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Conserved domains on  [gi|1109557646|ref|NP_460705|]
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oligopeptide transport protein with chaperone properties [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

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
40-582 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


:

Pssm-ID: 185059 [Multi-domain]  Cd Length: 543  Bit Score: 1158.38  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  40 MSNITKKSLIAAGILTALIAASAATAADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG 119
Cdd:PRK15104    1 MTNITKKSLIAAGVLAALMAGNVALAADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 120 HPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDL 199
Cdd:PRK15104   81 HPAPGVAESWDNKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 200 GVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNA 279
Cdd:PRK15104  161 GVKAIDDHTLEVTLSEPVPYFYKLLVHPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNA 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 280 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALK 359
Cdd:PRK15104  241 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALK 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 360 LALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKL 439
Cdd:PRK15104  321 LGLDRDIIVNKVKNQGDLPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKL 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 440 AIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTL 519
Cdd:PRK15104  401 AIAAASIWKKNLGVNVKLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETL 480
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1109557646 520 KVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 582
Cdd:PRK15104  481 KVKDEAQRAALYQKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
 
Name Accession Description Interval E-value
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
40-582 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059 [Multi-domain]  Cd Length: 543  Bit Score: 1158.38  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  40 MSNITKKSLIAAGILTALIAASAATAADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG 119
Cdd:PRK15104    1 MTNITKKSLIAAGVLAALMAGNVALAADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 120 HPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDL 199
Cdd:PRK15104   81 HPAPGVAESWDNKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 200 GVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNA 279
Cdd:PRK15104  161 GVKAIDDHTLEVTLSEPVPYFYKLLVHPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNA 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 280 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALK 359
Cdd:PRK15104  241 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALK 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 360 LALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKL 439
Cdd:PRK15104  321 LGLDRDIIVNKVKNQGDLPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKL 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 440 AIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTL 519
Cdd:PRK15104  401 AIAAASIWKKNLGVNVKLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETL 480
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1109557646 520 KVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 582
Cdd:PRK15104  481 KVKDEAQRAALYQKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
78-579 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 [Multi-domain]  Cd Length: 498  Bit Score: 668.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  78 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08504     1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDGKIVPGLAESWEvSDDGLTYTFHLRKDAKWSNGDPVTAQ 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRLADPNTASPYASYLQYghIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 236
Cdd:cd08504    81 DFVYSWRRALDPKTASPYAYLLYP--IKNAEAINAGKKPPDELGVKALDDYTLEVTLEKPTPYFLSLLAHPTFFPVNQKF 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 237 VEKFGDK-WTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPi 315
Cdd:cd08504   159 VEKYGGKyGTSPENIVYNGPFKLKEWTPNDKIVLVKNPNYWDAKNVKLDKINFLVIKDPNTALNLFEAGELDIAGLPPE- 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 316 elFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDLPAYSYTPPYTDGAKlv 393
Cdd:cd08504   238 --QVILKLKNNKDLKSTPYLGTYYLEFNTKKPPLDNKRVRKALSLAIDREALVEKVlgDAGGFVPAGLFVPPGTGGDF-- 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 394 ePEWFKWSQQKRNEEAKKLLAEAGFTADK-PLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQG 472
Cdd:cd08504   314 -RDEAGKLLEYNPEKAKKLLAEAGYELGKnPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVKVTLKNVEWKVFLDRRRKG 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 473 TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 552
Cdd:cd08504   393 DFDIARSGWGADYNDPSTFLDLFTSGSGNNYGGYSNPEYDKLLAKAATETDPEKRWELLAKAEKILLDDAPIIPLYQYVT 472
                         490       500
                  ....*....|....*....|....*..
gi 1109557646 553 ARLVKPWVGGYTgKDPLDNIYVKNLYI 579
Cdd:cd08504   473 AYLVKPKVKGLV-YNPLGGYDFKYAYL 498
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
70-581 0e+00

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


Pssm-ID: 226636 [Multi-domain]  Cd Length: 562  Bit Score: 546.23  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  70 AGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG-HPSPGVAEKWEN-KDFKVWTFHLRENAKW 147
Cdd:COG4166    30 HGTSLAGKQVLYVNNFSHPDSLDPQAPKGGVSTNVLRGLFEGLVRYDPKGgPALPGAAESWEVsDDGKTYTFHLRADAKW 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 148 SDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKK-PATDLGVKALDDHTFEVTLSEPVPYFYKLLVH 226
Cdd:COG4166   110 SNGDPVTAVDFVLSWKAAADPKTTAPYVYFLFNSVIKNAEPIFTGKKsPVDVLGVKALDDRTLEITLEKPTPYFLLLLAH 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 227 PSVSPVPKSAVEKFGDKWTQPA--NIVTNGAYKLKNWVV-NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRS 303
Cdd:COG4166   190 GTFLPVNPKHVEKYGDDFTKPLdeNPVGNGPYKLKSWVDpNQKIVLERNPDYWDKDNVVLDGITYDYIDDANTALEAFKA 269
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 304 GEIDMTYNN--MPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS 381
Cdd:COG4166   270 GEIDIASEPpaSPWALDYVLKLKDNGDVYKEPTLGTQYLAFNTRRPPFNDPRVRKALSLAIDREWLNKQVFGGRSTPATS 349
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 382 YTPPYTDGAKLVE-PEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-----HKKLAIAVASIWKKNLG--- 452
Cdd:COG4166   350 FTPPAASGLPGKElALLAPLPQKDPPEKAKELLKEAGYELGGRLNLTLKLLTSAGwkgsqHKNIATGLPFQWEKLLGlak 429
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 453 VNVNLENQEWKTFLDTRHQ-GTFDVARAGWCADYNEPTSFLNTMLSDSS--NNTAHYKSPAFDKLIADTLKVADDTQRSE 529
Cdd:COG4166   430 IGIKLVIREVKTQYTKRLQsGDFDMILSGWGADYNDPSEFLRLFFTSSSadNNAAGYKNPEYDALIEAALEAQDPEERLE 509
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1109557646 530 LYAK-AEQQLDKDSAIVPVYYYVNaRLVKPW-VGGYTGKDPLDNIYVKNLYIIK 581
Cdd:COG4166   510 LLARaAERILLQDAPVIPLYYYAN-RLARWDrPKGSPGYNPLGDVYWKDLYKKK 562
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
121-502 2.08e-102

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: 425718  Cd Length: 368  Bit Score: 313.96  E-value: 2.08e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 121 PSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYghianiddiiagkkPATDL 199
Cdd:pfam00496   2 VVPALAESWEvSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYASLLAY--------------DADIV 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 200 GVKALDDHTFEVTLSEPVPYFYKLLvhPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNa 279
Cdd:pfam00496  68 GVEAVDDYTVRFTLKKPDPLFLPLL--AALAAAPVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYWGG- 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 280 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALK 359
Cdd:pfam00496 145 KPKLDRIVFKVIPDSTARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSGPGGGTYYLAFNTKKPPFDDVRVRQALS 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 360 LALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEwfkwsQQKRNEEAKKLLAEAGFTA------DKPLTFDLLYNTS 433
Cdd:pfam00496 225 YAIDREAIVKAVLGGYATPANSLVPPGFPGYDDDPKP-----EYYDPEKAKALLAEAGYKDgdgggrRKLKLTLLVYSGN 299
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109557646 434 DLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNN 502
Cdd:pfam00496 300 PAAKAIAELIQQQLKK-IGIKVEIKTVDWATYLERVKDGDFDMALSGWGADYPDPDNFLYPFLSSTGGG 367
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
91-549 1.08e-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 [Multi-domain]  Cd Length: 500  Bit Score: 159.97  E-value: 1.08e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  91 LDPHKIEgvPESNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAhdfvyswqrladP 168
Cdd:TIGR02294  19 MNPHVYN--PNQMFAQSMvYEPLVRYTADGKIEPWLAKSWTvSEDGKTYTFKLRDDVKFSDGTPFDA------------E 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 169 NTAspyasylqyghiANIDDIIAGKKPATDLG-------VKALDDHTFEVTLSEPV-PYFYKLLVhpsVSPVPKSAVEKF 240
Cdd:TIGR02294  85 AVK------------KNFDAVLQNSQRHSWLElsnqldnVKALDKYTFELVLKEAYyPALQELAM---PRPYRFLSPSDF 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 241 GDKWTQPA--NIVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN---MPI 315
Cdd:TIGR02294 150 KNDTTKDGvkKPIGTGPWMLGESKQDEYAVFVRNENYW-GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGNegsIDL 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 316 ELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYTDGAkl 392
Cdd:TIGR02294 229 DTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPAdtlFAKNVPYADID-- 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 393 VEPewFKWSQQKrneeAKKLLAEAGFT--ADK--------PLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQE 461
Cdd:TIGR02294 307 LKP--YKYDVKK----ANALLDEAGWKlgKGKdvrekdgkPLELELYYdKTSALQKSLAEYLQAEWRK-IGIKLSLIGEE 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 462 WKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDS-SNNTAHYK---SPAFDKLIADTLKVADDTQRSELYAKAEQ 536
Cdd:TIGR02294 380 EDKIAARRRDGDFDMMFNyTWGAPY-DPHSFISAMRAKGhGDESAQSGlanKDEIDKSIGDALASTDETERQELYKNILT 458
                         490
                  ....*....|...
gi 1109557646 537 QLDKDSAIVPVYY 549
Cdd:TIGR02294 459 TLHDEAVYIPISY 471
 
Name Accession Description Interval E-value
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
40-582 0e+00

