDTFPlvmpNWWHDKSk--TPEFAKGyierLWFyn-qTPQPPTGLYLNTADplLRDLNVRLGIQHALNL-DKMLTTLLRg 358 Aeromonas hydro...
YP_001878284 331 lDIMNvrkpEVWETGLe--LPEVHRGyidkYSLea-nYACPPYGLYLNCSDklLKNPDIRRGLAHSVNM-GLVIDTLFRg 406 Akkermansia muc...
YP_001878448 364 lDVLNitkpELWHERMe--IPEVHNGyinrSTFyt-iYPRPPYGVFLNTSKapFNDLNVRRGFQHALNI-QNIIDITFRg 439 Akkermansia muc...
YP_001528829 295 iDAFPltmpDFWHDKTq--TPVFDKGyvhrIWFfn-dTQQSAMGMWLNQDIdiFKDVRVRYAFAHAMNI-QKVIDTVLRg 370 Desulfococcus o...
ZP_03727261  289 lDAFGlnlsEYYYDRLpdtHPLVARGliqkTIFyn-dIPRPNYALWMNTARplLANRDLRLGIQYATNW-QLVIDQYFRg 366 Opitutaceae bac...
YP_423752    362 QYKRTasyfanselaslglpsplelkvleplrgqippevftaefkppategdgniRPNLRAAMRLLEEAGWrvvdgk--l 439 Magnetospirillu...
YP_002604113 375 DYYRLaqafmgyge--------------------------------ytnndirprAFNIDKVESLMTEAGWqrgpdg--i 420 Desulfobacteriu...
ZP_01875277  436 DYERSetfnegygd--------------------------------ysnpnikarRFNPKKAVEYFEKAGYskigrdgir 483 Lentisphaera ar...
ZP_01076305  354 DYVHLqsfgsgkgi--------------------------------ydhptmkakPFDPKLAAEYFAKAGYdslgrdgir 401 Marinomonas sp....
YP_857919    348 DYDRAttfgsgfge--------------------------------ftdmqlperAYDIAKARDYFAKGGYakpgpdgil 395 Aeromonas hydro...
YP_857363    359 DYQRLnsygsgqge--------------------------------ftntdlkarPFDPELARQYFAKAGFtkpgpdgtl 406 Aeromonas hydro...
YP_001878284 407 NMRRLgsymegygd---------------------------------ltlplkapEYSKKKAMEYFARAGYremgtdgvl 453 Akkermansia muc...
YP_001878448 440 DYQRLnsynsgfgk--------------------------------ftnpyikarPYSPEQARAYFARAGYtipcpdgil 487 Akkermansia muc...
YP_001528829 371 DYFRLeqgfvgygd--------------------------------ytnpdvkarRFDLEKVNDYMTGAGWqrgtdg--i 416 Desulfococcus o...
ZP_03727261  367 DYTRLnttadgygs--------------------------------mtnpniharPFDIQRAAEHFAKAGYtqrgpdgil 414 Opitutaceae bac...
YP_423752    440 vdgaGRPFAFEILLVqp--awERITLPFVRNLSR-LGIEASVRtv-dPAQYKNRIDHfdfdMVVHVWgqs--qsPGNEQL 513 Magnetospirillu...
YP_002604113 421 wqkqGRRFSIEVTYGfd---eHTPRLVVLKEEALkAGVELVLQkl-dSTAAFKKFLEkkheVAWMGWstn--lrPSYWQG 494 Desulfobacteriu...
ZP_01875277  484 vnekGERLSFKILYAap--hhTQRILALQNEARK-LGLHLALDnf-dSTAVFKAMLSneheIAWNGWgag--frPKYRSQ 557 Lentisphaera ar...
ZP_01076305  402 inaqGERLVLVMNYSwk---aHSARTAVLREEAKkAGLDLQLNlvegATGFKAALEKkh-qAVFQGMgsg--mkPAYWQY 475 Marinomonas sp....
YP_857919    396 qndkGDRLTLALTYTsq--ehSKRLTVLKEEAKK-AGLDLELNlvdgATGFKAMLEKkheaAWLGWGggg--lyPQYWES 470 Aeromonas hydro...
YP_857363    407 qnsqGQPLTLAITYTta--ehAQRLTLLREEAKK-AGLNLELNlm-dASAGFKSMLEkkhqSAWMAWsgs--ryPAYWEF 480 Aeromonas hydro...
