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Conserved domains on  [gi|4139621|pdb|1B3G|A]
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Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kik

Protein Classification

oligopeptide ABC transporter substrate-binding protein OppA (domain architecture ID 11487649)

oligopeptide ABC transporter substrate-binding protein OppA is a component of the oligopeptide permease, a binding protein-dependent transport system, and functions as the initial receptor; it binds peptides up to five amino acids long with high affinity

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
1-517 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


:

Pssm-ID: 185059  Cd Length: 543  Bit Score: 1133.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         1 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENA 80
Cdd:PRK15104  27 ADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDGHPAPGVAESWDNKDFKVWTFHLRKDA 106
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        81 KWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLV 160
Cdd:PRK15104 107 KWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDLGVKAIDDHTLEVTLSEPVPYFYKLLV 186
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       161 HPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 240
Cdd:PRK15104 187 HPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       241 IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP 320
Cdd:PRK15104 267 IDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGLDRDIIVNKVKNQGDLPAYGYTPP 346
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       321 YTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 400
Cdd:PRK15104 347 YTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKLAIAAASIWKKNLGVNVKLENQEWKTF 426
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       401 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV 480
Cdd:PRK15104 427 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETLKVKDEAQRAALYQKAEQQLDKDSAIV 506
                        490       500       510
                 ....*....|....*....|....*....|....*..
1B3G_A       481 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 517
Cdd:PRK15104 507 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
 
Name Accession Description Interval E-value
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
1-517 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059  Cd Length: 543  Bit Score: 1133.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         1 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENA 80
Cdd:PRK15104  27 ADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDGHPAPGVAESWDNKDFKVWTFHLRKDA 106
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        81 KWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLV 160
Cdd:PRK15104 107 KWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDLGVKAIDDHTLEVTLSEPVPYFYKLLV 186
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       161 HPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 240
Cdd:PRK15104 187 HPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       241 IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP 320
Cdd:PRK15104 267 IDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGLDRDIIVNKVKNQGDLPAYGYTPP 346
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       321 YTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 400
Cdd:PRK15104 347 YTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKLAIAAASIWKKNLGVNVKLENQEWKTF 426
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       401 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV 480
Cdd:PRK15104 427 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETLKVKDEAQRAALYQKAEQQLDKDSAIV 506
                        490       500       510
                 ....*....|....*....|....*....|....*..
1B3G_A       481 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 517
Cdd:PRK15104 507 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
13-514 0e+00

The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. 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.


Pssm-ID: 173869  Cd Length: 498  Bit Score: 663.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       13 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08504   1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDGKIVPGLAESWEvSDDGLTYTFHLRKDAKWSNGDPVTAQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRLADPNTASPYASYLQYghIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 171
Cdd:cd08504  81 DFVYSWRRALDPKTASPYAYLLYP--IKNAEAINAGKKPPDELGVKALDDYTLEVTLEKPTPYFLSLLAHPTFFPVNQKF 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      172 VEKFGDK-WTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPi 250
Cdd:cd08504 159 VEKYGGKyGTSPENIVYNGPFKLKEWTPNDKIVLVKNPNYWDAKNVKLDKINFLVIKDPNTALNLFEAGELDIAGLPPE- 237
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      251 elFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDLPAYSYTPPYTDGAKlv 328
Cdd:cd08504 238 --QVILKLKNNKDLKSTPYLGTYYLEFNTKKPPLDNKRVRKALSLAIDREALVEKVlgDAGGFVPAGLFVPPGTGGDF-- 313
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      329 ePEWFKWSQQKRNEEAKKLLAEAGFTADK-PLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQG 407
Cdd:cd08504 314 -RDEAGKLLEYNPEKAKKLLAEAGYELGKnPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVKVTLKNVEWKVFLDRRRKG 392
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      408 TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 487
Cdd:cd08504 393 DFDIARSGWGADYNDPSTFLDLFTSGSGNNYGGYSNPEYDKLLAKAATETDPEKRWELLAKAEKILLDDAPIIPLYQYVT 472
                       490       500
                ....*....|....*....|....*..
1B3G_A      488 ARLVKPWVGGYTgKDPLDNIYVKNLYI 514
Cdd:cd08504 473 AYLVKPKVKGLV-YNPLGGYDFKYAYL 498
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
5-516 0e+00

ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 226636 [Multi-domain]  Cd Length: 562  Bit Score: 540.46  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        5 AGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG-HPSPGVAEKWEN-KDFKVWTFHLRENAKW 82
Cdd:COG4166  30 HGTSLAGKQVLYVNNFSHPDSLDPQAPKGGVSTNVLRGLFEGLVRYDPKGgPALPGAAESWEVsDDGKTYTFHLRADAKW 109
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       83 SDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKK-PATDLGVKALDDHTFEVTLSEPVPYFYKLLVH 161
Cdd:COG4166 110 SNGDPVTAVDFVLSWKAAADPKTTAPYVYFLFNSVIKNAEPIFTGKKsPVDVLGVKALDDRTLEITLEKPTPYFLLLLAH 189
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      162 PSVSPVPKSAVEKFGDKWTQPA--NIVTNGAYKLKNWVV-NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRS 238
Cdd:COG4166 190 GTFLPVNPKHVEKYGDDFTKPLdeNPVGNGPYKLKSWVDpNQKIVLERNPDYWDKDNVVLDGITYDYIDDANTALEAFKA 269
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      239 GEIDMTYNN--MPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS 316
Cdd:COG4166 270 GEIDIASEPpaSPWALDYVLKLKDNGDVYKEPTLGTQYLAFNTRRPPFNDPRVRKALSLAIDREWLNKQVFGGRSTPATS 349
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      317 YTPPYTDGAKLVE-PEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-----HKKLAIAVASIWKKNLG--- 387
Cdd:COG4166 350 FTPPAASGLPGKElALLAPLPQKDPPEKAKELLKEAGYELGGRLNLTLKLLTSAGwkgsqHKNIATGLPFQWEKLLGlak 429
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      388 VNVNLENQEWKTFLDTRHQ-GTFDVARAGWCADYNEPTSFLNTMLSDSS--NNTAHYKSPAFDKLIADTLKVADDTQRSE 464
Cdd:COG4166 430 IGIKLVIREVKTQYTKRLQsGDFDMILSGWGADYNDPSEFLRLFFTSSSadNNAAGYKNPEYDALIEAALEAQDPEERLE 509
                       490       500       510       520       530
                ....*....|....*....|....*....|....*....|....*....|....
1B3G_A      465 LYAK-AEQQLDKDSAIVPVYYYVNaRLVKPW-VGGYTGKDPLDNIYVKNLYIIK 516
Cdd:COG4166 510 LLARaAERILLQDAPVIPLYYYAN-RLARWDrPKGSPGYNPLGDVYWKDLYKKK 562
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
58-434 1.59e-101

Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family are based on the PDBSum definitions of the domain edges for Salmonella typhimurium oppA.


Pssm-ID: 334111  Cd Length: 360  Bit Score: 309.33  E-value: 1.59e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         58 PGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYghianiddiiagkkPATDLGV 136
Cdd:pfam00496   2 PALAESWEvSDDGKTYTFKLRKGVKFSDGTPFTADDVVFSFERILDPDTASPYASLLAY--------------SLDIVGV 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        137 KALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAvekfGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKT 216
Cdd:pfam00496  68 EAVDDYTVVFTLKKPNPLFLPLLAAPAAAIVEKAD----DDKKDLNEKPVGTGPYKLVEYKPGQKVVLERNPDYWWGGKP 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        217 VINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLA 296
Cdd:pfam00496 144 KLDRIVFRVIPDSTARAAALQSGEIDDAAEVPPPDIATLKKDKGLDVKVESPGGRTYYLAFNTKKPPFDDVRVRQALSYA 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        297 LDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvePEWFKWSQQKRNEEAKKLLAEAGFT---ADKPLTFDLLYNTSDLHKK 373
Cdd:pfam00496 224 IDREAIVKAVLGGYATPANSLVPPGFPGY----DDSYPPAYAYDPEKAKKLLAEAGYKdgdGDKLKLTLLVYNGSPAAKA 299
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
1B3G_A        374 LAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDS 434
Cdd:pfam00496 300 IAELIQQQLKK-IGIKVEIKTVDWATYLERVKDGDFDMALTGWGGDYPDPDNFLYPLLSST 359
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
26-484 2.12e-42

nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Most appear to be lipoproteins. This protein was previously (circa 2003) thought to mediate binding to nickel through water molecules, but is now thought to involve a chelating organic molecule, perhaps butane-1,2,4-tricarboxylate, acting as a metallophore. [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 274072  Cd Length: 500  Bit Score: 157.66  E-value: 2.12e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         26 LDPHKIEgvPESNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAhdfvyswqrladP 103
Cdd:TIGR02294  19 MNPHVYN--PNQMFAQSMvYEPLVRYTADGKIEPWLAKSWTvSEDGKTYTFKLRDDVKFSDGTPFDA------------E 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        104 NTAspyasylqyghiANIDDIIAGKKPATDLG-------VKALDDHTFEVTLSEPV-PYFYKLLVhpsVSPVPKSAVEKF 175
Cdd:TIGR02294  85 AVK------------KNFDAVLQNSQRHSWLElsnqldnVKALDKYTFELVLKEAYyPALQELAM---PRPYRFLSPSDF 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        176 GDKWTQPA--NIVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN---MPI 250
Cdd:TIGR02294 150 KNDTTKDGvkKPIGTGPWMLGESKQDEYAVFVRNENYW-GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGNegsIDL 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        251 ELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYTDGAkl 327
Cdd:TIGR02294 229 DTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPAdtlFAKNVPYADID-- 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        328 VEPewFKWSQQKrneeAKKLLAEAGFT--ADK--------PLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQE 396
Cdd:TIGR02294 307 LKP--YKYDVKK----ANALLDEAGWKlgKGKdvrekdgkPLELELYYdKTSALQKSLAEYLQAEWRK-IGIKLSLIGEE 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        397 WKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDS-SNNTAHYK---SPAFDKLIADTLKVADDTQRSELYAKAEQ 471
Cdd:TIGR02294 380 EDKIAARRRDGDFDMMFNyTWGAPY-DPHSFISAMRAKGhGDESAQSGlanKDEIDKSIGDALASTDETERQELYKNILT 458
                         490
                  ....*....|...
1B3G_A        472 QLDKDSAIVPVYY 484
Cdd:TIGR02294 459 TLHDEAVYIPISY 471
 
Name Accession Description Interval E-value
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
1-517 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059  Cd Length: 543  Bit Score: 1133.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         1 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENA 80
Cdd:PRK15104  27 ADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDGHPAPGVAESWDNKDFKVWTFHLRKDA 106
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        81 KWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLV 160
Cdd:PRK15104 107 KWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDLGVKAIDDHTLEVTLSEPVPYFYKLLV 186
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       161 HPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 240
Cdd:PRK15104 187 HPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       241 IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP 320
Cdd:PRK15104 267 IDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGLDRDIIVNKVKNQGDLPAYGYTPP 346
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       321 YTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 400
Cdd:PRK15104 347 YTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKLAIAAASIWKKNLGVNVKLENQEWKTF 426
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       401 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV 480
Cdd:PRK15104 427 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETLKVKDEAQRAALYQKAEQQLDKDSAIV 506
                        490       500       510
                 ....*....|....*....|....*....|....*..
1B3G_A       481 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 517
Cdd:PRK15104 507 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
13-514 0e+00

The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. 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.