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059 [Multi-domain]  Cd Length: 543  Bit Score: 1158.38  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  40 MSNITKKSLIAAGILTALIAASAATAADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG 119
Cdd:PRK15104    1 MTNITKKSLIAAGVLAALMAGNVALAADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 120 HPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDL 199
Cdd:PRK15104   81 HPAPGVAESWDNKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLADPKTASPYASYLQYGHIANIDDIIAGKKPPTDL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 200 GVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNA 279
Cdd:PRK15104  161 GVKAIDDHTLEVTLSEPVPYFYKLLVHPSMSPVPKAAVEKFGEKWTQPANIVTNGAYKLKDWVVNERIVLERNPTYWDNA 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 280 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALK 359
Cdd:PRK15104  241 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALK 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 360 LALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKL 439
Cdd:PRK15104  321 LGLDRDIIVNKVKNQGDLPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKL 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 440 AIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTL 519
Cdd:PRK15104  401 AIAAASIWKKNLGVNVKLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSNNTAHYKSPAFDKLMAETL 480
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1109557646 520 KVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 582
Cdd:PRK15104  481 KVKDEAQRAALYQKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
78-579 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 [Multi-domain]  Cd Length: 498  Bit Score: 668.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  78 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08504     1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDGKIVPGLAESWEvSDDGLTYTFHLRKDAKWSNGDPVTAQ 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRLADPNTASPYASYLQYghIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 236
Cdd:cd08504    81 DFVYSWRRALDPKTASPYAYLLYP--IKNAEAINAGKKPPDELGVKALDDYTLEVTLEKPTPYFLSLLAHPTFFPVNQKF 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 237 VEKFGDK-WTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPi 315
Cdd:cd08504   159 VEKYGGKyGTSPENIVYNGPFKLKEWTPNDKIVLVKNPNYWDAKNVKLDKINFLVIKDPNTALNLFEAGELDIAGLPPE- 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 316 elFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDLPAYSYTPPYTDGAKlv 393
Cdd:cd08504   238 --QVILKLKNNKDLKSTPYLGTYYLEFNTKKPPLDNKRVRKALSLAIDREALVEKVlgDAGGFVPAGLFVPPGTGGDF-- 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 394 ePEWFKWSQQKRNEEAKKLLAEAGFTADK-PLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQG 472
Cdd:cd08504   314 -RDEAGKLLEYNPEKAKKLLAEAGYELGKnPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVKVTLKNVEWKVFLDRRRKG 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 473 TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 552
Cdd:cd08504   393 DFDIARSGWGADYNDPSTFLDLFTSGSGNNYGGYSNPEYDKLLAKAATETDPEKRWELLAKAEKILLDDAPIIPLYQYVT 472
                         490       500
                  ....*....|....*....|....*..
gi 1109557646 553 ARLVKPWVGGYTgKDPLDNIYVKNLYI 579
Cdd:cd08504   473 AYLVKPKVKGLV-YNPLGGYDFKYAYL 498
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
70-581 0e+00

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


Pssm-ID: 226636 [Multi-domain]  Cd Length: 562  Bit Score: 546.23  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  70 AGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG-HPSPGVAEKWEN-KDFKVWTFHLRENAKW 147
Cdd:COG4166    30 HGTSLAGKQVLYVNNFSHPDSLDPQAPKGGVSTNVLRGLFEGLVRYDPKGgPALPGAAESWEVsDDGKTYTFHLRADAKW 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 148 SDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKK-PATDLGVKALDDHTFEVTLSEPVPYFYKLLVH 226
Cdd:COG4166   110 SNGDPVTAVDFVLSWKAAADPKTTAPYVYFLFNSVIKNAEPIFTGKKsPVDVLGVKALDDRTLEITLEKPTPYFLLLLAH 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 227 PSVSPVPKSAVEKFGDKWTQPA--NIVTNGAYKLKNWVV-NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRS 303
Cdd:COG4166   190 GTFLPVNPKHVEKYGDDFTKPLdeNPVGNGPYKLKSWVDpNQKIVLERNPDYWDKDNVVLDGITYDYIDDANTALEAFKA 269
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 304 GEIDMTYNN--MPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS 381
Cdd:COG4166   270 GEIDIASEPpaSPWALDYVLKLKDNGDVYKEPTLGTQYLAFNTRRPPFNDPRVRKALSLAIDREWLNKQVFGGRSTPATS 349
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 382 YTPPYTDGAKLVE-PEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-----HKKLAIAVASIWKKNLG--- 452
Cdd:COG4166   350 FTPPAASGLPGKElALLAPLPQKDPPEKAKELLKEAGYELGGRLNLTLKLLTSAGwkgsqHKNIATGLPFQWEKLLGlak 429
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 453 VNVNLENQEWKTFLDTRHQ-GTFDVARAGWCADYNEPTSFLNTMLSDSS--NNTAHYKSPAFDKLIADTLKVADDTQRSE 529
Cdd:COG4166   430 IGIKLVIREVKTQYTKRLQsGDFDMILSGWGADYNDPSEFLRLFFTSSSadNNAAGYKNPEYDALIEAALEAQDPEERLE 509
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1109557646 530 LYAK-AEQQLDKDSAIVPVYYYVNaRLVKPW-VGGYTGKDPLDNIYVKNLYIIK 581
Cdd:COG4166   510 LLARaAERILLQDAPVIPLYYYAN-RLARWDrPKGSPGYNPLGDVYWKDLYKKK 562
PRK09755 PRK09755
ABC transporter substrate-binding protein;
67-582 4.64e-161

ABC transporter substrate-binding protein;


Pssm-ID: 182060  Cd Length: 535  Bit Score: 470.78  E-value: 4.64e-161
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  67 DVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDF-KVWTFHLRENA 145
Cdd:PRK09755   22 DVPANTPLAPQQVFRYNNHSDPGTLDPQKVEENTAAQIVLDLFEGLVWMDGEGQVQPAQAERWEILDGgKRYIFHLRSGL 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 146 KWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLV 225
Cdd:PRK09755  102 QWSDGQPLTAEDFVLGWQRAVDPKTASPFAGYLAQAHINNAAAIVAGKADVTSLGVKATDDRTLEVTLEQPVPWFTTMLA 181
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 226 HPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE 305
Cdd:PRK09755  182 WPTLFPVPHHVIAKHGDSWSKPENMVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQVEYLALDNSVTGYNRYRAGE 261
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 306 IDMTYnnMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQgDLPAYSYTPP 385
Cdd:PRK09755  262 VDLTW--VPAQQIPAIEKSLPGELRIIPRLNSEYYNFNLEKPPFNDVRVRRALYLTVDRQLIAQKVLGL-RTPATTLTPP 338
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 386 YTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 465
Cdd:PRK09755  339 EVKGFSATTFDELQKPMSERVAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQVTLRTMEWKTY 418
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 466 LDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV 545
Cdd:PRK09755  419 LDARRAGDFMLSRQSWDATYNDASSFLNTLKSDSEENVGHWKNAQYDALLNQATQITDATKRNALYQQAEVIINQQAPLI 498
                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 1109557646 546 PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 582
Cdd:PRK09755  499 PIYYQPLIKLLKPYVGGFPLHNPQDYVYSKELYIKAH 535
PBP2_NikA_DppA_OppA_like cd00995
The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains ...
79-563 6.64e-135

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: 400.92  E-value: 6.64e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 157
Cdd:cd00995     1 TLTVALGSDPTSLDPAFATDASSGRVLRLIYDGLVRYDPDGELVPDLAESWEvSDDGKTYTFKLRDGVKFHDGTPLTAED 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 158 FVYSWQRLADPNTASPYASYLqyghiANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAV 237
Cdd:cd00995    81 VVFSFERLADPKNASPSAGKA-----DEIE------------GVEVVDDYTVTITLKEPDAPFLALLAYPAASPVPKAAA 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 238 EKFGDKWTQpaNIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIEL 317
Cdd:cd00995   144 EKDGKAFGT--KPVGTGPYKLVEWKPGESIVLERNDDYWGPGKPKIDKITFKVIPDASTRVAALQSGEIDIAD-DVPPSA 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 318 FQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEW 397
Cdd:cd00995   221 LETLKKNPGIRLVTVPSLGTGYLGFNTNKPPFDDKRVRQAISYAIDREEIIDAVLGGYGTPATSPLPPGSWGYYDKDLEP 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 398 FKwsqqKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDL-HKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGT-FD 475
Cdd:cd00995   301 YE----YDPEKAKELLAEAGYKDGKGLELTLLYNSDGPtRKEIAEAIQAQLKE-IGIKVEIEPLDFATLLDALDAGDdFD 375
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 476 VARAGWCADYNEPTSFLNTMLSDSS---NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVN 552
Cdd:cd00995   376 LFLLGWGADYPDPDNFLSPLFSSGAsgaGNYSGYSNPEFDALLDEARAETDPEERKALYQEAQEILAEDAPVIPLYYPNN 455
                         490
                  ....*....|.
gi 1109557646 553 ARLVKPWVGGY 563
Cdd:cd00995   456 VYAYSKRVKGF 466
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
121-502 2.08e-102

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: 425718  Cd Length: 368  Bit Score: 313.96  E-value: 2.08e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 121 PSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYghianiddiiagkkPATDL 199
Cdd:pfam00496   2 VVPALAESWEvSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYASLLAY--------------DADIV 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 200 GVKALDDHTFEVTLSEPVPYFYKLLvhPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNa 279
Cdd:pfam00496  68 GVEAVDDYTVRFTLKKPDPLFLPLL--AALAAAPVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYWGG- 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 280 KTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALK 359
Cdd:pfam00496 145 KPKLDRIVFKVIPDSTARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSGPGGGTYYLAFNTKKPPFDDVRVRQALS 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 360 LALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEwfkwsQQKRNEEAKKLLAEAGFTA------DKPLTFDLLYNTS 433
Cdd:pfam00496 225 YAIDREAIVKAVLGGYATPANSLVPPGFPGYDDDPKP-----EYYDPEKAKALLAEAGYKDgdgggrRKLKLTLLVYSGN 299
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109557646 434 DLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNN 502
Cdd:pfam00496 300 PAAKAIAELIQQQLKK-IGIKVEIKTVDWATYLERVKDGDFDMALSGWGADYPDPDNFLYPFLSSTGGG 367
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
38-581 3.42e-91