YP_001878284 454 knerGERLVVELTFAdsstlmTNVCSILRQEALK-CGVDLRLDsl-tYSVCSRKVFEkryqAALWAWpl---qtPFPRLY 528 Akkermansia muc...
YP_001878448 488 rkpdGTRLTAAITFPnsspslASTLGKLKEDARK-CGLEIQLDpldsTVAFRKIMEKra-qASFMAWgft-pphPMNEQG 564 Akkermansia muc...
YP_001528829 417 wekeGMRFSVDVTYShd--ghTPRLVVLKEEARK-AGIELNLRrldpSASYKQVLEKkh-eVGWVAWsts--lrPQYWEH 490 Desulfococcus o...
ZP_03727261  415 vndrGERLAVTLTTGye--alAPVLTILQQEARK-AGLHFEVEil-dSSTAWKKVQEknhdITFSAFnvgvelfPRYWEF 490 Opitutaceae bac...
YP_423752    514 gywgse----------------------sadeaGGQNVAGIKNKAVDALIEQVISAp-DRETLVARTRALDRVLLWnHYV 570 Magnetospirillu...
YP_002604113 495 whsdn------------------------ahktQTNNITNTDDPELDRLIDQYRSSl-SETERKSLSRTIQQKIHDqAAF 549 Desulfobacteriu...
ZP_01875277  558 fhken------------------------ahknQRNNLSNLDDDQVSEMIDKYRFAl-DSETRIKLAHQIEERLFElAAT 612 Lentisphaera ar...
ZP_01076305  476 fhsa-------------------------nakpQTNNFTNYQDPEMDKLIDAYDSEf-NVEKKAKFSHQIQEKIMAcDCF 529 Marinomonas sp....
YP_857919    471 fhsan------------------------ankpQTNNLFNVADKELDGLIDAYNVEf-DMTKRAELSRQIQQRIYDlAIF 525 Aeromonas hydro...
YP_857363    481 fhkin------------------------ankpQTNNIMNIDDDAITALVEQYDKEf-DFAKKAALSRQIQQRLYElASF 535 Aeromonas hydro...
YP_001878284 529 etfsselay----------------dargnpvgNTNNIMAVSDAGLDAALDAERNApdTGSLKLALHRAQQRLHEL-CVW 591 Akkermansia muc...
YP_001878448 565 fhsryayd------------------ergglitYTNNICAYADKEMDKLLDAETNAa-TEDELQKATWKVQQKIDDeALW 625 Akkermansia muc...
YP_001528829 491 fhsen------------------------ahkpQTNNITNTDDPEMDRLIEAYRASl-DAEERKVLSRQIQAKIHEiGAF 545 Desulfococcus o...
ZP_03727261  491 fhsanaydkpyltdatgtgaghktpnpdrkpkvQTNNLQSIAIPELDALIDAYDKSd-DLDAMRKMAWRMEGIIYEdGSY 569 Opitutaceae bac...
YP_423752    571 IPQWHLglDRLVWWDKFGMP 590 Magnetospirillum magneticum AMB-1
YP_002604113 550 VPTFMVpyVRQGFWRWLQLP 569 Desulfobacterium autotrophicum HRM2
ZP_01875277  613 IPTYKVpyFRQAAWRWVKYP 632 Lentisphaera araneosa HTCC2155
ZP_01076305  530 IPTYSVpyTRLAHWRYVRLP 549 Marinomonas sp. MED121
YP_857919    526 VPGVQLnyVRASSWRYVMLP 545 Aeromonas hydrophila subsp. hydrophila ATCC 7966
YP_857363    536 VPAYQVpyTREGAWRWIKLP 555 Aeromonas hydrophila subsp. hydrophila ATCC 7966
YP_001878284 592 IPGWREpyTHIACWRWIRWP 611 Akkermansia muciniphila ATCC BAA-835
YP_001878448 626 VPCWTTefIRLGYWRWVKWP 645 Akkermansia muciniphila ATCC BAA-835
YP_001528829 546 VPTFMVpyVRQACWRWWRLP 565 Desulfococcus oleovorans Hxd3
ZP_03727261  570 SPAFAMpfYRTGTWRWVGWP 589 Opitutaceae bacterium TAV2
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