Pssm-ID: 173869  Cd Length: 498  Bit Score: 663.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       13 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08504   1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDGKIVPGLAESWEvSDDGLTYTFHLRKDAKWSNGDPVTAQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRLADPNTASPYASYLQYghIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 171
Cdd:cd08504  81 DFVYSWRRALDPKTASPYAYLLYP--IKNAEAINAGKKPPDELGVKALDDYTLEVTLEKPTPYFLSLLAHPTFFPVNQKF 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      172 VEKFGDK-WTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPi 250
Cdd:cd08504 159 VEKYGGKyGTSPENIVYNGPFKLKEWTPNDKIVLVKNPNYWDAKNVKLDKINFLVIKDPNTALNLFEAGELDIAGLPPE- 237
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      251 elFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDLPAYSYTPPYTDGAKlv 328
Cdd:cd08504 238 --QVILKLKNNKDLKSTPYLGTYYLEFNTKKPPLDNKRVRKALSLAIDREALVEKVlgDAGGFVPAGLFVPPGTGGDF-- 313
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      329 ePEWFKWSQQKRNEEAKKLLAEAGFTADK-PLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQG 407
Cdd:cd08504 314 -RDEAGKLLEYNPEKAKKLLAEAGYELGKnPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVKVTLKNVEWKVFLDRRRKG 392
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      408 TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 487
Cdd:cd08504 393 DFDIARSGWGADYNDPSTFLDLFTSGSGNNYGGYSNPEYDKLLAKAATETDPEKRWELLAKAEKILLDDAPIIPLYQYVT 472
                       490       500
                ....*....|....*....|....*..
1B3G_A      488 ARLVKPWVGGYTgKDPLDNIYVKNLYI 514
Cdd:cd08504 473 AYLVKPKVKGLV-YNPLGGYDFKYAYL 498
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
5-516 0e+00

ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 226636 [Multi-domain]  Cd Length: 562  Bit Score: 540.46  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        5 AGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG-HPSPGVAEKWEN-KDFKVWTFHLRENAKW 82
Cdd:COG4166  30 HGTSLAGKQVLYVNNFSHPDSLDPQAPKGGVSTNVLRGLFEGLVRYDPKGgPALPGAAESWEVsDDGKTYTFHLRADAKW 109
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       83 SDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKK-PATDLGVKALDDHTFEVTLSEPVPYFYKLLVH 161
Cdd:COG4166 110 SNGDPVTAVDFVLSWKAAADPKTTAPYVYFLFNSVIKNAEPIFTGKKsPVDVLGVKALDDRTLEITLEKPTPYFLLLLAH 189
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      162 PSVSPVPKSAVEKFGDKWTQPA--NIVTNGAYKLKNWVV-NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRS 238
Cdd:COG4166 190 GTFLPVNPKHVEKYGDDFTKPLdeNPVGNGPYKLKSWVDpNQKIVLERNPDYWDKDNVVLDGITYDYIDDANTALEAFKA 269
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      239 GEIDMTYNN--MPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS 316
Cdd:COG4166 270 GEIDIASEPpaSPWALDYVLKLKDNGDVYKEPTLGTQYLAFNTRRPPFNDPRVRKALSLAIDREWLNKQVFGGRSTPATS 349
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      317 YTPPYTDGAKLVE-PEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-----HKKLAIAVASIWKKNLG--- 387
Cdd:COG4166 350 FTPPAASGLPGKElALLAPLPQKDPPEKAKELLKEAGYELGGRLNLTLKLLTSAGwkgsqHKNIATGLPFQWEKLLGlak 429
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      388 VNVNLENQEWKTFLDTRHQ-GTFDVARAGWCADYNEPTSFLNTMLSDSS--NNTAHYKSPAFDKLIADTLKVADDTQRSE 464
Cdd:COG4166 430 IGIKLVIREVKTQYTKRLQsGDFDMILSGWGADYNDPSEFLRLFFTSSSadNNAAGYKNPEYDALIEAALEAQDPEERLE 509
                       490       500       510       520       530
                ....*....|....*....|....*....|....*....|....*....|....
1B3G_A      465 LYAK-AEQQLDKDSAIVPVYYYVNaRLVKPW-VGGYTGKDPLDNIYVKNLYIIK 516
Cdd:COG4166 510 LLARaAERILLQDAPVIPLYYYAN-RLARWDrPKGSPGYNPLGDVYWKDLYKKK 562
PRK09755 PRK09755
putative ABC transporter periplasmic-binding protein; Provisional
1-517 2.00e-161

putative ABC transporter periplasmic-binding protein; Provisional


Pssm-ID: 182060  Cd Length: 535  Bit Score: 468.85  E-value: 2.00e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         1 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDF-KVWTFHLREN 79
Cdd:PRK09755  21 ADVPANTPLAPQQVFRYNNHSDPGTLDPQKVEENTAAQIVLDLFEGLVWMDGEGQVQPAQAERWEILDGgKRYIFHLRSG 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        80 AKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLL 159
Cdd:PRK09755 101 LQWSDGQPLTAEDFVLGWQRAVDPKTASPFAGYLAQAHINNAAAIVAGKADVTSLGVKATDDRTLEVTLEQPVPWFTTML 180
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       160 VHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSG 239
Cdd:PRK09755 181 AWPTLFPVPHHVIAKHGDSWSKPENMVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQVEYLALDNSVTGYNRYRAG 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       240 EIDMTYnnMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQgDLPAYSYTP 319
Cdd:PRK09755 261 EVDLTW--VPAQQIPAIEKSLPGELRIIPRLNSEYYNFNLEKPPFNDVRVRRALYLTVDRQLIAQKVLGL-RTPATTLTP 337
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       320 PYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKT 399
Cdd:PRK09755 338 PEVKGFSATTFDELQKPMSERVAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQVTLRTMEWKT 417
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       400 FLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAI 479
Cdd:PRK09755 418 YLDARRAGDFMLSRQSWDATYNDASSFLNTLKSDSEENVGHWKNAQYDALLNQATQITDATKRNALYQQAEVIINQQAPL 497
                        490       500       510
                 ....*....|....*....|....*....|....*...
1B3G_A       480 VPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 517
Cdd:PRK09755 498 IPIYYQPLIKLLKPYVGGFPLHNPQDYVYSKELYIKAH 535
PBP2_NikA_DppA_OppA_like cd00995
The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains ...
14-498 2.42e-134

The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. 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. Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel. 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 of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173853 [Multi-domain]  Cd Length: 466  Bit Score: 397.06  E-value: 2.42e-134
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 92
Cdd:cd00995   1 TLTVALGSDPTSLDPAFATDASSGRVLRLIYDGLVRYDPDGELVPDLAESWEvSDDGKTYTFKLRDGVKFHDGTPLTAED 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       93 FVYSWQRLADPNTASPYASYLqyghiANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAV 172
Cdd:cd00995  81 VVFSFERLADPKNASPSAGKA-----DEIE------------GVEVVDDYTVTITLKEPDAPFLALLAYPAASPVPKAAA 143
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      173 EKFGDKWTQpaNIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIEL 252
Cdd:cd00995 144 EKDGKAFGT--KPVGTGPYKLVEWKPGESIVLERNDDYWGPGKPKIDKITFKVIPDASTRVAALQSGEIDIAD-DVPPSA 220
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      253 FQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEW 332
Cdd:cd00995 221 LETLKKNPGIRLVTVPSLGTGYLGFNTNKPPFDDKRVRQAISYAIDREEIIDAVLGGYGTPATSPLPPGSWGYYDKDLEP 300
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      333 FKwsqqKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-HKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGT-FD 410
Cdd:cd00995 301 YE----YDPEKAKELLAEAGYKDGKGLELTLLYNSDGPtRKEIAEAIQAQLKE-IGIKVEIEPLDFATLLDALDAGDdFD 375
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      411 VARAGWCADYNEPTSFLNTMLSDSS---NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 487
Cdd:cd00995 376 LFLLGWGADYPDPDNFLSPLFSSGAsgaGNYSGYSNPEFDALLDEARAETDPEERKALYQEAQEILAEDAPVIPLYYPNN 455
                       490
                ....*....|.
1B3G_A      488 ARLVKPWVGGY 498
Cdd:cd00995 456 VYAYSKRVKGF 466
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
58-434 1.59e-101

Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family are based on the PDBSum definitions of the domain edges for Salmonella typhimurium oppA.


Pssm-ID: 334111  Cd Length: 360  Bit Score: 309.33  E-value: 1.59e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         58 PGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYghianiddiiagkkPATDLGV 136
Cdd:pfam00496   2 PALAESWEvSDDGKTYTFKLRKGVKFSDGTPFTADDVVFSFERILDPDTASPYASLLAY--------------SLDIVGV 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        137 KALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAvekfGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKT 216
Cdd:pfam00496  68 EAVDDYTVVFTLKKPNPLFLPLLAAPAAAIVEKAD----DDKKDLNEKPVGTGPYKLVEYKPGQKVVLERNPDYWWGGKP 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        217 VINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLA 296
Cdd:pfam00496 144 KLDRIVFRVIPDSTARAAALQSGEIDDAAEVPPPDIATLKKDKGLDVKVESPGGRTYYLAFNTKKPPFDDVRVRQALSYA 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        297 LDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvePEWFKWSQQKRNEEAKKLLAEAGFT---ADKPLTFDLLYNTSDLHKK 373
Cdd:pfam00496 224 IDREAIVKAVLGGYATPANSLVPPGFPGY----DDSYPPAYAYDPEKAKKLLAEAGYKdgdGDKLKLTLLVYNGSPAAKA 299
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
1B3G_A        374 LAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDS 434
Cdd:pfam00496 300 IAELIQQQLKK-IGIKVEIKTVDWATYLERVKDGDFDMALTGWGGDYPDPDNFLYPLLSST 359
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
4-516 1.76e-90

ABC-type transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 223818 [Multi-domain]  Cd Length: 556  Bit Score: 287.23  E-value: 1.76e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        4 PAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESN--VSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENA 80
Cdd:COG0747  32 TAAAAQLPTGTLTIALGGSPTTLDPATAFDGGTGGdvLGNLVYEGLVEYDENGELVPALAESWEvSEDGKTYTFKLRKGV 111
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       81 KWSDGTPVTAHDFVYSWQRLADPNTasPYASYLQYGHIANiddiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLL- 159
Cdd:COG0747 112 KFHDGTPFTADDVKFSFERALDPDG--PLLGALGLGVIAS---------------VEAVDDYTVRFTLKEPNAPFLLLLl 174
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      160 -VHPSVSPVPKSAVEKFGDKWTQPA---NIVTNGAYKLKNWVVNERIVLERNPQYW--DNAKTVINQVTYLPISSEVTDV 233
Cdd:COG0747 175 lAGGGASIVPKHAIEDKEADEGVPAalkNPVGTGPYKLVEWDPGQQIVLERNPDYWggDKPGPYLDRVTFRVVPDANARL 254
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      234 NRYRSGEIDMTYNNMPIEL-----FQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-K 307
Cdd:COG0747 255 AALESGEIDLAYGGVPPSAedlkrLKADPGYVVLPVVSAPGLNTGYLSFNPKKAPLDDVRVRQALAYAIDRDAIVDTVlK 334
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      308 NQGDLPAYSYTPPYTDGA--KLVEPEWFKWSQqkrnEEAKKLLAEAGFTA-----DKPLTFDLLYNTS-DLHKKLAIAVA 379
Cdd:COG0747 335 GLGAVPADGPVPPLVPGYnpDIEKYAADAYDP----EKAKALLDEAGYKDndgfgGGPLTLTLESAGYnPGARAIAELIQ 410
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      380 SIWKKnLGVNVNLENQEWKTFLDTRHQ-GTFDVARA----GWCADYN-EPTSFLNTMLSDS--SNNTAHYKSPAFDKLIA 451
Cdd:COG0747 411 AQLAK-IGIKVELQTLDWATYLDRALTnGDFDDAFGlflgGGAGGYGgDPDNFLSPLYGSSngPAGYSGYSNPEVDKLID 489
                       490       500       510       520       530       540
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
1B3G_A      452 DTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLV-KPWVGGYTGKDPLDNIYVKNLYIIK 516
Cdd:COG0747 490 KARATTDPAKRKALYKEAQKILLEEAPYIPLYQSTVVIVVvSKRVKGFPLSPTGLFSFLNVITGEV 555
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
11-498 4.51e-88

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.


Pssm-ID: 173877  Cd Length: 476  Bit Score: 278.33  E-value: 4.51e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       11 DKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPS--PGVAEKWE-NKDFKVWTFHLRENAKWSDGTP 87
Cdd:cd08512   1 PKDTLVVATSADINTLDPAVAYEVASGEVVQNVYDRLVTYDGEDTGKlvPELAESWEvSDDGKTYTFHLRDGVKFHDGNP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       88 VTAHDFVYSWQRLADPNTAspyASYLQYGHIANIDDIIagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPV 167
Cdd:cd08512  81 VTAEDVKYSFERALKLNKG---PAFILTQTSLNVPETI-----------KAVDDYTVVFKLDKPPALFLSTLAAPVASIV 146
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      168 PKSAVEK------FGDKWTQpANIVTNGAYKLKNWVVNERIVLERNPQYWDNA---KTVINQVtylpISSEVTDVNRYRS 238
Cdd:cd08512 147 DKKLVKEhgkdgdWGNAWLS-TNSAGSGPYKLKSWDPGEEVVLERNDDYWGGApklKRVIIRH----VPEAATRRLLLER 221
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      239 GEIDMTYnNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGdLPAYSY 317
Cdd:cd08512 222 GDADIAR-NLPPDDVAALEGNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVlKGQG-KPHPGP 299
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      318 TPPYTDGAKLVEPEWfkwsqqKRN-EEAKKLLAEAGFtaDKPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQ 395
Cdd:cd08512 300 LPDGLPGGAPDLPPY------KYDlEKAKELLAEAGY--PNGFKLTLSYNSGNePREDIAQLLQASLAQ-IGIKVEIEPV 370
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      396 EWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSN---NTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQ 472
Cdd:cd08512 371 PWAQLLEAARSREFDIFIGGWGPDYPDPDYFAATYNSDNGDnaaNRAWYDNPELDALIDEARAETDPAKRAALYKELQKI 450
                       490       500
                ....*....|....*....|....*.
1B3G_A      473 LDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08512 451 VYDDAPYIPLYQPVEVVAVRKNVKGY 476
PBP2_NikA_DppA_OppA_like_11 cd08516
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
21-498 2.51e-87

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.