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


Pssm-ID: 223818 [Multi-domain]  Cd Length: 556  Bit Score: 291.46  E-value: 3.42e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  38 NTMSNITKKSLIAAGILTALIAASAATAADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESN--VSRDLFEGLLIS 115
Cdd:COG0747     1 MLMMKLLLRALLALALLLSALLAAGALLAPATAAAAQLPTGTLTIALGGSPTTLDPATAFDGGTGGdvLGNLVYEGLVEY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 116 DVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTasPYASYLQYGHIANiddiiagkk 194
Cdd:COG0747    81 DENGELVPALAESWEvSEDGKTYTFKLRKGVKFHDGTPFTADDVKFSFERALDPDG--PLLGALGLGVIAS--------- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 195 patdlgVKALDDHTFEVTLSEPVPYFYKLL--VHPSVSPVPKSAVEKFGDKWTQPA---NIVTNGAYKLKNWVVNERIVL 269
Cdd:COG0747   150 ------VEAVDDYTVRFTLKEPNAPFLLLLllAGGGASIVPKHAIEDKEADEGVPAalkNPVGTGPYKLVEWDPGQQIVL 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 270 ERNPQYW--DNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIEL-----FQKLKKEIPNEVRVDPYLCTYYYEI 342
Cdd:COG0747   224 ERNPDYWggDKPGPYLDRVTFRVVPDANARLAALESGEIDLAYGGVPPSAedlkrLKADPGYVVLPVVSAPGLNTGYLSF 303
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 343 NNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDLPAYSYTPPYTDGA--KLVEPEWFKWSQqkrnEEAKKLLAEAGFT 419
Cdd:COG0747   304 NPKKAPLDDVRVRQALAYAIDRDAIVDTVlKGLGAVPADGPVPPLVPGYnpDIEKYAADAYDP----EKAKALLDEAGYK 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 420 A-----DKPLTFDLLYNTS-DLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQ-GTFDVARA----GWCADYN-E 487
Cdd:COG0747   380 DndgfgGGPLTLTLESAGYnPGARAIAELIQAQLAK-IGIKVELQTLDWATYLDRALTnGDFDDAFGlflgGGAGGYGgD 458
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 488 PTSFLNTMLSDS--SNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLV-KPWVGGYT 564
Cdd:COG0747   459 PDNFLSPLYGSSngPAGYSGYSNPEVDKLIDKARATTDPAKRKALYKEAQKILLEEAPYIPLYQSTVVIVVvSKRVKGFP 538
                         570
                  ....*....|....*..
gi 1109557646 565 GKDPLDNIYVKNLYIIK 581
Cdd:COG0747   539 LSPTGLFSFLNVITGEV 555
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
76-563 2.03e-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: 281.41  E-value: 2.03e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  76 DKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPS--PGVAEKWE-NKDFKVWTFHLRENAKWSDGTP 152
Cdd:cd08512     1 PKDTLVVATSADINTLDPAVAYEVASGEVVQNVYDRLVTYDGEDTGKlvPELAESWEvSDDGKTYTFHLRDGVKFHDGNP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 153 VTAHDFVYSWQRLADPNTAspyASYLQYGHIANIDDIIagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPV 232
Cdd:cd08512    81 VTAEDVKYSFERALKLNKG---PAFILTQTSLNVPETI-----------KAVDDYTVVFKLDKPPALFLSTLAAPVASIV 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 233 PKSAVEK------FGDKWTQpANIVTNGAYKLKNWVVNERIVLERNPQYWDNA---KTVINQVtylpISSEVTDVNRYRS 303
Cdd:cd08512   147 DKKLVKEhgkdgdWGNAWLS-TNSAGSGPYKLKSWDPGEEVVLERNDDYWGGApklKRVIIRH----VPEAATRRLLLER 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 304 GEIDMTYnNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGdLPAYSY 382
Cdd:cd08512   222 GDADIAR-NLPPDDVAALEGNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVlKGQG-KPHPGP 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 383 TPPYTDGAKLVEPEWfkwsqqKRN-EEAKKLLAEAGFtaDKPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQ 460
Cdd:cd08512   300 LPDGLPGGAPDLPPY------KYDlEKAKELLAEAGY--PNGFKLTLSYNSGNePREDIAQLLQASLAQ-IGIKVEIEPV 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 461 EWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSN---NTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQ 537
Cdd:cd08512   371 PWAQLLEAARSREFDIFIGGWGPDYPDPDYFAATYNSDNGDnaaNRAWYDNPELDALIDEARAETDPAKRAALYKELQKI 450
                         490       500
                  ....*....|....*....|....*.
gi 1109557646 538 LDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08512   451 VYDDAPYIPLYQPVEVVAVRKNVKGY 476
PBP2_NikA_DppA_OppA_like_11 cd08516
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
86-563 2.59e-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 [Multi-domain]  Cd Length: 457  Bit Score: 277.98  E-value: 2.59e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  86 SEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWEN-KDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 164
Cdd:cd08516     8 TDPDSLDPHKATAAASEEVLENIYEGLLGPDENGKLVPALAESWEVsDDGLTYTFKLRDGVKFHNGDPVTAADVKYSFNR 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 165 LADPNTASPYASylQYGHIANIDdiiagkkpatdlgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKsavEKFGDKW 244
Cdd:cd08516    88 IADPDSGAPLRA--LFQEIESVE---------------APDDATVVIKLKQPDAPLLSLLASVNSPIIPA---ASGGDLA 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 245 TQPaniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELFQKLKKE 324
Cdd:cd08516   148 TNP---IGTGPFKFASYEPGVSIVLEKNPDYWGKGLPKLDGITFKIYPDENTRLAALQSGDVDIIEYV-PPQQAAQLEED 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 325 IPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEwfkwSQQK 404
Cdd:cd08516   224 DGLKLASSPGNSYMYLALNNTREPFDDPKVRQAIAYAIDRDAIVDAAFFGRGTPLGGLPSPAGSPAYDPDDA----PCYK 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 405 RN-EEAKKLLAEAGFtaDKPLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFDVARAGWC 482
Cdd:cd08516   300 YDpEKAKALLAEAGY--PNGFDFTILVtSQYGMHVDTAQVIQAQLAA-IGINVEIELVEWATWLDDVNKGDYDATIAGTS 376
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 483 AdYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVG 561
Cdd:cd08516   377 G-NADPDGLYNRYFtSGGKLNFFNYSNPEVDELLAQGRAETDEAKRKEIYKELQQILAEDVPWVFLYWRSQYYAMNKNVQ 455

                  ..
gi 1109557646 562 GY 563
Cdd:cd08516   456 GF 457
PBP2_thermophilic_Hb8_like cd08513
The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like ...
87-563 2.31e-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: 268.38  E-value: 2.31e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  87 EVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRL 165
Cdd:cd08513     9 EPTTLNPLLASGATDAEAAQLLFEPLARIDPDGSLVPVLAEEIPtSENGLSVTFTLRPGVKWSDGTPVTADDVVFTWELI 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 166 ADPNTASPYASYLQyghiaNIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYklLVHPSVSPVPKSAVEK-FGDKW 244
Cdd:cd08513    89 KAPGVSAAYAAGYD-----NIAS------------VEAVDDYTVTVTLKKPTPYAP--FLFLTFPILPAHLLEGySGAAA 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 245 TQPAN---IVTNGAYKLKNWVVNERIVLERNPQYWDNAKTvINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKl 321
Cdd:cd08513   150 RQANFnlaPVGTGPYKLEEFVPGDSIELVRNPNYWGGKPY-IDRVVLKGVPDTDAARAALRSGEIDLAWLPGAKDLQQE- 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 322 KKEIPNEVRVDPYLCTYYY-EINNQKAP-FNDVRVRTALKLALDRDIIVNKV-KNQGdLPAYSYTPPYTDGAKLVEPEWf 398
Cdd:cd08513   228 ALLSPGYNVVVAPGSGYEYlAFNLTNHPiLADVRVRQALAYAIDRDAIVKTLyGGKA-TPAPTPVPPGSWADDPLVPAY- 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 399 kwsqqKRN-EEAKKLLAEAGFT----------ADKPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQEWKTFL 466
Cdd:cd08513   306 -----EYDpEKAKQLLDEAGWKlgpdggirekDGTPLSFTLLTTSGNaVRERVAELIQQQLAK-IGIDVEIENVPASVFF 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 467 DTRH-QGTFDVARAGWCADYN-EPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDK 540
Cdd:cd08513   380 SDDPgNRKFDLALFGWGLGSDpDLSPLFHSCASpangWGGQNFGGYSNPEADELLDAARTELDPEERKALYIRYQDLLAE 459
                         490       500
                  ....*....|....*....|...
gi 1109557646 541 DSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08513   460 DLPVIPLYFRNQVSAYKKNLKGV 482
PBP2_NikA_DppA_OppA_like_3 cd08490
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
78-570 1.04e-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 [Multi-domain]  Cd Length: 470  Bit Score: 266.39  E-value: 1.04e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  78 QTLVRNNGSEVQSLDPHKIEGVpesNVSR-DLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08490     1 KTLTVGLPFESTSLDPASDDGW---LLSRyGVAETLVKLDDDGKLEPWLAESWEQVDDTTWEFTLRDGVKFHDGTPLTAE 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRLADPNTaspyasylqyghianiddiiAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSA 236
Cdd:cd08490    78 AVKASLERALAKSP--------------------RAKGGALIISVIAVDDYTVTITTKEPYPALPARLADPNTAILDPAA 137
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 237 VEKFGDkwtqPANIVTnGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIE 316
Cdd:cd08490   138 YDDGVD----PAPIGT-GPYKVESFEPDQSLTLERNDDYW-GGKPKLDKVTVKFIPDANTRALALQSGEVDIAY-GLPPS 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 317 LFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDGAKLVEP 395
Cdd:cd08490   211 SVERLEKDDGYKVSSVPTPRTYFLYLNTEKGPLADVRVRQALSLAIDREGIADSVlEGSAA-PAKGPFPPSLPANPKLEP 289
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 396 ewfkwsqQKRN-EEAKKLLAEAGFTAD---------KPLTFDLL-YNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKT 464
Cdd:cd08490   290 -------YEYDpEKAKELLAEAGWTDGdgdgiekdgEPLELTLLtYTSRPELPPIAEAIQAQLKK-IGIDVEIRVVEYDA 361
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 465 FLDTRHQGTFDVARAGW-CADYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 542
Cdd:cd08490   362 IEEDLLDGDFDLALYSRnTAPTGDPDYFLNSDYkSDGSYNYGGYSNPEVDALIEELRTEFDPEERAELAAEIQQIIQDDA 441
                         490       500
                  ....*....|....*....|....*...
gi 1109557646 543 AIVPVYYYVNARLVKPWVGGYTgKDPLD 570
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 ...
79-563 4.17e-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 [Multi-domain]  Cd Length: 482  Bit Score: 265.20  E-value: 4.17e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLL-ISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08493     1 TLVYCSEGSPESLDPQLATDGESDAVTRQIYEGLVeFKPGTTELEPGLAESWEvSDDGLTYTFHLRKGVKFHDGRPFNAD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRLADPNTA--SPYASYLQYGHIANIDDIIAgkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPK 234
Cdd:cd08493    81 DVVFSFNRWLDPNHPyhKVGGGGYPYFYSMGLGSLIK--------SVEAVDDYTVKFTLTRPDAPFLANLAMPFASILSP 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 235 SAVEKFGDKwTQPANIVTN----GAYKLKNWVVNERIVLERNPQYW-DNAKtvINQVTYLPISSEVTDVNRYRSGEIDMT 309
Cdd:cd08493   153 EYADQLLAA-GKPEQLDLLpvgtGPFKFVSWQKDDRIRLEANPDYWgGKAK--IDTLVFRIIPDNSVRLAKLLAGECDIV 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 310 YNNMPIELFQKLKKEIpnEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP---- 385
Cdd:cd08493   230 AYPNPSDLAILADAGL--QLLERPGLNVGYLAFNTQKPPFDDPKVRQAIAHAINKEAIVDAVYQGTATVAKNPLPPtswg 307
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 386 YTDGAKLVE--PewfkwsqqkrnEEAKKLLAEAGFTADKPLTF-----DLLYNTSDlhKKLAIAVASIWKKnLGVNVNLE 458
Cdd:cd08493   308 YNDDVPDYEydP-----------EKAKALLAEAGYPDGFELTLwyppvSRPYNPNP--KKMAELIQADLAK-VGIKVEIV 373
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 459 NQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKA 534
Cdd:cd08493   374 TYEWGEYLERTKAGEHDLYLLGWTGDNGDPDNFLRPLLScdaaPSGTNRARWCNPEFDELLEKARRTTDQAERAKLYKQA 453
                         490       500
                  ....*....|....*....|....*....
gi 1109557646 535 EQQLDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08493   454 QEIIHEDAPWVPIAHSKRLLAVRKNVKGF 482
PBP2_NikA_DppA_OppA_like_17 cd08503
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
84-563 6.62e-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: 173868 [Multi-domain]  Cd Length: 460  Bit Score: 264.05  E-value: 6.62e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  84 NGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSW 162
Cdd:cd08503    13 GGSTADTLDPHTADSSADYVRGFALYEYLVEIDPDGTLVPDLAESWEpNDDATTWTFKLRKGVTFHDGKPLTADDVVASL 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 163 QRLADPNTASPYASYLqyghiANIDDIiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKsavekfGD 242
Cdd:cd08503    93 NRHRDPASGSPAKTGL-----LDVGAI------------EAVDDHTVRFTLKRPNADFPYLLSDYHFPIVPA------GD 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 243 KWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIELFQKLK 322
Cdd:cd08503   150 GGDDFKNPIGTGPFKLESFEPGVRAVLERNPDYWKPGRPYLDRIEFIDIPDPAARVNALLSGQVDVIN-QVDPKTADLLK 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 323 KeiPNEVRVD--PYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQG----DLPAYSyTPPYTDGaklvep 395
Cdd:cd08503   229 R--NPGVRVLrsPTGTHYTFVMRTDTAPFDDPRVRRALKLAVDREALVETVlLGYGtvgnDHPVAP-IPPYYAD------ 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 396 ewfkWSQQKRN-EEAKKLLAEAGFtadKPLTFDLlyNTSDL---HKKLAIAVASIWKKnLGVNVNLENQEWKTFLDtrhq 471
Cdd:cd08503   300 ----LPQREYDpDKAKALLAEAGL---PDLEVEL--VTSDAapgAVDAAVLFAEQAAQ-AGININVKRVPADGYWS---- 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 472 gtfDVAR-AGWCADYN----EPTSFLNT-MLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQL-DKDSAI 544
Cdd:cd08503   366 ---DVWMkKPFSATYWggrpTGDQMLSLaYRSGAPWNETHWANPEFDALLDAARAELDEAKRKELYAEMQQILhDEGGII 442
                         490       500
                  ....*....|....*....|
gi 1109557646 545 VPVYY-YVNArlVKPWVGGY 563
Cdd:cd08503   443 IPYFRsYLDA--HSDKVKGY 460
PBP2_NikA_DppA_OppA_like_2 cd08498
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
79-553 1.11e-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 [Multi-domain]  Cd Length: 481  Bit Score: 261.34  E-value: 1.11e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDF 158
Cdd:cd08498     1 TLRIALAADPTSLDPHFHNEGPTLAVLHNIYDTLVRRDADLKLEPGLATSWEAVDDTTWRFKLREGVKFHDGSPFTAEDV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 159 VYSWQRLADPntASPYASYLqyghIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPyfykLLVH-----PSVSPVP 233
Cdd:cd08498    81 VFSLERARDP--PSSPASFY----LRTIKE------------VEVVDDYTVDIKTKGPNP----LLPNdltniFIMSKPW 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 234 KSAVEKFGDKWTQPANIVTnGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTyNNM 313
Cdd:cd08498   139 AEAIAKTGDFNAGRNPNGT-GPYKFVSWEPGDRTVLERNDDYWG-GKPNWDEVVFRPIPNDATRVAALLSGEVDVI-EDV 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 314 PIELFQKLKK-------EIPnEVRV-----DPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGdLPAY 380
Cdd:cd08498   216 PPQDIARLKAnpgvkvvTGP-SLRViflglDQRRDELPAGSPLGKNPLKDPRVRQALSLAIDREAIVDRVmRGLA-TPAG 293
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 381 SYTPP-YTDGAKLVEPEwfkwsqqKRN-EEAKKLLAEAGFTADKPLTFDllyNTSDLH---KKLAIAVASIWKKnLGVNV 455
Cdd:cd08498   294 QLVPPgVFGGEPLDKPP-------PYDpEKAKKLLAEAGYPDGFELTLH---CPNDRYvndEAIAQAVAGMLAR-IGIKV 362
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 456 NLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDS-------SNNTAHYKSPAFDKLIADTLKVADDTQRS 528
Cdd:cd08498   363 NLETMPKSVYFPRATKGEADFYLLGWGVPTGDASSALDALLHTPdpekglgAYNRGGYSNPEVDALIEAAASEMDPAKRA 442
                         490       500
                  ....*....|....*....|....*
gi 1109557646 529 ELYAKAEQQLDKDSAIVPVYYYVNA 553
Cdd:cd08498   443 ALLQEAQEIVADDAAYIPLHQQVLI 467
PBP2_AppA_like cd08514
The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus ...
79-555 9.31e-78

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 [Multi-domain]  Cd Length: 483  Bit Score: 254.08  E-value: 9.31e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 157
Cdd:cd08514     1 TLVLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDKDLNFEPDLAESWEvSDDGKTYTFKLRKDVKWHDGEPLTADD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 158 FVYSWQRLADPNTASPYASYlQYGHIAniddiiagkkpatdlGVKALDDHTFEVTLSEP-VPYFYKLLVHPsvsPVPKSA 236
Cdd:cd08514    81 VKFTYKAIADPKYAGPRASG-DYDEIK---------------GVEVPDDYTVVFHYKEPyAPALESWALNG---ILPKHL 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 237 VE--KFGDKWTQPAN--IVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN 312
Cdd:cd08514   142 LEdvPIADFRHSPFNrnPVGTGPYKLKEWKRGQYIVLEANPDYFL-GRPYIDKIVFRIIPDPTTALLELKAGELDIVELP 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 313 MPIELFQKLKKEIPNEVRVDPYLCTYYYEI--NNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPP---- 385
Cdd:cd08514   221 PPQYDRQTEDKAFDKKINIYEYPSFSYTYLgwNLKRPLFQDKRVRQAITYAIDREEIIDGLlLGLGE-VANGPFSPgtwa 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 386 YTDGaklVEPewFKWSQQKrneeAKKLLAEAGFTAD----------KPLTFDLLYNTSDlhkKLAIAVASIWKKNL---G 452
Cdd:cd08514   300 YNPD---LKP--YPYDPDK----AKELLAEAGWVDGdddgildkdgKPFSFTLLTNQGN---PVREQAATIIQQQLkeiG 367
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 453 VNVNLENQEWKTFLDTRHQGTFDVARAGWCADyNEPTSFlntMLSDSS------NNTAHYKSPAFDKLIADTLKVADDTQ 526
Cdd:cd08514   368 IDVKIRVLEWAAFLEKVDDKDFDAVLLGWSLG-PDPDPY---DIWHSSgakpggFNFVGYKNPEVDKLIEKARSTLDREK 443
                         490       500       510
                  ....*....|....*....|....*....|....
gi 1109557646 527 RSELYAKAEQQLDKDSAIVPVYYY-----VNARL 555
Cdd:cd08514   444 RAEIYHEWQEILAEDQPYTFLYAPnslyaVNKRL 477
PBP2_Ylib_like cd08499
The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib ...
85-552 1.95e-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 [Multi-domain]  Cd Length: 474  Bit Score: 247.52  E-value: 1.95e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  85 GSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQ 163
Cdd:cd08499     7 LSDATSLDPHDTNDTPSASVQSNIYEGLVGFDKDMKIVPVLAESWEqSDDGTTWTFKLREGVKFHDGTPFNAEAVKANLD 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 164 RLADPNTASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDk 243
Cdd:cd08499    87 RVLDPETASPRASLF-----SMIEE------------VEVVDDYTVKITLKEPFAPLLAHLAHPGGSIISPKAIEEYGK- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 244 wTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTViNQVTYLPISSEVTDVNRYRSGEIDMTYNnMPIELFQKLKK 323
Cdd:cd08499   149 -EISKHPVGTGPFKFESWTPGDEVTLVKNDDYWGGLPKV-DTVTFKVVPEDGTRVAMLETGEADIAYP-VPPEDVDRLEN 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 324 EIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP----YTDGAKLVE--Pew 397
Cdd:cd08499   226 SPGLNVYRSPSISVVYIGFNTQKEPFDDVRVRQAINYAIDKEAIIKGILNGYGTPADSPIAPgvfgYSEQVGPYEydP-- 303
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 398 fkwsqqkrnEEAKKLLAEAGFTadKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD-TRHQGTFDV 476
Cdd:cd08499   304 ---------EKAKELLAEAGYP--DGFETTLWTNDNRERIKIAEFIQQQLAQ-IGIDVEIEVMEWGAYLEeTGNGEEHQM 371
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 477 ARAGWC-----ADYNeptsfLNTMLSDSS----NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 547
Cdd:cd08499   372 FLLGWStstgdADYG-----LRPLFHSSNwgapGNRAFYSNPEVDALLDEARREADEEERLELYAKAQEIIWEDAPWVFL 446

                  ....*
gi 1109557646 548 YYYVN 552
Cdd:cd08499   447 YHPET 451
PBP2_clavulanate_OppA2 cd08506
The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis ...
79-563 7.16e-75