Pssm-ID: 173881  Cd Length: 457  Bit Score: 276.05  E-value: 2.51e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       21 SEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWEN-KDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 99
Cdd:cd08516   8 TDPDSLDPHKATAAASEEVLENIYEGLLGPDENGKLVPALAESWEVsDDGLTYTFKLRDGVKFHNGDPVTAADVKYSFNR 87
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      100 LADPNTASPYASylQYGHIANIDdiiagkkpatdlgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKsavEKFGDKW 179
Cdd:cd08516  88 IADPDSGAPLRA--LFQEIESVE---------------APDDATVVIKLKQPDAPLLSLLASVNSPIIPA---ASGGDLA 147
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      180 TQPaniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELFQKLKKE 259
Cdd:cd08516 148 TNP---IGTGPFKFASYEPGVSIVLEKNPDYWGKGLPKLDGITFKIYPDENTRLAALQSGDVDIIEYV-PPQQAAQLEED 223
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      260 IPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEwfkwSQQK 339
Cdd:cd08516 224 DGLKLASSPGNSYMYLALNNTREPFDDPKVRQAIAYAIDRDAIVDAAFFGRGTPLGGLPSPAGSPAYDPDDA----PCYK 299
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      340 RN-EEAKKLLAEAGFtaDKPLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWC 417
Cdd:cd08516 300 YDpEKAKALLAEAGY--PNGFDFTILVtSQYGMHVDTAQVIQAQLAA-IGINVEIELVEWATWLDDVNKGDYDATIAGTS 376
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      418 AdYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVG 496
Cdd:cd08516 377 G-NADPDGLYNRYFtSGGKLNFFNYSNPEVDELLAQGRAETDEAKRKEIYKELQQILAEDVPWVFLYWRSQYYAMNKNVQ 455

                ..
1B3G_A      497 GY 498
Cdd:cd08516 456 GF 457
PBP2_thermophilic_Hb8_like cd08513
The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like ...
22-498 4.83e-83

The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold; This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. 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. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. 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.


Pssm-ID: 173878  Cd Length: 482  Bit Score: 265.69  E-value: 4.83e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       22 EVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRL 100
Cdd:cd08513   9 EPTTLNPLLASGATDAEAAQLLFEPLARIDPDGSLVPVLAEEIPtSENGLSVTFTLRPGVKWSDGTPVTADDVVFTWELI 88
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      101 ADPNTASPYASYLQyghiaNIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYklLVHPSVSPVPKSAVEK-FGDKW 179
Cdd:cd08513  89 KAPGVSAAYAAGYD-----NIA------------SVEAVDDYTVTVTLKKPTPYAP--FLFLTFPILPAHLLEGySGAAA 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      180 TQPAN---IVTNGAYKLKNWVVNERIVLERNPQYWDNAKTvINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKl 256
Cdd:cd08513 150 RQANFnlaPVGTGPYKLEEFVPGDSIELVRNPNYWGGKPY-IDRVVLKGVPDTDAARAALRSGEIDLAWLPGAKDLQQE- 227
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      257 KKEIPNEVRVDPYLCTYYY-EINNQKAP-FNDVRVRTALKLALDRDIIVNKV-KNQGdLPAYSYTPPYTDGAKLVEPEWf 333
Cdd:cd08513 228 ALLSPGYNVVVAPGSGYEYlAFNLTNHPiLADVRVRQALAYAIDRDAIVKTLyGGKA-TPAPTPVPPGSWADDPLVPAY- 305
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      334 kwsqqKRN-EEAKKLLAEAGFT----------ADKPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQEWKTFL 401
Cdd:cd08513 306 -----EYDpEKAKQLLDEAGWKlgpdggirekDGTPLSFTLLTTSGNaVRERVAELIQQQLAK-IGIDVEIENVPASVFF 379
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      402 DTRH-QGTFDVARAGWCADYN-EPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDK 475
Cdd:cd08513 380 SDDPgNRKFDLALFGWGLGSDpDLSPLFHSCASpangWGGQNFGGYSNPEADELLDAARTELDPEERKALYIRYQDLLAE 459
                       490       500
                ....*....|....*....|...
1B3G_A      476 DSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08513 460 DLPVIPLYFRNQVSAYKKNLKGV 482
PBP2_NikA_DppA_OppA_like_3 cd08490
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
13-505 1.19e-82

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.


Pssm-ID: 173855  Cd Length: 470  Bit Score: 264.08  E-value: 1.19e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       13 QTLVRNNGSEVQSLDPHKIEGVpesNVSR-DLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08490   1 KTLTVGLPFESTSLDPASDDGW---LLSRyGVAETLVKLDDDGKLEPWLAESWEQVDDTTWEFTLRDGVKFHDGTPLTAE 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRLADPNTaspyasylqyghianiddiiAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 171
Cdd:cd08490  78 AVKASLERALAKSP--------------------RAKGGALIISVIAVDDYTVTITTKEPYPALPARLADPNTAILDPAA 137
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      172 VEKFGDkwtqPANIVTnGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIE 251
Cdd:cd08490 138 YDDGVD----PAPIGT-GPYKVESFEPDQSLTLERNDDYW-GGKPKLDKVTVKFIPDANTRALALQSGEVDIAY-GLPPS 210
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      252 LFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDGAKLVEP 330
Cdd:cd08490 211 SVERLEKDDGYKVSSVPTPRTYFLYLNTEKGPLADVRVRQALSLAIDREGIADSVlEGSAA-PAKGPFPPSLPANPKLEP 289
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      331 ewfkwsqQKRN-EEAKKLLAEAGFTAD---------KPLTFDLL-YNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKT 399
Cdd:cd08490 290 -------YEYDpEKAKELLAEAGWTDGdgdgiekdgEPLELTLLtYTSRPELPPIAEAIQAQLKK-IGIDVEIRVVEYDA 361
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      400 FLDTRHQGTFDVARAGW-CADYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 477
Cdd:cd08490 362 IEEDLLDGDFDLALYSRnTAPTGDPDYFLNSDYkSDGSYNYGGYSNPEVDALIEELRTEFDPEERAELAAEIQQIIQDDA 441
                       490       500
                ....*....|....*....|....*...
1B3G_A      478 AIVPVYYYVNARLVKPWVGGYTgKDPLD 505
Cdd:cd08490 442 PVIPVAHYNQVVAVSKRVKGYK-VDPTE 468
PBP2_DppA_like cd08493
The substrate-binding component of an ABC-type dipeptide import system contains the type 2 ...
14-498 7.12e-82

The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. 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.


Pssm-ID: 173858  Cd Length: 482  Bit Score: 262.50  E-value: 7.12e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLL-ISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08493   1 TLVYCSEGSPESLDPQLATDGESDAVTRQIYEGLVeFKPGTTELEPGLAESWEvSDDGLTYTFHLRKGVKFHDGRPFNAD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRLADPNTA--SPYASYLQYGHIANIDDIIAgkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPK 169
Cdd:cd08493  81 DVVFSFNRWLDPNHPyhKVGGGGYPYFYSMGLGSLIK--------SVEAVDDYTVKFTLTRPDAPFLANLAMPFASILSP 152
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      170 SAVEKFGDKwTQPANIVTN----GAYKLKNWVVNERIVLERNPQYW-DNAKtvINQVTYLPISSEVTDVNRYRSGEIDMT 244
Cdd:cd08493 153 EYADQLLAA-GKPEQLDLLpvgtGPFKFVSWQKDDRIRLEANPDYWgGKAK--IDTLVFRIIPDNSVRLAKLLAGECDIV 229
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      245 YNNMPIELFQKLKKEIpnEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP---- 320
Cdd:cd08493 230 AYPNPSDLAILADAGL--QLLERPGLNVGYLAFNTQKPPFDDPKVRQAIAHAINKEAIVDAVYQGTATVAKNPLPPtswg 307
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      321 YTDGAKLVE--PewfkwsqqkrnEEAKKLLAEAGFTADKPLTF-----DLLYNTSDlhKKLAIAVASIWKKnLGVNVNLE 393
Cdd:cd08493 308 YNDDVPDYEydP-----------EKAKALLAEAGYPDGFELTLwyppvSRPYNPNP--KKMAELIQADLAK-VGIKVEIV 373
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      394 NQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKA 469
Cdd:cd08493 374 TYEWGEYLERTKAGEHDLYLLGWTGDNGDPDNFLRPLLScdaaPSGTNRARWCNPEFDELLEKARRTTDQAERAKLYKQA 453
                       490       500
                ....*....|....*....|....*....
1B3G_A      470 EQQLDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08493 454 QEIIHEDAPWVPIAHSKRLLAVRKNVKGF 482
PBP2_NikA_DppA_OppA_like_17 cd08503
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
19-498 1.57e-81

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.


Pssm-ID: 173868  Cd Length: 460  Bit Score: 260.97  E-value: 1.57e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       19 NGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSW 97
Cdd:cd08503  13 GGSTADTLDPHTADSSADYVRGFALYEYLVEIDPDGTLVPDLAESWEpNDDATTWTFKLRKGVTFHDGKPLTADDVVASL 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       98 QRLADPNTASPYASYLqyghiANIDDIiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKsavekfGD 177
Cdd:cd08503  93 NRHRDPASGSPAKTGL-----LDVGAI------------EAVDDHTVRFTLKRPNADFPYLLSDYHFPIVPA------GD 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      178 KWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIELFQKLK 257
Cdd:cd08503 150 GGDDFKNPIGTGPFKLESFEPGVRAVLERNPDYWKPGRPYLDRIEFIDIPDPAARVNALLSGQVDVIN-QVDPKTADLLK 228
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      258 KeiPNEVRVD--PYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQG----DLPAYSyTPPYTDGaklvep 330
Cdd:cd08503 229 R--NPGVRVLrsPTGTHYTFVMRTDTAPFDDPRVRRALKLAVDREALVETVlLGYGtvgnDHPVAP-IPPYYAD------ 299
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      331 ewfkWSQQKRN-EEAKKLLAEAGFtadKPLTFDLlyNTSDL---HKKLAIAVASIWKKnLGVNVNLENQEWKTFLDtrhq 406
Cdd:cd08503 300 ----LPQREYDpDKAKALLAEAGL---PDLEVEL--VTSDAapgAVDAAVLFAEQAAQ-AGININVKRVPADGYWS---- 365
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      407 gtfDVAR-AGWCADYN----EPTSFLNT-MLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQL-DKDSAI 479
Cdd:cd08503 366 ---DVWMkKPFSATYWggrpTGDQMLSLaYRSGAPWNETHWANPEFDALLDAARAELDEAKRKELYAEMQQILhDEGGII 442
                       490       500
                ....*....|....*....|
1B3G_A      480 VPVYY-YVNArlVKPWVGGY 498
Cdd:cd08503 443 IPYFRsYLDA--HSDKVKGY 460
PBP2_NikA_DppA_OppA_like_2 cd08498
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
14-488 1.41e-80

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.


Pssm-ID: 173863  Cd Length: 481  Bit Score: 259.03  E-value: 1.41e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDF 93
Cdd:cd08498   1 TLRIALAADPTSLDPHFHNEGPTLAVLHNIYDTLVRRDADLKLEPGLATSWEAVDDTTWRFKLREGVKFHDGSPFTAEDV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       94 VYSWQRLADPntASPYASYLqyghIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPyfykLLVH-----PSVSPVP 168
Cdd:cd08498  81 VFSLERARDP--PSSPASFY----LRTIKE------------VEVVDDYTVDIKTKGPNP----LLPNdltniFIMSKPW 138
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      169 KSAVEKFGDKWTQPANIVTnGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTyNNM 248
Cdd:cd08498 139 AEAIAKTGDFNAGRNPNGT-GPYKFVSWEPGDRTVLERNDDYWG-GKPNWDEVVFRPIPNDATRVAALLSGEVDVI-EDV 215
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      249 PIELFQKLKK-------EIPnEVRV-----DPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS 316
Cdd:cd08498 216 PPQDIARLKAnpgvkvvTGP-SLRViflglDQRRDELPAGSPLGKNPLKDPRVRQALSLAIDREAIVDRVMRGLATPAGQ 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      317 YTPP-YTDGAKLVEPEwfkwsqqKRN-EEAKKLLAEAGFTADKPLTFDllyNTSDLH---KKLAIAVASIWKKnLGVNVN 391
Cdd:cd08498 295 LVPPgVFGGEPLDKPP-------PYDpEKAKKLLAEAGYPDGFELTLH---CPNDRYvndEAIAQAVAGMLAR-IGIKVN 363
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      392 LENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDS-------SNNTAHYKSPAFDKLIADTLKVADDTQRSE 464
Cdd:cd08498 364 LETMPKSVYFPRATKGEADFYLLGWGVPTGDASSALDALLHTPdpekglgAYNRGGYSNPEVDALIEAAASEMDPAKRAA 443
                       490       500
                ....*....|....*....|....
1B3G_A      465 LYAKAEQQLDKDSAIVPVYYYVNA 488
Cdd:cd08498 444 LLQEAQEIVADDAAYIPLHQQVLI 467
PBP2_AppA_like cd08514
The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus ...
14-490 4.37e-77

The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also 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.