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 [Multi-domain]  Cd Length: 466  Bit Score: 245.63  E-value: 7.16e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGH-----PSPGVAEKW--ENKDFKVWTFHLRENAKWSDGT 151
Cdd:cd08506     1 TLRLLSSADFDHLDPARTYYADGWQVLRLIYRQLTTYKPAPGaegteVVPDLATDTgtVSDDGKTWTYTLRDGLKFEDGT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 152 PVTAHDFVYSWQRLADpntaspyasylqyghianiddiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSP 231
Cdd:cd08506    81 PITAKDVKYGIERSFA---------------------------------IETPDDKTIVFHLNRPDSDFPYLLALPAAAP 127
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 232 VPKSAVEKfgDKWTQpaNIVTNGAYKLKNWVVNERIVLERNPqYWDNAKTVIN-----QVTY-LPISSEvTDVNRYRSGE 305
Cdd:cd08506   128 VPAEKDTK--ADYGR--APVSSGPYKIESYDPGKGLVLVRNP-HWDAETDPIRdaypdKIVVtFGLDPE-TIDQRLQAGD 201
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 306 IDM--TYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV--KNQGDlPAYS 381
Cdd:cd08506   202 ADLalDGDGVPRAPAAELVEELKARLHNVPGGGVYYLAINTNVPPFDDVKVRQAVAYAVDRAALVRAFggPAGGE-PATT 280
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 382 YTPPYTDGAKLVEPEWFKWSQQKRnEEAKKLLAEAGFtadKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQE 461
Cdd:cd08506   281 ILPPGIPGYEDYDPYPTKGPKGDP-DKAKELLAEAGV---PGLKLTLAYRDTAVDKKIAEALQASLAR-AGIDVTLKPID 355
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 462 WKTFLDTRHQGT---FDVARAGWCADYNEPTSFLNTMLS------DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYA 532
Cdd:cd08506   356 SATYYDTIANPDgaaYDLFITGWGPDWPSASTFLPPLFDgdaigpGGNSNYSGYDDPEVNALIDEALATTDPAEAAALWA 435
                         490       500       510
                  ....*....|....*....|....*....|.
gi 1109557646 533 KAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08506   436 ELDRQIMEDAPIVPLVYPKALDLRSSRVTNY 466
PBP2_NikA_DppA_OppA_like_15 cd08492
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
79-562 3.15e-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: 244.83  E-value: 3.15e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 157
Cdd:cd08492     3 TLTYALGQDPTCLDPHTLDFYPNGSVLRQVVDSLVYQDPTGEIVPWLAESWEvSDDGTTYTFHLRDGVTFSDGTPLDAEA 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 158 FVYSWQRLADPNTASPYASYLqyghIANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAV 237
Cdd:cd08492    83 VKANFDRILDGSTKSGLAASY----LGPYK------------STEVVDPYTVKVHFSEPYAPFLQALSTPGLGILSPATL 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 238 EKFGDKWTQPaNIVTNGAYKLKNWVVNERIVLERNPQY-W--DNAK----TVINQVTYLPISSEVTDVNRYRSGEIDMTY 310
Cdd:cd08492   147 ARPGEDGGGE-NPVGSGPFVVESWVRGQSIVLVRNPDYnWapALAKhqgpAYLDKIVFRFIPEASVRVGALQSGQVDVIT 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 311 NNMPIELFQKLKKEIPN-EVRVDPYLcTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVkNQGDLPAYSY-TPPYTD 388
Cdd:cd08492   226 DIPPQDEKQLAADGGPViETRPTPGV-PYSLYLNTTRPPFDDVRVRQALQLAIDREAIVETV-FFGSYPAASSlLSSTTP 303
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 389 GAKLVEPEWfkwsqqKRN-EEAKKLLAEAGFTAD----------KPLTFDLLYNT-SDLHKKLAIAVASIWKKnLGVNVN 456
Cdd:cd08492   304 YYKDLSDAY------AYDpEKAKKLLDEAGWTARgadgirtkdgKRLTLTFLYSTgQPQSQSVLQLIQAQLKE-VGIDLQ 376
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 457 LENQEWKTFLDTRHQGTFDVARAGWCADYNEPtsfLNTMLSDSSNNT----AHYKSPAFDKLIADTLKVADDTQRSELYA 532
Cdd:cd08492   377 LKVLDAGTLTARRASGDYDLALSYYGRADPDI---LRTLFHSANRNPpggySRFADPELDDLLEKAAATTDPAERAALYA 453
                         490       500       510
                  ....*....|....*....|....*....|
gi 1109557646 533 KAEQQLDKDSAIVPVYYYVNARLVKPWVGG 562
Cdd:cd08492   454 DAQKYLIEQAYVVPLYEEPQVVAAAPNVKG 483
PBP2_NikA_DppA_OppA_like_20 cd08519
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
88-547 2.43e-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 [Multi-domain]  Cd Length: 469  Bit Score: 228.66  E-value: 2.43e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  88 VQSLDPHKIEGVPESNVSRDLFEGLLISDVE-GHPSPGVAEKWE--NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 164
Cdd:cd08519    10 VRTLDPAGAYDLGSWQLLSNLGDTLYTYEPGtTELVPDLATSLPfvSDDGLTYTIPLRQGVKFHDGTPFTAKAVKFSLDR 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 165 L----ADPntaspyaSYLqyghianIDDIIAgkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKF 240
Cdd:cd08519    90 FikigGGP-------ASL-------LADRVE--------SVEAPDDYTVTFRLKKPFATFPALLATPALTPVSPKAYPAD 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 241 GDKwTQPANIVTNGAYKLKNWvVNERIVLERNPQYW-DNAKTVINQVTYLpiSSEVTDVNRYRSGEIDMTYNNMPIELFQ 319
Cdd:cd08519   148 ADL-FLPNTFVGTGPYKLKSF-RSESIRLEPNPDYWgEKPKNDGVDIRFY--SDSSNLFLALQTGEIDVAYRSLSPEDIA 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 320 KLKKEIPNEVRV--DPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDGAKlvepE 396
Cdd:cd08519   224 DLLLAKDGDLQVveGPGGEIRYIVFNVNQPPLDNLAVRQALAYLIDRDLIVNRVyYGTAE-PLYSLVPTGFWGHK----P 298
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 397 WFKWSQQKRN-EEAKKLLAEAGFTADKPLTFDLLYNTS-DLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTF 474
Cdd:cd08519   299 VFKEKYGDPNvEKARQLLQQAGYSAENPLKLELWYRSNhPADKLEAATLKAQLEADGLFKVNLKSVEWTTYYKQLSKGAY 378
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1109557646 475 DVARAGWCADYNEPTSFLNTMLSDSSN--NTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 547
Cdd:cd08519   379 PVYLLGWYPDYPDPDNYLTPFLSCGNGvfLGSFYSNPKVNQLIDKSRTELDPAARLKILAEIQDILAEDVPYIPL 453
PBP2_NikA_DppA_OppA_like_13 cd08517
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
104-547 6.74e-65

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: 219.73  E-value: 6.74e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 104 VSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASpyasylqYGH 182
Cdd:cd08517    28 ISGKIFEGLLRYDFDLNPQPDLATSWEvSEDGLTYTFKLRPGVKWHDGKPFTSADVKFSIDTLKEEHPRR-------RRT 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 183 IANIDDIiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVhPSVSP-VPKSAVEKfGDKWTQPAN--IVTNGAYKLK 259
Cdd:cd08517   101 FANVESI------------ETPDDLTVVFKLKKPAPALLSALS-WGESPiVPKHIYEG-TDILTNPANnaPIGTGPFKFV 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 260 NWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELF--QKLKKeIPN-EVRVDPYLC 336
Cdd:cd08517   167 EWVRGSHIILERNPDYWDKGKPYLDRIVFRIIPDAAARAAAFETGEVDVLPFG-PVPLSdiPRLKA-LPNlVVTTKGYEY 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 337 ---TYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDL---PAYSYTPPYTDgAKLVEPEwFKWsqqkrnEEA 409
Cdd:cd08517   245 fspRSYLEFNLRNPPLKDVRVRQAIAHAIDRQFIVDTVfFGYGKPatgPISPSLPFFYD-DDVPTYP-FDV------AKA 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 410 KKLLAEAGFTAD---KPLTFDLLYNTS-DLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD------------TRHQGT 473
Cdd:cd08517   317 EALLDEAGYPRGadgIRFKLRLDPLPYgEFWKRTAEYVKQALKE-VGIDVELRSQDFATWLKrvytdrdfdlamNGGYQG 395
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1109557646 474 FD----VARAGWCADYNEPTSFlntmlsdssNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 547
Cdd:cd08517   396 GDpavgVQRLYWSGNIKKGVPF---------SNASGYSNPEVDALLEKAAVETDPAKRKALYKEFQKILAEDLPIIPL 464
PBP2_NikA_DppA_OppA_like_5 cd08511
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
78-563 4.46e-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 [Multi-domain]  Cd Length: 467  Bit Score: 214.84  E-value: 4.46e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  78 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08511     1 GTLRIGLEADPDRLDPALSRTFVGRQVFAALCDKLVDIDADLKIVPQLATSWEiSPDGKTLTLKLRKGVKFHDGTPFDAA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRLADPNTASpyasylQYGHIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPS---VSP-V 232
Cdd:cd08511    81 AVKANLERLLTLPGSN------RKSELASVES------------VEVVDPATVRFRLKQPFAPLLAVLSDRAgmmVSPkA 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 233 PKSAVEKFGDKwtqPaniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN 312
Cdd:cd08511   143 AKAAGADFGSA---P---VGTGPFKFVERVQQDRIVLERNPHYWNAGKPHLDRLVYRPIPDATVRLANLRSGDLDIIERL 216
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 313 MPIELfQKLKKEipNEVRVDPYLCTYYYEI--NNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYT--D 388
Cdd:cd08511   217 SPSDV-AAVKKD--PKLKVLPVPGLGYQGItfNIGNGPFNDPRVRQALALAIDREAINQVVFNGTFKPANQPFPPGSpyY 293
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 389 GAKLVEPewfkwsqqKRN-EEAKKLLAEAGFTAdkpLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLD 467
Cdd:cd08511   294 GKSLPVP--------GRDpAKAKALLAEAGVPT---VTFELTTANTPTGRQLAQVIQAMAAE-AGFTVKLRPTEFATLLD 361
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 468 TRHQGTFDVARAGWcADYNEPTSFLNTML-SDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVP 546
Cdd:cd08511   362 RALAGDFQATLWGW-SGRPDPDGNIYQFFtSKGGQNYSRYSNPEVDALLEKARASADPAERKALYNQAAKILADDLPYIY 440
                         490
                  ....*....|....*..
gi 1109557646 547 VYYYVNARLVKPWVGGY 563
Cdd:cd08511   441 LYHQPYYIAASKKVRGL 457
PBP2_NikA_DppA_OppA_like_8 cd08495
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
87-562 3.96e-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 [Multi-domain]  Cd Length: 482  Bit Score: 212.58  E-value: 3.96e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  87 EVQSLDPHK------IEGVP--ESNVSRDLFEGLLISDVEghpsPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHD 157
Cdd:cd08495     9 PLTTLDPDQgaeglrFLGLPvyDPLVRWDLSTADRPGEIV----PGLAESWEvSPDGRRWTFTLRPGVKFHDGTPFDADA 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 158 FVYSWQRLADPNTA--SPYASYLQYGHIANIDdiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHP-SVSPVPK 234
Cdd:cd08495    85 VVWNLDRMLDPDSPqyDPAQAGQVRSRIPSVT------------SVEAIDDNTVRITTSEPFADLPYVLTTGlASSPSPK 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 235 SAVEKFGDKWTQPAniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMP 314
Cdd:cd08495   153 EKAGDAWDDFAAHP--AGTGPFRITRFVPRERIELVRNDGYWDKRPPKNDKLVLIPMPDANARLAALLSGQVDAIEAPAP 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 315 IELFQklKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPytdgaklvE 394
Cdd:cd08495   231 DAIAQ--LKSAGFQLVTNPSPHVWIYQLNMAEGPLSDPRVRQALNLAIDREGLVDLLLGGLAAPATGPVPP--------G 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 395 PEWFKWSQQ--KRN-EEAKKLLAEAGFTADKPLTFDLLYNTSdlHKKLAIAVASIWKKNL---GVNVNLENQEWKTFLDT 468
Cdd:cd08495   301 HPGFGKPTFpyKYDpDKARALLKEAGYGPGLTLKLRVSASGS--GQMQPLPMNEFIQQNLaeiGIDLDIEVVEWADLYNA 378
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 469 RHQGTFDVARAG---------WCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLD 539
Cdd:cd08495   379 WRAGAKDGSRDGanainmssaMDPFLALVRFLSSKIDPPVGSNWGGYHNPEFDALIDQARVTFDPAERAALYREAHAIVV 458
                         490       500
                  ....*....|....*....|...
gi 1109557646 540 KDSAIVPVYYYVNARLVKPWVGG 562
Cdd:cd08495   459 DDAPWLFVVHDRNPRALSPKVKG 481
PBP2_NikA cd08489
The substrate-binding component of an ABC-type nickel import system contains the type 2 ...
79-564 2.46e-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 [Multi-domain]  Cd Length: 488  Bit Score: 202.46  E-value: 2.46e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGvpeSNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAH 156
Cdd:cd08489     1 TLTYAWPKDIGDLNPHLYSN---QMFAQNMvYEPLVKYGEDGKIEPWLAESWEiSEDGKTYTFHLRKGVKFSDGTPFNAE 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 157 DFVYSWQRlADPNTASPYASYLqyghIANIDDiiagkkpatdlgVKALDDHTFEVTLSEPV-PYFYKL-LVHP--SVSPv 232
Cdd:cd08489    78 AVKKNFDA-VLANRDRHSWLEL----VNKIDS------------VEVVDEYTVRLHLKEPYyPTLNELaLVRPfrFLSP- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 233 pkSAVEKFGDKWTQPANIVTnGAYKLKNWVVNERIVLERNPQYWDNaKTVINQVTYLPISSEVTDVNRYRSGEIDMTY-- 310
Cdd:cd08489   140 --KAFPDGGTKGGVKKPIGT-GPWVLAEYKKGEYAVFVRNPNYWGE-KPKIDKITVKVIPDAQTRLLALQSGEIDLIYga 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 311 NNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYT 387
Cdd:cd08489   216 DGISADAFKQLKKDKGYGTAVSEPTSTRFLALNTASEPLSDLKVREAINYAIDKEAISKGILYGLEKPAdtlFAPNVPYA 295
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 388 DgaklVEPEwfKWSQQKrnEEAKKLLAEAGFTAD----------KPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVN 456
Cdd:cd08489   296 D----IDLK--PYSYDP--EKANALLDEAGWTLNegdgirekdgKPLSLELVYQTDNaLQKSIAEYLQSELKK-IGIDLN 366
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 457 LENQEWKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDSSnntAHYKS-------PAFDKLIADTLKVADDTQRS 528
Cdd:cd08489   367 IIGEEEQAYYDRQKDGDFDLIFYrTWGAPY-DPHSFLSSMRVPSH---ADYQAqvglankAELDALINEVLATTDEEKRQ 442
                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 1109557646 529 ELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYT 564
Cdd:cd08489   443 ELYDEILTTLHDQAVYIPLTYPRNKAVYNPKVKGVT 478
PBP2_NikA_DppA_OppA_like_16 cd08502
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
86-563 3.37e-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: 173867 [Multi-domain]  Cd Length: 472  Bit Score: 198.95  E-value: 3.37e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  86 SEVQSLDPHkiegVPESNVSRD----LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVY 160
Cdd:cd08502     8 ADLRTLDPI----VTTAYITRNhgymIYDTLFGMDANGEPQPQMAESWEvSDDGKTYTFTLRDGLKFHDGSPVTAADVVA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 161 SWQRLADPNTAspyasylqyghianiddiiaGKK--PATDLgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPV---PKS 235
Cdd:cd08502    84 SLKRWAKRDAM--------------------GQAlmAAVES-LEAVDDKTVVITLKEPFGLLLDALAKPSSQPAfimPKR 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 236 AVEKFGDK-WTQPaniVTNGAYKLKNWVVNERIVLERNPQY--------W-DNAKTVI-NQVTYLPISSEVTDVNRYRSG 304
Cdd:cd08502   143 IAATPPDKqITEY---IGSGPFKFVEWEPDQYVVYEKFADYvprkeppsGlAGGKVVYvDRVEFIVVPDANTAVAALQSG 219
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 305 EIDMtYNNMPIELFQKLKKEiPNEVrVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVknQGDLPAYSY-- 382
Cdd:cd08502   220 EIDF-AEQPPADLLPTLKAD-PVVV-LKPLGGQGVLRFNHLQPPFDNPKIRRAVLAALDQEDLLAAA--VGDPDFYKVcg 294
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 383 ------TPPYTDGAKlvepEWFKwsqqKRN-EEAKKLLAEAGFtADKPLTfdLLYNTS-DLHKKLAIAVASIWKKnLGVN 454
Cdd:cd08502   295 smfpcgTPWYSEAGK----EGYN----KPDlEKAKKLLKEAGY-DGEPIV--ILTPTDyAYLYNAALVAAQQLKA-AGFN 362
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 455 VNLENQEWKTFLDTRHQ--GTFDVARAGWC-ADYNEPtsFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELY 531
Cdd:cd08502   363 VDLQVMDWATLVQRRAKpdGGWNIFITSWSgLDLLNP--LLNTGLNAGKAWFGWPDDPEIEALRAAFIAATDPAERKALA 440
                         490       500       510
                  ....*....|....*....|....*....|..
gi 1109557646 532 AKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08502   441 AEIQKRAYEDVPYIPLGQFTQPTAYRSKLEGL 472
PBP2_NikA_DppA_OppA_like_1 cd08508
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
79-563 3.96e-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: 198.76  E-value: 3.96e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  79 TLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLlISDVEGHPSPG-----VAEKWENKDFK-VWTFHLRENAKWSDGT- 151
Cdd:cd08508     2 LRIGSAADDIRTLDPHFATGTTDKGVISWVFNGL-VRFPPGSADPYeiepdLAESWESSDDPlTWTFKLRKGVMFHGGYg 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 152 PVTAHDFVYSWQRLADPNTASpYASylqyghianidDIIAGKKpatdlgVKALDDHTFEVTLSEPVPYFYKLLV-HPSVS 230
Cdd:cd08508    81 EVTAEDVVFSLERAADPKRSS-FSA-----------DFAALKE------VEAHDPYTVRITLSRPVPSFLGLVSnYHSGL 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 231 PVPKSAVEKFGDKWTQPAniVTNGAYKLKNWVVNERIVLERNPQYWDNAKTvINQVTYLPISSEVTDVNRYRSGEIDMTY 310
Cdd:cd08508   143 IVSKKAVEKLGEQFGRKP--VGTGPFEVEEHSPQQGVTLVANDGYFRGAPK-LERINYRFIPNDASRELAFESGEIDMTQ 219
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 311 NNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGa 390
Cdd:cd08508   220 GKRDQRWVQRREANDGVVVDVFEPAEFRTLGLNITKPPLDDLKVRQAIAAAVNVDEVVEFVGAGVAQPGNSVIPPGLLG- 298
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 391 klvepEWFKWSQQKRN-EEAKKLLAEAGFTADKPLTFdllyNTSDLHKKLAIA-VASIWKKNLGVNVNLENQEWKTFLDT 468
Cdd:cd08508   299 -----EDADAPVYPYDpAKAKALLAEAGFPNGLTLTF----LVSPAAGQQSIMqVVQAQLAEAGINLEIDVVEHATFHAQ 369
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 469 RHQGTFDVARAGwCADYNEPTSFL------NTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 542
Cdd:cd08508   370 IRKDLSAIVLYG-AARFPIADSYLtefydsASIIGAPTAVTNFSHCPVADKRIEAARVEPDPESRSALWKEAQKKIDEDV 448
                         490       500
                  ....*....|....*....|..
gi 1109557646 543 AIVPVYYYVNARLVKPWVG-GY 563
Cdd:cd08508   449 CAIPLTNLVQAWARKPALDyGY 470
PBP2_TmCBP_oligosaccharides_like cd08509
The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains ...
113-568 4.11e-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 [Multi-domain]  Cd Length: 509  Bit Score: 194.46  E-value: 4.11e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 113 LISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADpnTASPYASYLQYghiaNIDDiia 191
Cdd:cd08509    39 IYNPLTGEFIPWLAESWTwSDDFTTLTVTLRKGVKWSDGEPFTADDVVFTFELLKK--YPALDYSGFWY----YVES--- 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 192 gkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVH--PSVSPVPKSAVEKFGDKWTQPANI--VTNGAYKLKNWvVNERI 267
Cdd:cd08509   110 ---------VEAVDDYTVVFTFKKPSPTEAFYFLYtlGLVPIVPKHVWEKVDDPLITFTNEppVGTGPYTLKSF-SPQWI 179
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 268 VLERNPQYWDNAKTV-INQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQK 346
Cdd:cd08509   180 VLERNPNYWGAFGKPkPDYVVYPAYSSNDQALLALANGEVDWAGLFIPDIQKTVLKDPENNKYWYFPYGGTVGLYFNTKK 259
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 347 APFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPY--TDGAKLVEPEWFKWSQQKRN---EEAKKLLAEAGFTAD 421
Cdd:cd08509   260 YPFNDPEVRKALALAIDRTAIVKIAGYGYATPAPLPGPPYkvPLDPSGIAKYFGSFGLGWYKydpDKAKKLLESAGFKKD 339
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 422 ----------KPLTFDLL--YNTSDlhkklAIAVASIWKKNL---GVNVNLENQEWKTFLDTRHQGTFDVARAG--WCAD 484
Cdd:cd08509   340 kdgkwytpdgTPLKFTIIvpSGWTD-----WMAAAQIIAEQLkefGIDVTVKTPDFGTYWAALTKGDFDTFDAAtpWGGP 414
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 485 YNEPTSFLNTMLS--------DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLV 556
Cdd:cd08509   415 GPTPLGYYNSAFDppnggpggSAAGNFGRWKNPELDELIDELNKTTDEAEQKELGNELQKIFAEEMPVIPLFYNPIWYEY 494
                         490
                  ....*....|....
gi 1109557646 557 --KPWVGGYTGKDP 568
Cdd:cd08509   495 ntKYWTGWPTEENP 508
PBP2_NikA_DppA_OppA_like_4 cd08500
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
102-553 5.84e-55