Pssm-ID: 173879  Cd Length: 483  Bit Score: 250.23  E-value: 4.37e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 92
Cdd:cd08514   1 TLVLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDKDLNFEPDLAESWEvSDDGKTYTFKLRKDVKWHDGEPLTADD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       93 FVYSWQRLADPNTASPYASYlQYGHIAniddiiagkkpatdlGVKALDDHTFEVTLSEP-VPYFYKLLVHPsvsPVPKSA 171
Cdd:cd08514  81 VKFTYKAIADPKYAGPRASG-DYDEIK---------------GVEVPDDYTVVFHYKEPyAPALESWALNG---ILPKHL 141
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      172 VE--KFGDKWTQPAN--IVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN 247
Cdd:cd08514 142 LEdvPIADFRHSPFNrnPVGTGPYKLKEWKRGQYIVLEANPDYFL-GRPYIDKIVFRIIPDPTTALLELKAGELDIVELP 220
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      248 MPIELFQKLKKEIPNEVRVDPYLCTYYYEI--NNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPP---- 320
Cdd:cd08514 221 PPQYDRQTEDKAFDKKINIYEYPSFSYTYLgwNLKRPLFQDKRVRQAITYAIDREEIIDGLlLGLGE-VANGPFSPgtwa 299
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      321 YTDGaklVEPewFKWSQQKrneeAKKLLAEAGFTAD----------KPLTFDLLYNTSDlhkKLAIAVASIWKKNL---G 387
Cdd:cd08514 300 YNPD---LKP--YPYDPDK----AKELLAEAGWVDGdddgildkdgKPFSFTLLTNQGN---PVREQAATIIQQQLkeiG 367
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      388 VNVNLENQEWKTFLDTRHQGTFDVARAGWCADyNEPTSFlntMLSDSS------NNTAHYKSPAFDKLIADTLKVADDTQ 461
Cdd:cd08514 368 IDVKIRVLEWAAFLEKVDDKDFDAVLLGWSLG-PDPDPY---DIWHSSgakpggFNFVGYKNPEVDKLIEKARSTLDREK 443
                       490       500       510
                ....*....|....*....|....*....|....
1B3G_A      462 RSELYAKAEQQLDKDSAIVPVYYY-----VNARL 490
Cdd:cd08514 444 RAEIYHEWQEILAEDQPYTFLYAPnslyaVNKRL 477
PBP2_Ylib_like cd08499
The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib ...
20-487 2.39e-75

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.


Pssm-ID: 173864  Cd Length: 474  Bit Score: 245.21  E-value: 2.39e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       20 GSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQ 98
Cdd:cd08499   7 LSDATSLDPHDTNDTPSASVQSNIYEGLVGFDKDMKIVPVLAESWEqSDDGTTWTFKLREGVKFHDGTPFNAEAVKANLD 86
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       99 RLADPNTASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDk 178
Cdd:cd08499  87 RVLDPETASPRASLF-----SMIEE------------VEVVDDYTVKITLKEPFAPLLAHLAHPGGSIISPKAIEEYGK- 148
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      179 wTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTViNQVTYLPISSEVTDVNRYRSGEIDMTYNnMPIELFQKLKK 258
Cdd:cd08499 149 -EISKHPVGTGPFKFESWTPGDEVTLVKNDDYWGGLPKV-DTVTFKVVPEDGTRVAMLETGEADIAYP-VPPEDVDRLEN 225
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      259 EIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP----YTDGAKLVE--Pew 332
Cdd:cd08499 226 SPGLNVYRSPSISVVYIGFNTQKEPFDDVRVRQAINYAIDKEAIIKGILNGYGTPADSPIAPgvfgYSEQVGPYEydP-- 303
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      333 fkwsqqkrnEEAKKLLAEAGFTadKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD-TRHQGTFDV 411
Cdd:cd08499 304 ---------EKAKELLAEAGYP--DGFETTLWTNDNRERIKIAEFIQQQLAQ-IGIDVEIEVMEWGAYLEeTGNGEEHQM 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      412 ARAGWC-----ADYNeptsfLNTMLSDSS----NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 482
Cdd:cd08499 372 FLLGWStstgdADYG-----LRPLFHSSNwgapGNRAFYSNPEVDALLDEARREADEEERLELYAKAQEIIWEDAPWVFL 446

                ....*
1B3G_A      483 YYYVN 487
Cdd:cd08499 447 YHPET 451
PBP2_clavulanate_OppA2 cd08506
The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis ...
14-498 1.54e-74

The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold; Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. 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.


Pssm-ID: 173871  Cd Length: 466  Bit Score: 242.94  E-value: 1.54e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGH-----PSPGVAEKW--ENKDFKVWTFHLRENAKWSDGT 86
Cdd:cd08506   1 TLRLLSSADFDHLDPARTYYADGWQVLRLIYRQLTTYKPAPGaegteVVPDLATDTgtVSDDGKTWTYTLRDGLKFEDGT 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       87 PVTAHDFVYSWQRLADpntaspyasylqyghianiddiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSP 166
Cdd:cd08506  81 PITAKDVKYGIERSFA---------------------------------IETPDDKTIVFHLNRPDSDFPYLLALPAAAP 127
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      167 VPKSAVEKfgDKWTQpaNIVTNGAYKLKNWVVNERIVLERNPqYWDNAKTVIN-----QVTY-LPISSEvTDVNRYRSGE 240
Cdd:cd08506 128 VPAEKDTK--ADYGR--APVSSGPYKIESYDPGKGLVLVRNP-HWDAETDPIRdaypdKIVVtFGLDPE-TIDQRLQAGD 201
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      241 IDM--TYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDlPAYS 316
Cdd:cd08506 202 ADLalDGDGVPRAPAAELVEELKARLHNVPGGGVYYLAINTNVPPFDDVKVRQAVAYAVDRAALVRAFggPAGGE-PATT 280
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      317 YTPPYTDGAKLVEPEWFKWSQQKRnEEAKKLLAEAGFtadKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQE 396
Cdd:cd08506 281 ILPPGIPGYEDYDPYPTKGPKGDP-DKAKELLAEAGV---PGLKLTLAYRDTAVDKKIAEALQASLAR-AGIDVTLKPID 355
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      397 WKTFLDTRHQGT---FDVARAGWCADYNEPTSFLNTMLS------DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYA 467
Cdd:cd08506 356 SATYYDTIANPDgaaYDLFITGWGPDWPSASTFLPPLFDgdaigpGGNSNYSGYDDPEVNALIDEALATTDPAEAAALWA 435
                       490       500       510
                ....*....|....*....|....*....|.
1B3G_A      468 KAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08506 436 ELDRQIMEDAPIVPLVYPKALDLRSSRVTNY 466
PBP2_NikA_DppA_OppA_like_15 cd08492
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
14-497 6.70e-74

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.


Pssm-ID: 173857 [Multi-domain]  Cd Length: 484  Bit Score: 241.75  E-value: 6.70e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 92
Cdd:cd08492   3 TLTYALGQDPTCLDPHTLDFYPNGSVLRQVVDSLVYQDPTGEIVPWLAESWEvSDDGTTYTFHLRDGVTFSDGTPLDAEA 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       93 FVYSWQRLADPNTASPYASYLqyghIANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAV 172
Cdd:cd08492  83 VKANFDRILDGSTKSGLAASY----LGPYK------------STEVVDPYTVKVHFSEPYAPFLQALSTPGLGILSPATL 146
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      173 EKFGDKWTQPaNIVTNGAYKLKNWVVNERIVLERNPQY-W--DNAK----TVINQVTYLPISSEVTDVNRYRSGEIDMTY 245
Cdd:cd08492 147 ARPGEDGGGE-NPVGSGPFVVESWVRGQSIVLVRNPDYnWapALAKhqgpAYLDKIVFRFIPEASVRVGALQSGQVDVIT 225
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      246 NNMPIELFQKLKKEIPN-EVRVDPYLcTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVkNQGDLPAYSY-TPPYTD 323
Cdd:cd08492 226 DIPPQDEKQLAADGGPViETRPTPGV-PYSLYLNTTRPPFDDVRVRQALQLAIDREAIVETV-FFGSYPAASSlLSSTTP 303
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      324 GAKLVEPEWfkwsqqKRN-EEAKKLLAEAGFTAD----------KPLTFDLLYNT-SDLHKKLAIAVASIWKKnLGVNVN 391
Cdd:cd08492 304 YYKDLSDAY------AYDpEKAKKLLDEAGWTARgadgirtkdgKRLTLTFLYSTgQPQSQSVLQLIQAQLKE-VGIDLQ 376
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      392 LENQEWKTFLDTRHQGTFDVARAGWCADYNEPtsfLNTMLSDSSNNT----AHYKSPAFDKLIADTLKVADDTQRSELYA 467
Cdd:cd08492 377 LKVLDAGTLTARRASGDYDLALSYYGRADPDI---LRTLFHSANRNPpggySRFADPELDDLLEKAAATTDPAERAALYA 453
                       490       500       510
                ....*....|....*....|....*....|
1B3G_A      468 KAEQQLDKDSAIVPVYYYVNARLVKPWVGG 497
Cdd:cd08492 454 DAQKYLIEQAYVVPLYEEPQVVAAAPNVKG 483
PBP2_NikA_DppA_OppA_like_20 cd08519
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
23-482 4.11e-68

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.


Pssm-ID: 173884  Cd Length: 469  Bit Score: 226.35  E-value: 4.11e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       23 VQSLDPHKIEGVPESNVSRDLFEGLLISDVE-GHPSPGVAEKWE--NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 99
Cdd:cd08519  10 VRTLDPAGAYDLGSWQLLSNLGDTLYTYEPGtTELVPDLATSLPfvSDDGLTYTIPLRQGVKFHDGTPFTAKAVKFSLDR 89
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      100 L----ADPntaspyaSYLqyghianIDDIIAgkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKF 175
Cdd:cd08519  90 FikigGGP-------ASL-------LADRVE--------SVEAPDDYTVTFRLKKPFATFPALLATPALTPVSPKAYPAD 147
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      176 GDKwTQPANIVTNGAYKLKNWvVNERIVLERNPQYW-DNAKTVINQVTYLpiSSEVTDVNRYRSGEIDMTYNNMPIELFQ 254
Cdd:cd08519 148 ADL-FLPNTFVGTGPYKLKSF-RSESIRLEPNPDYWgEKPKNDGVDIRFY--SDSSNLFLALQTGEIDVAYRSLSPEDIA 223
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      255 KLKKEIPNEVRV--DPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDGAKlvepE 331
Cdd:cd08519 224 DLLLAKDGDLQVveGPGGEIRYIVFNVNQPPLDNLAVRQALAYLIDRDLIVNRVyYGTAE-PLYSLVPTGFWGHK----P 298
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      332 WFKWSQQKRN-EEAKKLLAEAGFTADKPLTFDLLYNTS-DLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTF 409
Cdd:cd08519 299 VFKEKYGDPNvEKARQLLQQAGYSAENPLKLELWYRSNhPADKLEAATLKAQLEADGLFKVNLKSVEWTTYYKQLSKGAY 378
                       410       420       430       440       450       460       470
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
1B3G_A      410 DVARAGWCADYNEPTSFLNTMLSDSSN--NTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 482
Cdd:cd08519 379 PVYLLGWYPDYPDPDNYLTPFLSCGNGvfLGSFYSNPKVNQLIDKSRTELDPAARLKILAEIQDILAEDVPYIPL 453
PBP2_NikA_DppA_OppA_like_13 cd08517
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
39-482 2.01e-64

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.


Pssm-ID: 173882 [Multi-domain]  Cd Length: 480  Bit Score: 216.65  E-value: 2.01e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       39 VSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASpyasylqYGH 117
Cdd:cd08517  28 ISGKIFEGLLRYDFDLNPQPDLATSWEvSEDGLTYTFKLRPGVKWHDGKPFTSADVKFSIDTLKEEHPRR-------RRT 100
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      118 IANIDDIiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVhPSVSP-VPKSAVEKfGDKWTQPAN--IVTNGAYKLK 194
Cdd:cd08517 101 FANVESI------------ETPDDLTVVFKLKKPAPALLSALS-WGESPiVPKHIYEG-TDILTNPANnaPIGTGPFKFV 166
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      195 NWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELF--QKLKKeIPN-EVRVDPYLC 271
Cdd:cd08517 167 EWVRGSHIILERNPDYWDKGKPYLDRIVFRIIPDAAARAAAFETGEVDVLPFG-PVPLSdiPRLKA-LPNlVVTTKGYEY 244
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      272 ---TYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDL---PAYSYTPPYTDgAKLVEPEwFKWsqqkrnEEA 344
Cdd:cd08517 245 fspRSYLEFNLRNPPLKDVRVRQAIAHAIDRQFIVDTVfFGYGKPatgPISPSLPFFYD-DDVPTYP-FDV------AKA 316
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      345 KKLLAEAGFTAD---KPLTFDLLYNTS-DLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD------------TRHQGT 408
Cdd:cd08517 317 EALLDEAGYPRGadgIRFKLRLDPLPYgEFWKRTAEYVKQALKE-VGIDVELRSQDFATWLKrvytdrdfdlamNGGYQG 395
                       410       420       430       440       450       460       470
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1B3G_A      409 FD----VARAGWCADYNEPTSFlntmlsdssNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 482
Cdd:cd08517 396 GDpavgVQRLYWSGNIKKGVPF---------SNASGYSNPEVDALLEKAAVETDPAKRKALYKEFQKILAEDLPIIPL 464
PBP2_NikA_DppA_OppA_like_5 cd08511
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
13-498 7.24e-63

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This family 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.