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: 193.61  E-value: 5.84e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 102 SNVSRDLFEGLLISDVEGH-PSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYAsylq 179
Cdd:cd08500    31 RDIIGLGYAGLVRYDPDTGeLVPNLAESWEvSEDGREFTFKLREGLKWSDGQPFTADDVVFTYEDIYLNPEIPPSA---- 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 180 yghianIDDIIAGKKPATdlgVKALDDHTFEVTLSEPVPYFykllvhpsvspvpksaVEKFGdkwtqPANIVTNGAYKLK 259
Cdd:cd08500   107 ------PDTLLVGGKPPK---VEKVDDYTVRFTLPAPNPLF----------------LAYLA-----PPDIPTLGPWKLE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 260 NWVVNERIVLERNPQYWD-----NAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKeipNE------ 328
Cdd:cd08500   157 SYTPGERVVLERNPYYWKvdtegNQLPYIDRIVYQIVEDAEAQLLKFLAGEIDLQGRHPEDLDYPLLKE---NEekggyt 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 329 -VRVDPYLCTYYYEIN-NQKAP-----FNDVRVRTALKLALDRDIIVNKV-KNQGDLPAYSYTPPYTdgaklvePEWFKW 400
Cdd:cd08500   234 vYNLGPATSTLFINFNlNDKDPvkrklFRDVRFRQALSLAINREEIIETVyFGLGEPQQGPVSPGSP-------YYYPEW 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 401 SQQKRN---EEAKKLLAEAGFT---AD--------KPLTFDLLYNTSD-LHKKLAIAVASIWKKnLGVNVNLENQEWKTF 465
Cdd:cd08500   307 ELKYYEydpDKANKLLDEAGLKkkdADgfrldpdgKPVEFTLITNAGNsIREDIAELIKDDWRK-IGIKVNLQPIDFNLL 385
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 466 LDTRHQG-TFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAF---------------DKLIADTLKVADDTQRSE 529
Cdd:cd08500   386 VTRLSANeDWDAILLGLTGGGPDPALGAPVWRSGGSLHLWNQPYPGGgppggpepppwekkiDDLYDKGAVELDQEKRKA 465
                         490       500
                  ....*....|....*....|....
gi 1109557646 530 LYAKAeQQLDKDSaiVPVYYYVNA 553
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 ...
87-563 7.41e-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 [Multi-domain]  Cd Length: 448  Bit Score: 189.38  E-value: 7.41e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  87 EVQSLDP-----HKIEGVPESNVsrdlFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVY 160
Cdd:cd08494     9 EPTSLDItttagAAIDQVLLGNV----YETLVRRDEDGKVQPGLAESWTiSDDGLTYTFTLRSGVTFHDGTPFDAADVKF 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 161 SWQRLADPNTASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKF 240
Cdd:cd08494    85 SLQRARAPDSTNADKALL-----AAIAS------------VEAPDAHTVVVTLKHPDPSLLFNLGGRAGVVVDPASAADL 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 241 GdkwTQPaniVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIEL--- 317
Cdd:cd08494   148 A---TKP---VGTGPFTVAAWARGSSITLVRNDDYWG-AKPKLDKVTFRYFSDPTALTNALLAGDIDAAPPFDAPELeqf 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 318 -----FQKLKKEIPNEVRVdpylctyyyEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGakl 392
Cdd:cd08494   221 addprFTVLVGTTTGKVLL---------AMNNARAPFDDVRVRQAIRYAIDRKALIDAAWDGYGTPIGGPISPLDPG--- 288
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 393 vepeWFKWSQQKRN--EEAKKLLAEAGFTAdkPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRH 470
Cdd:cd08494   289 ----YVDLTGLYPYdpDKARQLLAEAGAAY--GLTLTLTLPPLPYARRIGEIIASQLAE-VGITVKIEVVEPATWLQRVY 361
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 471 QG-TFDVAragwCADYNEPTSFLNTMLSDSsnnTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYY 549
Cdd:cd08494   362 KGkDYDLT----LIAHVEPDDIGIFADPDY---YFGYDNPEFQELYAQALAATDADERAELLKQAQRTLAEDAAADWLYT 434
                         490
                  ....*....|....
gi 1109557646 550 YVNARLVKPWVGGY 563
Cdd:cd08494   435 RPNIVVARKGVTGY 448
PBP2_NikA_DppA_OppA_like_19 cd08518
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
108-549 2.20e-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: 185.87  E-value: 2.20e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 108 LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASylqyghiaNI 186
Cdd:cd08518    29 IFSGLLKRDENLNLVPDLATSYKvSDDGLTWTFTLRDDVKFSDGEPLTAEDVAFTYNTAKDPGSASDILS--------NL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 187 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVhpSVSPVPKSAVEKFGDKWTQPaniVTNGAYKLKNWVVNER 266
Cdd:cd08518   101 ED------------VEAVDDYTVKFTLKKPDSTFLDKLA--SLGIVPKHAYENTDTYNQNP---IGTGPYKLVQWDKGQQ 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 267 IVLERNPQYWDNaKTVINQVTYLpISSEVTDVNRYRSGEIDMTYnnMPIELfqkLKKEIPNE--VRVD---------PYL 335
Cdd:cd08518   164 VIFEANPDYYGG-KPKFKKLTFL-FLPDDAAAAALKSGEVDLAL--IPPSL---AKQGVDGYklYSIKsadyrgislPFV 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 336 CTYYYEI-NNQKApfnDVRVRTALKLALDRDIIVNKVKN-QGDlPAYSytppYTDGAKLVEPEWFKWSQQKrnEEAKKLL 413
Cdd:cd08518   237 PATGKKIgNNVTS---DPAIRKALNYAIDRQAIVDGVLNgYGT-PAYS----PPDGLPWGNPDAAIYDYDP--EKAKKIL 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 414 AEAGF--TAD-------KPLTFDLLYNTSDLHKK-LAIAVASIWKKnLGVNVNLENQEWKTFLDTRHQGTFdvaRAGWCA 483
Cdd:cd08518   307 EEAGWkdGDDggrekdgQKAEFTLYYPSGDQVRQdLAVAVASQAKK-LGIEVKLEGKSWDEIDPRMHDNAV---LLGWGS 382
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1109557646 484 DYNEPT-SFLNTMLSDS-SNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYY 549
Cdd:cd08518   383 PDDTELySLYHSSLAGGgYNNPGHYSNPEVDAYLDKARTSTDPEERKKYWKKAQWDGAEDPPWLWLVN 450
PBP2_NikA_DppA_OppA_like_18 cd08505
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
90-563 8.37e-49