Pssm-ID: 173876  Cd Length: 467  Bit Score: 212.14  E-value: 7.24e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       13 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08511   1 GTLRIGLEADPDRLDPALSRTFVGRQVFAALCDKLVDIDADLKIVPQLATSWEiSPDGKTLTLKLRKGVKFHDGTPFDAA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRLADPNTASpyasylQYGHIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPS---VSP-V 167
Cdd:cd08511  81 AVKANLERLLTLPGSN------RKSELASVES------------VEVVDPATVRFRLKQPFAPLLAVLSDRAgmmVSPkA 142
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      168 PKSAVEKFGDKwtqPaniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN 247
Cdd:cd08511 143 AKAAGADFGSA---P---VGTGPFKFVERVQQDRIVLERNPHYWNAGKPHLDRLVYRPIPDATVRLANLRSGDLDIIERL 216
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      248 MPIELfQKLKKEipNEVRVDPYLCTYYYEI--NNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYT--D 323
Cdd:cd08511 217 SPSDV-AAVKKD--PKLKVLPVPGLGYQGItfNIGNGPFNDPRVRQALALAIDREAINQVVFNGTFKPANQPFPPGSpyY 293
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      324 GAKLVEPewfkwsqqKRN-EEAKKLLAEAGFTAdkpLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD 402
Cdd:cd08511 294 GKSLPVP--------GRDpAKAKALLAEAGVPT---VTFELTTANTPTGRQLAQVIQAMAAE-AGFTVKLRPTEFATLLD 361
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      403 TRHQGTFDVARAGWcADYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVP 481
Cdd:cd08511 362 RALAGDFQATLWGW-SGRPDPDGNIYQFFtSKGGQNYSRYSNPEVDALLEKARASADPAERKALYNQAAKILADDLPYIY 440
                       490
                ....*....|....*..
1B3G_A      482 VYYYVNARLVKPWVGGY 498
Cdd:cd08511 441 LYHQPYYIAASKKVRGL 457
PBP2_NikA_DppA_OppA_like_8 cd08495
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
22-497 9.54e-62

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.


Pssm-ID: 173860  Cd Length: 482  Bit Score: 209.89  E-value: 9.54e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       22 EVQSLDPHK------IEGVP--ESNVSRDLFEGLLISDVEghpsPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 92
Cdd:cd08495   9 PLTTLDPDQgaeglrFLGLPvyDPLVRWDLSTADRPGEIV----PGLAESWEvSPDGRRWTFTLRPGVKFHDGTPFDADA 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       93 FVYSWQRLADPNTA--SPYASYLQYGHIANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHP-SVSPVPK 169
Cdd:cd08495  85 VVWNLDRMLDPDSPqyDPAQAGQVRSRIPSVT------------SVEAIDDNTVRITTSEPFADLPYVLTTGlASSPSPK 152
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      170 SAVEKFGDKWTQPAniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMP 249
Cdd:cd08495 153 EKAGDAWDDFAAHP--AGTGPFRITRFVPRERIELVRNDGYWDKRPPKNDKLVLIPMPDANARLAALLSGQVDAIEAPAP 230
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      250 IELFQklKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPytdgaklvE 329
Cdd:cd08495 231 DAIAQ--LKSAGFQLVTNPSPHVWIYQLNMAEGPLSDPRVRQALNLAIDREGLVDLLLGGLAAPATGPVPP--------G 300
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      330 PEWFKWSQQ--KRN-EEAKKLLAEAGFTADKPLTFDLLYNTSdlHKKLAIAVASIWKKNL---GVNVNLENQEWKTFLDT 403
Cdd:cd08495 301 HPGFGKPTFpyKYDpDKARALLKEAGYGPGLTLKLRVSASGS--GQMQPLPMNEFIQQNLaeiGIDLDIEVVEWADLYNA 378
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      404 RHQGTFDVARAG---------WCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLD 474
Cdd:cd08495 379 WRAGAKDGSRDGanainmssaMDPFLALVRFLSSKIDPPVGSNWGGYHNPEFDALIDQARVTFDPAERAALYREAHAIVV 458
                       490       500
                ....*....|....*....|...
1B3G_A      475 KDSAIVPVYYYVNARLVKPWVGG 497
Cdd:cd08495 459 DDAPWLFVVHDRNPRALSPKVKG 481
PBP2_NikA cd08489
The substrate-binding component of an ABC-type nickel import system contains the type 2 ...
14-499 2.78e-58

The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. 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.


Pssm-ID: 173854  Cd Length: 488  Bit Score: 200.53  E-value: 2.78e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGvpeSNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 91
Cdd:cd08489   1 TLTYAWPKDIGDLNPHLYSN---QMFAQNMvYEPLVKYGEDGKIEPWLAESWEiSEDGKTYTFHLRKGVKFSDGTPFNAE 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       92 DFVYSWQRlADPNTASPYASYLqyghIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPV-PYFYKL-LVHP--SVSPv 167
Cdd:cd08489  78 AVKKNFDA-VLANRDRHSWLEL----VNKIDS------------VEVVDEYTVRLHLKEPYyPTLNELaLVRPfrFLSP- 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      168 pkSAVEKFGDKWTQPANIVTnGAYKLKNWVVNERIVLERNPQYWDNaKTVINQVTYLPISSEVTDVNRYRSGEIDMTY-- 245
Cdd:cd08489 140 --KAFPDGGTKGGVKKPIGT-GPWVLAEYKKGEYAVFVRNPNYWGE-KPKIDKITVKVIPDAQTRLLALQSGEIDLIYga 215
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      246 NNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYT 322
Cdd:cd08489 216 DGISADAFKQLKKDKGYGTAVSEPTSTRFLALNTASEPLSDLKVREAINYAIDKEAISKGILYGLEKPAdtlFAPNVPYA 295
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      323 DgaklVEPEwfKWSQQKrnEEAKKLLAEAGFTAD----------KPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVN 391
Cdd:cd08489 296 D----IDLK--PYSYDP--EKANALLDEAGWTLNegdgirekdgKPLSLELVYQTDNaLQKSIAEYLQSELKK-IGIDLN 366
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      392 LENQEWKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDSSnntAHYKS-------PAFDKLIADTLKVADDTQRS 463
Cdd:cd08489 367 IIGEEEQAYYDRQKDGDFDLIFYrTWGAPY-DPHSFLSSMRVPSH---ADYQAqvglankAELDALINEVLATTDEEKRQ 442
                       490       500       510
                ....*....|....*....|....*....|....*.
1B3G_A      464 ELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYT 499
Cdd:cd08489 443 ELYDEILTTLHDQAVYIPLTYPRNKAVYNPKVKGVT 478
PBP2_NikA_DppA_OppA_like_16 cd08502
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
21-498 4.63e-57

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.


Pssm-ID: 173867  Cd Length: 472  Bit Score: 197.03  E-value: 4.63e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       21 SEVQSLDPHkiegVPESNVSRD----LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVY 95
Cdd:cd08502   8 ADLRTLDPI----VTTAYITRNhgymIYDTLFGMDANGEPQPQMAESWEvSDDGKTYTFTLRDGLKFHDGSPVTAADVVA 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       96 SWQRLADPNTAspyasylqyghianiddiiaGKK--PATDLgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPV---PKS 170
Cdd:cd08502  84 SLKRWAKRDAM--------------------GQAlmAAVES-LEAVDDKTVVITLKEPFGLLLDALAKPSSQPAfimPKR 142
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      171 AVEKFGDK-WTQPaniVTNGAYKLKNWVVNERIVLERNPQY--------W-DNAKTVI-NQVTYLPISSEVTDVNRYRSG 239
Cdd:cd08502 143 IAATPPDKqITEY---IGSGPFKFVEWEPDQYVVYEKFADYvprkeppsGlAGGKVVYvDRVEFIVVPDANTAVAALQSG 219
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      240 EIDMtYNNMPIELFQKLKKEiPNEVrVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVknQGDLPAYSY-- 317
Cdd:cd08502 220 EIDF-AEQPPADLLPTLKAD-PVVV-LKPLGGQGVLRFNHLQPPFDNPKIRRAVLAALDQEDLLAAA--VGDPDFYKVcg 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      318 ------TPPYTDGAKlvepEWFKwsqqKRN-EEAKKLLAEAGFtADKPLTfdLLYNTS-DLHKKLAIAVASIWKKnLGVN 389
Cdd:cd08502 295 smfpcgTPWYSEAGK----EGYN----KPDlEKAKKLLKEAGY-DGEPIV--ILTPTDyAYLYNAALVAAQQLKA-AGFN 362
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      390 VNLENQEWKTFLDTRHQ--GTFDVARAGWC-ADYNEPtsFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELY 466
Cdd:cd08502 363 VDLQVMDWATLVQRRAKpdGGWNIFITSWSgLDLLNP--LLNTGLNAGKAWFGWPDDPEIEALRAAFIAATDPAERKALA 440
                       490       500       510
                ....*....|....*....|....*....|..
1B3G_A      467 AKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08502 441 AEIQKRAYEDVPYIPLGQFTQPTAYRSKLEGL 472
PBP2_NikA_DppA_OppA_like_1 cd08508
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
14-498 6.37e-57

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.


Pssm-ID: 173873  Cd Length: 470  Bit Score: 196.45  E-value: 6.37e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       14 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLlISDVEGHPSPG-----VAEKWENKDFK-VWTFHLRENAKWSDGT- 86
Cdd:cd08508   2 LRIGSAADDIRTLDPHFATGTTDKGVISWVFNGL-VRFPPGSADPYeiepdLAESWESSDDPlTWTFKLRKGVMFHGGYg 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       87 PVTAHDFVYSWQRLADPNTASpYASylqyghianidDIIAGKKpatdlgVKALDDHTFEVTLSEPVPYFYKLLV-HPSVS 165
Cdd:cd08508  81 EVTAEDVVFSLERAADPKRSS-FSA-----------DFAALKE------VEAHDPYTVRITLSRPVPSFLGLVSnYHSGL 142
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      166 PVPKSAVEKFGDKWTQPAniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTvINQVTYLPISSEVTDVNRYRSGEIDMTY 245
Cdd:cd08508 143 IVSKKAVEKLGEQFGRKP--VGTGPFEVEEHSPQQGVTLVANDGYFRGAPK-LERINYRFIPNDASRELAFESGEIDMTQ 219
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      246 NNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGa 325
Cdd:cd08508 220 GKRDQRWVQRREANDGVVVDVFEPAEFRTLGLNITKPPLDDLKVRQAIAAAVNVDEVVEFVGAGVAQPGNSVIPPGLLG- 298
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      326 klvepEWFKWSQQKRN-EEAKKLLAEAGFTADKPLTFdllyNTSDLHKKLAIA-VASIWKKNLGVNVNLENQEWKTFLDT 403
Cdd:cd08508 299 -----EDADAPVYPYDpAKAKALLAEAGFPNGLTLTF----LVSPAAGQQSIMqVVQAQLAEAGINLEIDVVEHATFHAQ 369
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      404 RHQGTFDVARAGwCADYNEPTSFL------NTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 477
Cdd:cd08508 370 IRKDLSAIVLYG-AARFPIADSYLtefydsASIIGAPTAVTNFSHCPVADKRIEAARVEPDPESRSALWKEAQKKIDEDV 448
                       490       500
                ....*....|....*....|..
1B3G_A      478 AIVPVYYYVNARLVKPWVG-GY 498
Cdd:cd08508 449 CAIPLTNLVQAWARKPALDyGY 470
PBP2_TmCBP_oligosaccharides_like cd08509
The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains ...
48-503 8.01e-55

The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold; This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. 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.


Pssm-ID: 173874  Cd Length: 509  Bit Score: 191.77  E-value: 8.01e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       48 LISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADpnTASPYASYLQYghiaNIDDiia 126
Cdd:cd08509  39 IYNPLTGEFIPWLAESWTwSDDFTTLTVTLRKGVKWSDGEPFTADDVVFTFELLKK--YPALDYSGFWY----YVES--- 109
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      127 gkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVH--PSVSPVPKSAVEKFGDKWTQPANI--VTNGAYKLKNWvVNERI 202
Cdd:cd08509 110 ---------VEAVDDYTVVFTFKKPSPTEAFYFLYtlGLVPIVPKHVWEKVDDPLITFTNEppVGTGPYTLKSF-SPQWI 179
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      203 VLERNPQYWDNAKTV-INQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQK 281
Cdd:cd08509 180 VLERNPNYWGAFGKPkPDYVVYPAYSSNDQALLALANGEVDWAGLFIPDIQKTVLKDPENNKYWYFPYGGTVGLYFNTKK 259
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      282 APFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPY--TDGAKLVEPEWFKWSQQKRN---EEAKKLLAEAGFTAD 356
Cdd:cd08509 260 YPFNDPEVRKALALAIDRTAIVKIAGYGYATPAPLPGPPYkvPLDPSGIAKYFGSFGLGWYKydpDKAKKLLESAGFKKD 339
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      357 ----------KPLTFDLL--YNTSDlhkklAIAVASIWKKNL---GVNVNLENQEWKTFLDTRHQGTFDVARAG--WCAD 419
Cdd:cd08509 340 kdgkwytpdgTPLKFTIIvpSGWTD-----WMAAAQIIAEQLkefGIDVTVKTPDFGTYWAALTKGDFDTFDAAtpWGGP 414
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      420 YNEPTSFLNTMLS--------DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLV 491
Cdd:cd08509 415 GPTPLGYYNSAFDppnggpggSAAGNFGRWKNPELDELIDELNKTTDEAEQKELGNELQKIFAEEMPVIPLFYNPIWYEY 494
                       490
                ....*....|....
1B3G_A      492 --KPWVGGYTGKDP 503
Cdd:cd08509 495 ntKYWTGWPTEENP 508
PBP2_NikA_DppA_OppA_like_4 cd08500
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
37-488 2.46e-54

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.


Pssm-ID: 173865 [Multi-domain]  Cd Length: 499  Bit Score: 190.14  E-value: 2.46e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       37 SNVSRDLFEGLLISDVEGH-PSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYAsylq 114
Cdd:cd08500  31 RDIIGLGYAGLVRYDPDTGeLVPNLAESWEvSEDGREFTFKLREGLKWSDGQPFTADDVVFTYEDIYLNPEIPPSA---- 106
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      115 yghianIDDIIAGKKPATdlgVKALDDHTFEVTLSEPVPYFYKLLVhpsvspvpksavekfgdkwtqPANIVTNGAYKLK 194
Cdd:cd08500 107 ------PDTLLVGGKPPK---VEKVDDYTVRFTLPAPNPLFLAYLA---------------------PPDIPTLGPWKLE 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      195 NWVVNERIVLERNPQYWD-----NAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKeipNE------ 263
Cdd:cd08500 157 SYTPGERVVLERNPYYWKvdtegNQLPYIDRIVYQIVEDAEAQLLKFLAGEIDLQGRHPEDLDYPLLKE---NEekggyt 233
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      264 -VRVDPYLCTYYYEIN-NQKAP-----FNDVRVRTALKLALDRDIIVNKV-KNQGDLPAYSYTPPYTdgaklvePEWFKW 335
Cdd:cd08500 234 vYNLGPATSTLFINFNlNDKDPvkrklFRDVRFRQALSLAINREEIIETVyFGLGEPQQGPVSPGSP-------YYYPEW 306
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      336 SQQKRN---EEAKKLLAEAGFT---AD--------KPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQEWKTF 400
Cdd:cd08500 307 ELKYYEydpDKANKLLDEAGLKkkdADgfrldpdgKPVEFTLITNAGNsIREDIAELIKDDWRK-IGIKVNLQPIDFNLL 385
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      401 LDTRHQG-TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAF---------------DKLIADTLKVADDTQRSE 464
Cdd:cd08500 386 VTRLSANeDWDAILLGLTGGGPDPALGAPVWRSGGSLHLWNQPYPGGgppggpepppwekkiDDLYDKGAVELDQEKRKA 465
                       490       500
                ....*....|....*....|....
1B3G_A      465 LYAKAeQQLDKDSaiVPVYYYVNA 488
Cdd:cd08500 466 LYAEI-QKIAAEN--LPVIGTVGP 486
PBP2_NikA_DppA_OppA_like_6 cd08494
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
22-498 5.17e-54

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.


Pssm-ID: 173859  Cd Length: 448  Bit Score: 188.22  E-value: 5.17e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       22 EVQSLDP-----HKIEGVPESNVsrdlFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVY 95
Cdd:cd08494   9 EPTSLDItttagAAIDQVLLGNV----YETLVRRDEDGKVQPGLAESWTiSDDGLTYTFTLRSGVTFHDGTPFDAADVKF 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       96 SWQRLADPNTASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKF 175
Cdd:cd08494  85 SLQRARAPDSTNADKALL-----AAIAS------------VEAPDAHTVVVTLKHPDPSLLFNLGGRAGVVVDPASAADL 147
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      176 GdkwTQPaniVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIEL--- 252
Cdd:cd08494 148 A---TKP---VGTGPFTVAAWARGSSITLVRNDDYWG-AKPKLDKVTFRYFSDPTALTNALLAGDIDAAPPFDAPELeqf 220
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      253 -----FQKLKKEIPNEVRVdpylctyyyEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGakl 327
Cdd:cd08494 221 addprFTVLVGTTTGKVLL---------AMNNARAPFDDVRVRQAIRYAIDRKALIDAAWDGYGTPIGGPISPLDPG--- 288
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      328 vepeWFKWSQQKRN--EEAKKLLAEAGFTAdkPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRH 405
Cdd:cd08494 289 ----YVDLTGLYPYdpDKARQLLAEAGAAY--GLTLTLTLPPLPYARRIGEIIASQLAE-VGITVKIEVVEPATWLQRVY 361
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      406 QG-TFDVAragwCADYNEPTSFLNTMLSDSsnnTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYY 484
Cdd:cd08494 362 KGkDYDLT----LIAHVEPDDIGIFADPDY---YFGYDNPEFQELYAQALAATDADERAELLKQAQRTLAEDAAADWLYT 434
                       490
                ....*....|....
1B3G_A      485 YVNARLVKPWVGGY 498
Cdd:cd08494 435 RPNIVVARKGVTGY 448
PBP2_NikA_DppA_OppA_like_19 cd08518
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
43-484 3.77e-52

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.


Pssm-ID: 173883 [Multi-domain]  Cd Length: 464  Bit Score: 183.56  E-value: 3.77e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       43 LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASylqyghiaNI 121
Cdd:cd08518  29 IFSGLLKRDENLNLVPDLATSYKvSDDGLTWTFTLRDDVKFSDGEPLTAEDVAFTYNTAKDPGSASDILS--------NL 100
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      122 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVhpSVSPVPKSAVEKFGDKWTQPaniVTNGAYKLKNWVVNER 201
Cdd:cd08518 101 ED------------VEAVDDYTVKFTLKKPDSTFLDKLA--SLGIVPKHAYENTDTYNQNP---IGTGPYKLVQWDKGQQ 163
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      202 IVLERNPQYWDNaKTVINQVTYLpISSEVTDVNRYRSGEIDMTYnnMPIELfqkLKKEIPNE--VRVD---------PYL 270
Cdd:cd08518 164 VIFEANPDYYGG-KPKFKKLTFL-FLPDDAAAAALKSGEVDLAL--IPPSL---AKQGVDGYklYSIKsadyrgislPFV 236
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      271 CTYYYEI-NNQKApfnDVRVRTALKLALDRDIIVNKVKN-QGDlPAYSytppYTDGAKLVEPEWFKWSQQKrnEEAKKLL 348
Cdd:cd08518 237 PATGKKIgNNVTS---DPAIRKALNYAIDRQAIVDGVLNgYGT-PAYS----PPDGLPWGNPDAAIYDYDP--EKAKKIL 306
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      349 AEAGF--TAD-------KPLTFDLLYNTSDLHKK-LAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFdvaRAGWCA 418
Cdd:cd08518 307 EEAGWkdGDDggrekdgQKAEFTLYYPSGDQVRQdLAVAVASQAKK-LGIEVKLEGKSWDEIDPRMHDNAV---LLGWGS 382
                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1B3G_A      419 DYNEPT-SFLNTMLSDS-SNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYY 484
Cdd:cd08518 383 PDDTELySLYHSSLAGGgYNNPGHYSNPEVDAYLDKARTSTDPEERKKYWKKAQWDGAEDPPWLWLVN 450
PBP2_Lpqw cd08501
The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic ...
65-483 2.70e-48

The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold; LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. 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.


Pssm-ID: 173866  Cd Length: 486  Bit Score: 173.69  E-value: 2.70e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       65 ENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAD-PNTASPyASYLQYGHIANIddiiagkkPATDlgvkalDDHT 143
Cdd:cd08501  58 TSDDPQTVTYTINPEAQWSDGTPITAADFEYLWKAMSGePGTYDP-ASTDGYDLIESV--------EKGD------GGKT 122
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      144 FEVTLSEPVPYfYKLL---VHPSvSPVPKSAveKFGDKWTQPANIVTNGAYKLKNWVVN-ERIVLERNPQYWDNAKTVIN 219
Cdd:cd08501 123 VVVTFKQPYAD-WRALfsnLLPA-HLVADEA--GFFGTGLDDHPPWSAGPYKVESVDRGrGEVTLVRNDRWWGDKPPKLD 198
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      220 QVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELFQKLKKEIPN-EVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALD 298
Cdd:cd08501 199 KITFRAMEDPDAQINALRNGEIDAADVG-PTEDTLEALGLLPGvEVRTGDGPRYLHLTLNTKSPALADVAVRKAFLKAID 277
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      299 RDIIVNKV--------KNQGDLPAYSYTPPYTDGaklvEPEWFKWSQqkrnEEAKKLLAEAGFTAD--------KPLTFD 362
Cdd:cd08501 278 RDTIARIAfgglppeaEPPGSHLLLPGQAGYEDN----SSAYGKYDP----EAAKKLLDDAGYTLGgdgiekdgKPLTLR 349
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      363 LLYNTSDlhkKLAIAVASIWKKNL---GVNVNLEN---QEW-KTFLDtrhQGTFDVARAGWCADYNEPTSFLNTMLSDSS 435
Cdd:cd08501 350 IAYDGDD---PTAVAAAELIQDMLakaGIKVTVVSvpsNDFsKTLLS---GGDYDAVLFGWQGTPGVANAGQIYGSCSES 423
                       410       420       430       440
                ....*....|....*....|....*....|....*....|....*...
1B3G_A      436 NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVY 483
Cdd:cd08501 424 SNFSGFCDPEIDELIAEALTTTDPDEQAELLNEADKLLWEQAYTLPLY 471
PBP2_NikA_DppA_OppA_like_18 cd08505
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
25-498 5.37e-48

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.


Pssm-ID: 173870  Cd Length: 528  Bit Score: 173.61  E-value: 5.37e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       25 SLDPHKIEGVPESNVSRDLFEGLLISDVEGHP---SPGVAEK-----WENKDFKVWTFHLRENAKWSD--------GTPV 88
Cdd:cd08505  12 GLDPAQSYDSYSAEIIEQIYEPLLQYHYLKRPyelVPNTAAAmpevsYLDVDGSVYTIRIKPGIYFQPdpafpkgkTREL 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       89 TAHDFVYSWQRLADPNTAspyasylqyghianiddiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVP 168
Cdd:cd08505  92 TAEDYVYSIKRLADPPLE----------------------------GVEAVDRYTLRIRLTGPYPQFLYWLAMPFFAPVP 143
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      169 KSAVEKFGDKWTQPANIVTN------GAYKLKNWVVNERIVLERNPQY------------WDNA-------KTV--INQV 221
Cdd:cd08505 144 WEAVEFYGQPGMAEKNLTLDwhpvgtGPYMLTENNPNSRMVLVRNPNYrgevypfegsadDDQAglladagKRLpfIDRI 223
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      222 TYLPISSEVTDVNRYRSGEIDM---TYNNMPI----------ELFQKLKKE---IPNEVRVDpylcTYYYEINnqkapFN 285
Cdd:cd08505 224 VFSLEKEAQPRWLKFLQGYYDVsgiSSDAFDQalrvsaggepELTPELAKKgirLSRAVEPS----IFYIGFN-----ML 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      286 DVRV----------RTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvEPEWFKWSQQKRNEEAKKLLAEAGFTA 355
Cdd:cd08505 295 DPVVggyskekrklRQAISIAFDWEEYISIFRNGRAVPAQGPIPPGIFGY---RPGEDGKPVRYDLELAKALLAEAGYPD 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      356 D------KPLTFDLLYNTSDLHKklaiAVASIWKKN---LGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSF 426
Cdd:cd08505 372 GrdgptgKPLVLNYDTQATPDDK----QRLEWWRKQfakLGIQLNVRATDYNRFQDKLRKGNAQLFSWGWNADYPDPENF 447
                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
1B3G_A      427 LntMLSDSSN------NTAHYKSPAFDKLIaDTLKVADDT-QRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08505 448 L--FLLYGPNaksggeNAANYSNPEFDRLF-EQMKTMPDGpERQALIDQMNRILREDAPWIFGFHPKSNGLAHPWVGNY 523
PBP2_NikA_DppA_OppA_like_10 cd08515
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
12-487 7.88e-45

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.


Pssm-ID: 173880  Cd Length: 460  Bit Score: 163.54  E-value: 7.88e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       12 KQTLVRNNGSEVQSLDPHKI---EGVPesnVSRDLFEGLLISDVE-GHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTP 87
Cdd:cd08515   1 RDTLVIAVQKEPPTLDPYYNtsrEGVI---ISRNIFDTLIYRDPDtGELVPGLATSWKWIDDTTLEFTLREGVKFHDGSP 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       88 VTAHDFVYSWQRLADPNTASP-YASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSP 166
Cdd:cd08515  78 MTAEDVVFTFNRVRDPDSKAPrGRQNF-----NWLDK------------VEKVDPYTVRIVTKKPDPAALERLAGLVGPI 140
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      167 VPKSAVEKFGDKWTqPANIVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYn 246
Cdd:cd08515 141 VPKAYYEKVGPEGF-ALKPVGTGPYKVTEFVPGERVVLEAFDDYWG-GKPPIEKITFRVIPDVSTRVAELLSGGVDIIT- 217
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      247 NMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIV-NKVKNQGDLPAYSYTPP----Y 321
Cdd:cd08515 218 NVPPDQAERLKSSPGLTVVGGPTMRIGFITFDAAGPPLKDVRVRQALNHAIDRQAIVkALWGGRAKVPNTACQPPqfgcE 297
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      322 TDGAKLVE--PewfkwsqqkrnEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKT 399
Cdd:cd08515 298 FDVDTKYPydP-----------EKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAEAIVGMWKA-VGINAELNVLSKYR 365
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      400 FLDTRHQGTFDVaragwcadynePTSFLN---TMLSDSSNNTAHYKS---PAFDKLIADTLKVADDTQRSELYAKAEQQL 473
Cdd:cd08515 366 ALRAWSKGGLFV-----------PAFFYTwgsNGINDASASTSTWFKardAEFDELLEKAETTTDPAKRKAAYKKALKII 434
                       490
                ....*....|....*
1B3G_A      474 DKDSAIVPVY-YYVN 487
Cdd:cd08515 435 AEEAYWTPLYqYSQN 449
PBP2_NikA_DppA_OppA_like_9 cd08496
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
43-485 5.01e-44

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 can bind 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.


Pssm-ID: 173861  Cd Length: 454  Bit Score: 161.35  E-value: 5.01e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       43 LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTAspyasylQYGHIANI 121
Cdd:cd08496  30 LYDTLIKLDPDGKLEPGLAESWEyNADGTTLTLHLREGLTFSDGTPLDAAAVKANLDRGKSTGGS-------QVKQLASI 102
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      122 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVH---PSVSPvpkSAVEKFGDKWTQPaniVTNGAYKLKNWVV 198
Cdd:cd08496 103 SS------------VEVVDDTTVTLTLSQPDPAIPALLSDragMIVSP---TALEDDGKLATNP---VGAGPYVLTEWVP 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      199 NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIelfQKLKKEIPNEVRVDPYLCTYYYEIN 278
Cdd:cd08496 165 NSKYVFERNEDYWDAANPHLDKLELSVIPDPTARVNALQSGQVDFAQLLAAQ---VKIARAAGLDVVVEPTLAATLLLLN 241
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      279 NQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDG--AKLVEPewFKWSQQKrneeAKKLLAEAGFta 355
Cdd:cd08496 242 ITGAPFDDPKVRQAINYAIDRKAFVDALlFGLGE-PASQPFPPGSWAydPSLENT--YPYDPEK----AKELLAEAGY-- 312
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      356 dkPLTFDL-LYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRH-QGTFDVARAGWCADYNEPTSFLNTMLSD 433
Cdd:cd08496 313 --PNGFSLtIPTGAQNADTLAEIVQQQLAK-VGIKVTIKPLTGANAAGEFFaAEKFDLAVSGWVGRPDPSMTLSNMFGKG 389
                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|..
1B3G_A      434 SSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYY 485
Cdd:cd08496 390 GYYNPGKATDPELSALLKEVRATLDDPARKTALRAANKVVVEQAWFVPLFFQ 441
PBP2_NikA_DppA_OppA_like_21 cd08520
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
43-498 8.88e-44

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.


Pssm-ID: 173885  Cd Length: 468  Bit Score: 160.95  E-value: 8.88e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       43 LFEGLLISDvEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAdpntASPYASYlqYGHIANI 121
Cdd:cd08520  32 IFDSLVWKD-EKGFIPWLAESWEvSEDGLTYTFHLREGAKWHDGEPLTAEDVAFTFDYMK----KHPYVWV--DIELSII 104
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      122 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYF-YKLLvhpSVSPV-PKSAVEKFGD--KWTQPANIVTNGAYKLKNWV 197
Cdd:cd08520 105 ER------------VEALDDYTVKITLKRPYAPFlEKIA---TTVPIlPKHIWEKVEDpeKFTGPEAAIGSGPYKLVDYN 169
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      198 -VNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRyrsGEIDMTynNMPIELFQKLKKEIPNEVRVDPYLCTYYYE 276
Cdd:cd08520 170 kEQGTYLYEANEDYW-GGKPKVKRLEFVPVSDALLALEN---GEVDAI--SILPDTLAALENNKGFKVIEGPGFWVYRLM 243
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      277 INNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS-YTPPYTDgaklvepeWFKWSQQKRN---EEAKKLLAEAG 352
Cdd:cd08520 244 FNHDKNPFSDKEFRQAIAYAIDRQELVEKAARGAAALGSPgYLPPDSP--------WYNPNVPKYPydpEKAKELLKGLG 315
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      353 FTAD--------KPLTFDLLYNTSDLHKKlaiaVASIWKKNL---GVNVNLENQEWKTfLDTR-HQGTFDVA---RAGWC 417
Cdd:cd08520 316 YTDNggdgekdgEPLSLELLTSSSGDEVR----VAELIKEQLervGIKVNVKSLESKT-LDSAvKDGDYDLAisgHGGIG 390
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      418 ADYNeptsFLNTMLSDSSNNTAH-YKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVG 496
Cdd:cd08520 391 GDPD----ILREVYSSNTKKSARgYDNEELNALLRQQLQEMDPEKRKELVFEIQELYAEELPMIPLYYPTMYTVHRGKYD 466

                ..
1B3G_A      497 GY 498
Cdd:cd08520 467 GW 468
PBP2_NikA_DppA_OppA_like_12 cd08491
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
38-486 7.00e-43

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.


Pssm-ID: 173856  Cd Length: 473  Bit Score: 158.69  E-value: 7.00e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       38 NVSRDLFEGLLISDVE-GHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPntaspyasylqyg 116
Cdd:cd08491  26 VIRSNVTEPLTEIDPEsGTVGPRLATEWEQVDDNTWRFKLRPGVKFHDGTPFDAEAVAFSIERSMNG------------- 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      117 hiANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPvPKSAVEKFGDKwtqPaniVTNGAYKLKNW 196
Cdd:cd08491  93 --KLTCETRGYYFGDAKLTVKAVDDYTVEIKTDEPDPILPLLLSYVDVVS-PNTPTDKKVRD---P---IGTGPYKFDSW 163
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      197 VVNERIVLERNPQYWDNaKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIEL------FQKLKKEipnevrvdpyl 270
Cdd:cd08491 164 EPGQSIVLSRFDGYWGE-KPEVTKATYVWRSESSVRAAMVETGEADLAPSIAVQDAtnpdtdFAYLNSE----------- 231
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      271 cTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvEPEWFKWSQQKrnEEAKKLLAE 350
Cdd:cd08491 232 -TTALRIDAQIPPLDDVRVRKALNLAIDRDGIVGALFGGQGRPATQLVVPGINGH---NPDLKPWPYDP--EKAKALVAE 305
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      351 A---GFTADKPLTF----DLLYNTSDLHKklaiAVASIWKKnLGVNVNLENQE---W-----KTFLDTRHQGTFDVARAG 415
Cdd:cd08491 306 AkadGVPVDTEITLigrnGQFPNATEVME----AIQAMLQQ-VGLNVKLRMLEvadWlrylrKPFPEDRGPTLLQSQHDN 380
                       410       420       430       440       450       460       470
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
1B3G_A      416 WCADynEPTSFLNTMLSDSSNNTahYKSPAFDKLIADTLKVADDtQRSELYAKAEQQL-DKDSAIVPVYYYV 486
Cdd:cd08491 381 NSGD--ASFTFPVYYLSEGSQST--FGDPELDALIKAAMAATGD-ERAKLFQEIFAYVhDEIVADIPMFHMV 447
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
26-484 2.12e-42

nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Most appear to be lipoproteins. This protein was previously (circa 2003) thought to mediate binding to nickel through water molecules, but is now thought to involve a chelating organic molecule, perhaps butane-1,2,4-tricarboxylate, acting as a metallophore. [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 274072  Cd Length: 500  Bit Score: 157.66  E-value: 2.12e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         26 LDPHKIEgvPESNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAhdfvyswqrladP 103
Cdd:TIGR02294  19 MNPHVYN--PNQMFAQSMvYEPLVRYTADGKIEPWLAKSWTvSEDGKTYTFKLRDDVKFSDGTPFDA------------E 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        104 NTAspyasylqyghiANIDDIIAGKKPATDLG-------VKALDDHTFEVTLSEPV-PYFYKLLVhpsVSPVPKSAVEKF 175
Cdd:TIGR02294  85 AVK------------KNFDAVLQNSQRHSWLElsnqldnVKALDKYTFELVLKEAYyPALQELAM---PRPYRFLSPSDF 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        176 GDKWTQPA--NIVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN---MPI 250
Cdd:TIGR02294 150 KNDTTKDGvkKPIGTGPWMLGESKQDEYAVFVRNENYW-GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGNegsIDL 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        251 ELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYTDGAkl 327
Cdd:TIGR02294 229 DTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPAdtlFAKNVPYADID-- 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        328 VEPewFKWSQQKrneeAKKLLAEAGFT--ADK--------PLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQE 396
Cdd:TIGR02294 307 LKP--YKYDVKK----ANALLDEAGWKlgKGKdvrekdgkPLELELYYdKTSALQKSLAEYLQAEWRK-IGIKLSLIGEE 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        397 WKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDS-SNNTAHYK---SPAFDKLIADTLKVADDTQRSELYAKAEQ 471
Cdd:TIGR02294 380 EDKIAARRRDGDFDMMFNyTWGAPY-DPHSFISAMRAKGhGDESAQSGlanKDEIDKSIGDALASTDETERQELYKNILT 458
                         490
                  ....*....|...
1B3G_A        472 QLDKDSAIVPVYY 484
Cdd:TIGR02294 459 TLHDEAVYIPISY 471
PBP2_NikA_DppA_OppA_like_14 cd08497
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
25-490 3.65e-41

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.


Pssm-ID: 173862  Cd Length: 491  Bit Score: 154.22  E-value: 3.65e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       25 SLDPHKIEGVPESNVSRDLFEGLLIS--DVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLA 101
Cdd:cd08497  28 SLNPFILKGTAAAGLFLLVYETLMTRspDEPFSLYGLLAESVEyPPDRSWVTFHLRPEARFSDGTPVTAEDVVFSFETLK 107
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      102 DPNtASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEP----VPYFYKLLvhpsvSPVPKSAVEKFGD 177
Cdd:cd08497 108 SKG-PPYYRAYY-----ADVEK------------VEALDDHTVRFTFKEKanreLPLIVGGL-----PVLPKHWYEGRDF 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      178 K-----WTQPaniVTNGAYKLKNWVVNERIVLERNPQYW----------DNAKTVInqVTYlpISSEVTDVNRYRSGEID 242
Cdd:cd08497 165 DkkrynLEPP---PGSGPYVIDSVDPGRSITYERVPDYWgkdlpvnrgrYNFDRIR--YEY--YRDRTVAFEAFKAGEYD 237
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      243 MTYNNMP--------IELFQK---LKKEIPNEVRVDPylctYYYEINNQKAPFNDVRVRTALKLALDrdiivnkvknqgd 311
Cdd:cd08497 238 FREENSAkrwatgydFPAVDDgrvIKEEFPHGNPQGM----QGFVFNTRRPKFQDIRVREALALAFD------------- 300
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      312 lpaysytppytdgaklvepewFKWS-------QQKRNE----EAKKLLAEAGFTAD----------KPLTFDLLYNTSDL 370
Cdd:cd08497 301 ---------------------FEWMnknlfygQYTRTRfnlrKALELLAEAGWTVRggdilvnadgEPLSFEILLDSPTF 359
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      371 HKklaiaVASIWKKNL---GVNVNLE---NQEWKTFLDTRHqgtFDVARAGWCADY---NEPTSFLNTMLSD--SSNNTA 439
Cdd:cd08497 360 ER-----VLLPYVRNLkklGIDASLRlvdSAQYQKRLRSFD---FDMITAAWGQSLspgNEQRFHWGSAAADkpGSNNLA 431
                       490       500       510       520       530
                ....*....|....*....|....*....|....*....|....*....|....*
1B3G_A      440 HYKSPAFDKLIaDTLKVADDtqRSELYAkAEQQLDK----DSAIVPVYYYVNARL 490
Cdd:cd08497 432 GIKDPAVDALI-EAVLAADD--REELVA-AVRALDRvlraGHYVIPQWYLPYHRV 482
PBP2_Lactococcal_OppA_like cd08510
The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; ...
32-498 2.35e-36

The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 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.


Pssm-ID: 173875  Cd Length: 516  Bit Score: 141.25  E-value: 2.35e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       32 EGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASP-Y 109
Cdd:cd08510  24 EDNTDAEIMGFGNEGLFDTDKNYKITDSGAAKFKlDDKAKTVTITIKDGVKWSDGKPVTAKDLEYSYEIIANKDYTGVrY 103
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      110 ASYLQygHIANIDDIIAGKKPaTDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPA-----N 184
Cdd:cd08510 104 TDSFK--NIVGMEEYHDGKAD-TISGIKKIDDKTVEITFKEMSPSMLQSGNGYFEYAEPKHYLKDVPVKKLESSdqvrkN 180
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      185 IVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEvTDVNRYRSGEIDMTyNNMPIELFQKLKKEIPNEV 264
Cdd:cd08510 181 PLGFGPYKVKKIVPGESVEYVPNEYYW-RGKPKLDKIVIKVVSPS-TIVAALKSGKYDIA-ESPPSQWYDQVKDLKNYKF 257
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      265 RVDPYLcTYYY--------------EINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP----YTDGak 326
Cdd:cd08510 258 LGQPAL-SYSYigfklgkwdkkkgeNVMDPNAKMADKNLRQAMAYAIDNDAVGKKFYNGLRTRANSLIPPvfkdYYDS-- 334
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      327 lvEPEWFKWSQQKrneeAKKLLAEAGF---TAD--------KPLTFDLL-YNTSDLHKKLAIAVASIWKKnLGVNVNLEN 394
Cdd:cd08510 335 --ELKGYTYDPEK----AKKLLDEAGYkdvDGDgfredpdgKPLTINFAaMSGSETAEPIAQYYIQQWKK-IGLNVELTD 407
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      395 ---QEWKTFLDTRHQG--TFDVARAGWCADYN-EPTSFLntmLSDSSNNTAHYKSPAFDKLIA--DTLKVADDTQRSELY 466
Cdd:cd08510 408 grlIEFNSFYDKLQADdpDIDVFQGAWGTGSDpSPSGLY---GENAPFNYSRFVSEENTKLLDaiDSEKAFDEEYRKKAY 484
                       490       500       510
                ....*....|....*....|....*....|..
1B3G_A      467 AKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 498
Cdd:cd08510 485 KEWQKYMNEEAPVIPTLYRYSITPVNKRVKGY 516
PBP2_SgrR_like cd08507
The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related ...
25-483 1.46e-27

The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery from glucose-phosphate stress. Most of 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.


Pssm-ID: 173872  Cd Length: 448  Bit Score: 114.67  E-value: 1.46e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       25 SLDPHKIEGVPESNVSRDLFEGLLISDVE-GHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAD 102
Cdd:cd08507  17 TLDPGTPLRRSESHLVRQIFDGLVRYDEEnGEIEPDLAHHWEsNDDLTHWTFYLRKGVRFHNGRELTAEDVVFTLLRLRE 96
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      103 PNTASPyasylQYGHIANIddiiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFgDKWTQP 182
Cdd:cd08507  97 LESYSW-----LLSHIEQI---------------ESPSPYTVDIKLSKPDPLFPRLLASANASILPADILFDP-DFARHP 155
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      183 aniVTNGAYKLKNWvVNERIVLERNPQYWdNAKTVINQVTYLpISSEVTDVNRYRSGEIDMTYNNMPIElFQKlkkeipn 262
Cdd:cd08507 156 ---IGTGPFRVVEN-TDKRLVLEAFDDYF-GERPLLDEVEIW-VVPELYENLVYPPQSTYLQYEESDSD-EQQ------- 221
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      263 EVRVDPylCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKN---QGDLPAYSYTPPYTDgaklvepewfkwsqqk 339
Cdd:cd08507 222 ESRLEE--GCYFLLFNQRKPGAQDPAFRRALSELLDPEALIQHLGGerqRGWFPAYGLLPEWPR---------------- 283
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      340 rnEEAKKLLAEAGFtADKPLTfdLLYNTSDLHKKLAIAVASIWKKnlgVNVNLENQEWktFLDTRHQGTFDVARAGWCA- 418
Cdd:cd08507 284 --EKIRRLLKESEY-PGEELT--LATYNQHPHREDAKWIQQRLAK---HGIRLEIHIL--SYEELLEGDADSMADLWLGs 353
                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1B3G_A      419 ---DYNEPTSFLNTMLsDSSNNTAHYKSPAFDKLIADTLKvadDTQRSELYAKAEQQLDKDSAIVPVY 483
Cdd:cd08507 354 anfADDLEFSLFAWLL-DKPLLRHGCILEDLDALLAQWRN---EELAQAPLEEIEEQLVDEAWLLPLF 417
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
20-482 5.95e-27

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311  Cd Length: 512  Bit Score: 113.83  E-value: 5.95e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        20 GSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQ 98
Cdd:PRK15413  35 GSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTvSDDGLTYTVKLREGVKFQDGTDFNAAAVKANLD 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        99 RLADPNtaSPYASYLQYGHIANIDdiiagkkpatdlgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFG-D 177
Cdd:PRK15413 115 RASNPD--NHLKRYNLYKNIAKTE---------------AVDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGkE 177
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       178 KWTQPaniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIELFQKLK 257
Cdd:PRK15413 178 IGFHP---VGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAF-PIPYEQAALLE 253
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       258 KEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVnKVKNQG-DLPAYSYTPPYTDGAKLVEPewfkWS 336
Cdd:PRK15413 254 KNKNLELVASPSIMQRYISMNVTQKPFDNPKVREALNYAINRQALV-KVAFAGyATPATGVVPPSIAYAQSYKP----WP 328
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       337 QQKrnEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVN-LENQEWKTFLDTRHQGTFDVAR-- 413
Cdd:PRK15413 329 YDP--AKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTaMDAGQRAAEVEGKGQKESGVRMfy 406
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1B3G_A       414 AGWCADYNEPTSFLNTMLSDSS-----NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 482
Cdd:PRK15413 407 TGWSASTGEADWALSPLFASQNwpptlFNTAFYSNKQVDDDLAQALKTNDPAEKTRLYKAAQDIIWKESPWIPL 480
PRK15109 PRK15109
antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
58-484 9.88e-18

antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional


Pssm-ID: 185064  Cd Length: 547  Bit Score: 85.90  E-value: 9.88e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        58 PGVAEKWENKDF-KVWTFHLREN-----AKWSDGT-PVTAHDFVYSWQRLADPN--------TASPYASYLQYGhianiD 122
Cdd:PRK15109  81 PELAESWEVLDNgATYRFHLRRDvpfqkTDWFTPTrKMNADDVVFSFQRIFDRNhpwhnvngGNYPYFDSLQFA-----D 155
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       123 DIiagkkpatdLGVKALDDHTFEVTLSEPVPYF-YKLLVH--PSVSPVPKSAVEKFGDK----WtQPaniVTNGAYKLKN 195
Cdd:PRK15109 156 NV---------KSVRKLDNYTVEFRLAQPDASFlWHLATHyaSVLSAEYAAKLTKEDRQeqldR-QP---VGTGPFQLSE 222
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       196 WVVNERIVLERNPQYWdNAKTVINQVtylpisseVTDV--------NRYRSGEID-MTY---NNMPIelfqklkkeipne 263
Cdd:PRK15109 223 YRAGQFIRLQRHDDYW-RGKPLMPQV--------VVDLgsggtgrlSKLLTGECDvLAYpaaSQLSI------------- 280
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       264 VRVDPYL--------CTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTP----PYTDGAKLVE-- 329
Cdd:PRK15109 281 LRDDPRLrltlrpgmNIAYLAFNTRKPPLNNPAVRHALALAINNQRLMQSIYYGTAETAASILPraswAYDNEAKITEyn 360
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       330 PEwfkwsqqkrneEAKKLLAEAGFTAdkpLTFDLL-------YNTSDLhKKLAIAVASIwkKNLGVNVNLENQEWKtFLD 402
Cdd:PRK15109 361 PE-----------KSREQLKALGLEN---LTLKLWvptasqaWNPSPL-KTAELIQADL--AQVGVKVVIVPVEGR-FQE 422
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       403 TR-HQGTFDVARAGWCADYNEPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 477
Cdd:PRK15109 423 ARlMDMNHDLTLSGWATDSNDPDSFFRPLLScaaiRSQTNYAHWCDPAFDSVLRKALSSQQLASRIEAYDEAQSILAQEL 502

                 ....*..
1B3G_A       478 AIVPVYY 484
Cdd:PRK15109 503 PILPLAS 509
SgrR COG4533
DNA-binding transcriptional regulator SgrR of sgrS sRNA, contains a MarR-type HTH domain and ...
22-210 1.00e-11

DNA-binding transcriptional regulator SgrR of sgrS sRNA, contains a MarR-type HTH domain and a periplasmic-type solute-binding domain [Transcription];


Pssm-ID: 226909 [Multi-domain]  Cd Length: 564  Bit Score: 66.97  E-value: 1.00e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A       22 EVQSLDPHKIEGVPESNVSRDLFEGLLISD-VEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 99
Cdd:COG4533 130 PLEPLDPGQALRRSEQHLARQIFSGLTRYDeEKGELEPDLAHHWQqSDDGLRWRFYLRPGVLFHNGRELDASDVIASLLR 209
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A      100 LADPNTASPyasylQYGHIANIDdiiagkkpatdlgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVekfgdkw 179
Cdd:COG4533 210 LLQLPALAW-----LFSHIKTIT---------------SPHPYTLEIHLHRPDPWLPLLLASVPAMILPRDVP------- 262
                       170       180       190
                ....*....|....*....|....*....|...
1B3G_A      180 TQPANIVTNGAYKlknWVVN--ERIVLERNPQY 210
Cdd:COG4533 263 TDPDHPIGTGPFK---VQENtdNRLVLEAFDHY 292
SBP_KPN_01854 TIGR04028
ABC transporter substrate binding protein, KPN_01854 family; Members of this protein family ...
57-499 3.25e-04

ABC transporter substrate binding protein, KPN_01854 family; Members of this protein family are ABC transporter substrate-binding proteins related to KPN_01854 from Klebsiella pneumoniae, and occur in both Gram-positive and Gram-negative species. This transport protein family is closely associated with a putative FMN-dependent luciferase-like monooxygenase of unknown function (TIGR04027), as well as with the other proteins of its transporter complex. [Transport and binding proteins, Unknown substrate]


Pssm-ID: 274929  Cd Length: 509  Bit Score: 43.14  E-value: 3.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A         57 SPGVAEKWE--NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR--LADPNTASPYASylqygHIANIDdiiagkkpat 132
Cdd:TIGR04028  45 EPWIAESWPevNADATEYTFKIRKGVTYSDGTPLDAENVAKNFDLygLGDKDRKLTVSE-----VINNYD---------- 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        133 dlGVKALDDHTFEVTLSEPVPYFYKL-------LVHPSVSPVPKsavEKFGDKwtQPANIVTNGAYKLKNWVVNERIVLE 205
Cdd:TIGR04028 110 --RSEVVDPLTVKFYFSKPSPGFLQGtsvinsgLVSLATLALPF---EGFGPG--NATKIIGSGPFVVESEELGTELVLK 182
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        206 RNPQY-WDNAKTV------INQVTYLPISSEVTDVNRYRSGEIDMTYnnmpielfqklKKEIPNEVRVDPYLCTYYYE-- 276
Cdd:TIGR04028 183 AREDYdWAPPSRAhqgrayLDGIKYIVAAEDSVRVGALLAGQADLAR-----------QIEAPDEKQVEDQGFAIYAApt 251
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        277 --INNQKA-----PF-NDVRVRTALKLALDRDIIVNKVknqgdlpaysYTPPYTDGAKLVEPEWFKWSQQKRN-----EE 343
Cdd:TIGR04028 252 rgVNNSFAfrfdnPLlADIRVRQALIHATDRKEIVDTL----------FSDSYPLATSVLASTALGYVDLSDKytfdpEK 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        344 AKKLLAEAGFTAD---------KPLTfdLLYNTSDLH---KKLAIAVASIWKKnLGVNVNLE--NQEWKTfLDTRHQGTF 409
Cdd:TIGR04028 322 AAALLDEAGWKPGpdgirqkdgQRLA--LTFNEALPQprnKEVLTLVQQQLAK-VGVKLNVLagDQAAQT-ADSLDPDKT 397
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1B3G_A        410 DVARA--GWcADYNEPTSFL-----NTMLS-DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVP 481
Cdd:TIGR04028 398 QVYHSmvGR-ADPDVLKSQYyptnrNALLNkGGDSDKVKFGDEKLNALLEAIASEPDEEKRLAASGAVQDYLTDQAYVLP 476
                         490
                  ....*....|....*...
1B3G_A        482 VYYYVNARLVKPWVGGYT 499
Cdd:TIGR04028 477 IFEEPQVFAGAPYVKGFA 494
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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