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 [Multi-domain]  Cd Length: 528  Bit Score: 177.47  E-value: 8.37e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  90 SLDPHKIEGVPESNVSRDLFEGLLISDVEGHP---SPGVAEK-----WENKDFKVWTFHLRENAKWSD--------GTPV 153
Cdd:cd08505    12 GLDPAQSYDSYSAEIIEQIYEPLLQYHYLKRPyelVPNTAAAmpevsYLDVDGSVYTIRIKPGIYFQPdpafpkgkTREL 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 154 TAHDFVYSWQRLADPNTAspyasylqyghianiddiiagkkpatdlGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVP 233
Cdd:cd08505    92 TAEDYVYSIKRLADPPLE----------------------------GVEAVDRYTLRIRLTGPYPQFLYWLAMPFFAPVP 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 234 KSAVEKFGDKWTQPANIVTN------GAYKLKNWVVNERIVLERNPQY------------WDNA-------KTV--INQV 286
Cdd:cd08505   144 WEAVEFYGQPGMAEKNLTLDwhpvgtGPYMLTENNPNSRMVLVRNPNYrgevypfegsadDDQAglladagKRLpfIDRI 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 287 TYLPISSEVTDVNRYRSGEIDM---TYNNMPI----------ELFQKLKKE---IPNEVRVDpylcTYYYEINnqkapFN 350
Cdd:cd08505   224 VFSLEKEAQPRWLKFLQGYYDVsgiSSDAFDQalrvsaggepELTPELAKKgirLSRAVEPS----IFYIGFN-----ML 294
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 351 DVRV----------RTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvEPEWFKWSQQKRNEEAKKLLAEAGFTA 420
Cdd:cd08505   295 DPVVggyskekrklRQAISIAFDWEEYISIFRNGRAVPAQGPIPPGIFGY---RPGEDGKPVRYDLELAKALLAEAGYPD 371
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 421 D------KPLTFDLLYNTSDLHKklaiAVASIWKKN---LGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSF 491
Cdd:cd08505   372 GrdgptgKPLVLNYDTQATPDDK----QRLEWWRKQfakLGIQLNVRATDYNRFQDKLRKGNAQLFSWGWNADYPDPENF 447
                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1109557646 492 LntMLSDSSN------NTAHYKSPAFDKLIaDTLKVADDT-QRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08505   448 L--FLLYGPNaksggeNAANYSNPEFDRLF-EQMKTMPDGpERQALIDQMNRILREDAPWIFGFHPKSNGLAHPWVGNY 523
PBP2_Lpqw cd08501
The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic ...
130-548 2.18e-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 [Multi-domain]  Cd Length: 486  Bit Score: 175.61  E-value: 2.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 130 ENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAD-PNTASPyASYLQYGHIANIddiiagkkPATDlgvkalDDHT 208
Cdd:cd08501    58 TSDDPQTVTYTINPEAQWSDGTPITAADFEYLWKAMSGePGTYDP-ASTDGYDLIESV--------EKGD------GGKT 122
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 209 FEVTLSEPVPYfYKLL---VHPSvSPVPKSAveKFGDKWTQPANIVTNGAYKLKNWVVN-ERIVLERNPQYWDNAKTVIN 284
Cdd:cd08501   123 VVVTFKQPYAD-WRALfsnLLPA-HLVADEA--GFFGTGLDDHPPWSAGPYKVESVDRGrGEVTLVRNDRWWGDKPPKLD 198
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 285 QVTYLPISSEVTDVNRYRSGEIDMTYNNmPIELFQKLKKEIPN-EVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALD 363
Cdd:cd08501   199 KITFRAMEDPDAQINALRNGEIDAADVG-PTEDTLEALGLLPGvEVRTGDGPRYLHLTLNTKSPALADVAVRKAFLKAID 277
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 364 RDIIVNKV--------KNQGDLPAYSYTPPYTDGaklvEPEWFKWSQqkrnEEAKKLLAEAGFTAD--------KPLTFD 427
Cdd:cd08501   278 RDTIARIAfgglppeaEPPGSHLLLPGQAGYEDN----SSAYGKYDP----EAAKKLLDDAGYTLGgdgiekdgKPLTLR 349
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 428 LLYNTSDlhkKLAIAVASIWKKNL---GVNVNLEN---QEW-KTFLDtrhQGTFDVARAGWCADYNEPTSFLNTMLSDSS 500
Cdd:cd08501   350 IAYDGDD---PTAVAAAELIQDMLakaGIKVTVVSvpsNDFsKTLLS---GGDYDAVLFGWQGTPGVANAGQIYGSCSES 423
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 1109557646 501 NNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVY 548
Cdd:cd08501   424 SNFSGFCDPEIDELIAEALTTTDPDEQAELLNEADKLLWEQAYTLPLY 471
PBP2_NikA_DppA_OppA_like_10 cd08515
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
77-552 3.74e-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 [Multi-domain]  Cd Length: 460  Bit Score: 165.85  E-value: 3.74e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  77 KQTLVRNNGSEVQSLDPHKI---EGVPesnVSRDLFEGLLISDVE-GHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTP 152
Cdd:cd08515     1 RDTLVIAVQKEPPTLDPYYNtsrEGVI---ISRNIFDTLIYRDPDtGELVPGLATSWKWIDDTTLEFTLREGVKFHDGSP 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 153 VTAHDFVYSWQRLADPNTASP-YASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVHPSVSP 231
Cdd:cd08515    78 MTAEDVVFTFNRVRDPDSKAPrGRQNF-----NWLDK------------VEKVDPYTVRIVTKKPDPAALERLAGLVGPI 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 232 VPKSAVEKFGDKWTqPANIVTNGAYKLKNWVVNERIVLERNPQYWDnAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYN 311
Cdd:cd08515   141 VPKAYYEKVGPEGF-ALKPVGTGPYKVTEFVPGERVVLEAFDDYWG-GKPPIEKITFRVIPDVSTRVAELLSGGVDIITN 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 312 NMP-----IELFQKLKKEIPNEVRVdpylctYYYEINNQKAPFNDVRVRTALKLALDRDIIV-NKVKNQGDLPAYSYTPP 385
Cdd:cd08515   219 VPPdqaerLKSSPGLTVVGGPTMRI------GFITFDAAGPPLKDVRVRQALNHAIDRQAIVkALWGGRAKVPNTACQPP 292
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 386 ----YTDGAKLVE--PewfkwsqqkrnEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKnLGVNVNLEN 459
Cdd:cd08515   293 qfgcEFDVDTKYPydP-----------EKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAEAIVGMWKA-VGINAELNV 360
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 460 QEWKTFLDTRHQGTFDVaragwcadynePTSFLN---TMLSDSSNNTAHYKS---PAFDKLIADTLKVADDTQRSELYAK 533
Cdd:cd08515   361 LSKYRALRAWSKGGLFV-----------PAFFYTwgsNGINDASASTSTWFKardAEFDELLEKAETTTDPAKRKAAYKK 429
                         490       500
                  ....*....|....*....|
gi 1109557646 534 AEQQLDKDSAIVPVY-YYVN 552
Cdd:cd08515   430 ALKIIAEEAYWTPLYqYSQN 449
PBP2_NikA_DppA_OppA_like_21 cd08520
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
108-563 2.18e-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 [Multi-domain]  Cd Length: 468  Bit Score: 164.03  E-value: 2.18e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 108 LFEGLLISDvEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAdpntASPYASYlqYGHIANI 186
Cdd:cd08520    32 IFDSLVWKD-EKGFIPWLAESWEvSEDGLTYTFHLREGAKWHDGEPLTAEDVAFTFDYMK----KHPYVWV--DIELSII 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 187 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYF-YKLLvhpSVSPV-PKSAVEKFGD--KWTQPANIVTNGAYKLKNWV 262
Cdd:cd08520   105 ER------------VEALDDYTVKITLKRPYAPFlEKIA---TTVPIlPKHIWEKVEDpeKFTGPEAAIGSGPYKLVDYN 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 263 -VNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRyrsGEIDMTynNMPIELFQKLKKEIPNEVRVDPYLCTYYYE 341
Cdd:cd08520   170 kEQGTYLYEANEDYW-GGKPKVKRLEFVPVSDALLALEN---GEVDAI--SILPDTLAALENNKGFKVIEGPGFWVYRLM 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 342 INNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYS-YTPPYTDgaklvepeWF-----KWSQQKrnEEAKKLLAE 415
Cdd:cd08520   244 FNHDKNPFSDKEFRQAIAYAIDRQELVEKAARGAAALGSPgYLPPDSP--------WYnpnvpKYPYDP--EKAKELLKG 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 416 AGFTAD--------KPLTFDLLYNTSDLHKKlaiaVASIWKKNL---GVNVNLENQEWKTfLDTR-HQGTFDVA---RAG 480
Cdd:cd08520   314 LGYTDNggdgekdgEPLSLELLTSSSGDEVR----VAELIKEQLervGIKVNVKSLESKT-LDSAvKDGDYDLAisgHGG 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 481 WCADYNeptsFLNTMLSDSSNNTAH-YKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPW 559
Cdd:cd08520   389 IGGDPD----ILREVYSSNTKKSARgYDNEELNALLRQQLQEMDPEKRKELVFEIQELYAEELPMIPLYYPTMYTVHRGK 464

                  ....
gi 1109557646 560 VGGY 563
Cdd:cd08520   465 YDGW 468
PBP2_NikA_DppA_OppA_like_9 cd08496
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
108-550 5.04e-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 [Multi-domain]  Cd Length: 454  Bit Score: 162.89  E-value: 5.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 108 LFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTAspyasylQYGHIANI 186
Cdd:cd08496    30 LYDTLIKLDPDGKLEPGLAESWEyNADGTTLTLHLREGLTFSDGTPLDAAAVKANLDRGKSTGGS-------QVKQLASI 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 187 DDiiagkkpatdlgVKALDDHTFEVTLSEPVPYFYKLLVH---PSVSPvpkSAVEKFGDKWTQPaniVTNGAYKLKNWVV 263
Cdd:cd08496   103 SS------------VEVVDDTTVTLTLSQPDPAIPALLSDragMIVSP---TALEDDGKLATNP---VGAGPYVLTEWVP 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 264 NERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIelfQKLKKEIPNEVRVDPYLCTYYYEIN 343
Cdd:cd08496   165 NSKYVFERNEDYWDAANPHLDKLELSVIPDPTARVNALQSGQVDFAQLLAAQ---VKIARAAGLDVVVEPTLAATLLLLN 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 344 NQKAPFNDVRVRTALKLALDRDIIVNKV-KNQGDlPAYSYTPPYTDG-AKLVEPEWfkwsqQKRNEEAKKLLAEAGFtad 421
Cdd:cd08496   242 ITGAPFDDPKVRQAINYAIDRKAFVDALlFGLGE-PASQPFPPGSWAyDPSLENTY-----PYDPEKAKELLAEAGY--- 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 422 kPLTFDL-LYNTSDLHKKLAIAVASIWKKnLGVNVNLENQEWKTFLDTRH-QGTFDVARAGWCADYNEPTSFLNTMLSDS 499
Cdd:cd08496   313 -PNGFSLtIPTGAQNADTLAEIVQQQLAK-VGIKVTIKPLTGANAAGEFFaAEKFDLAVSGWVGRPDPSMTLSNMFGKGG 390
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1109557646 500 SNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYY 550
Cdd:cd08496   391 YYNPGKATDPELSALLKEVRATLDDPARKTALRAANKVVVEQAWFVPLFFQ 441
PBP2_NikA_DppA_OppA_like_12 cd08491
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
103-568 5.11e-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: 160.24  E-value: 5.11e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 103 NVSRDLFEGLLISDVE-GHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPntaspyasylqyg 181
Cdd:cd08491    26 VIRSNVTEPLTEIDPEsGTVGPRLATEWEQVDDNTWRFKLRPGVKFHDGTPFDAEAVAFSIERSMNG------------- 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 182 hiANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPvPKSAVEKFGDKwtqPaniVTNGAYKLKNW 261
Cdd:cd08491    93 --KLTCETRGYYFGDAKLTVKAVDDYTVEIKTDEPDPILPLLLSYVDVVS-PNTPTDKKVRD---P---IGTGPYKFDSW 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 262 VVNERIVLERNPQYWDNaKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIEL------FQKLKKEipnevrvdpyl 335
Cdd:cd08491   164 EPGQSIVLSRFDGYWGE-KPEVTKATYVWRSESSVRAAMVETGEADLAPSIAVQDAtnpdtdFAYLNSE----------- 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 336 cTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAklvEPEWFKWSQQKrnEEAKKLLAE 415
Cdd:cd08491   232 -TTALRIDAQIPPLDDVRVRKALNLAIDRDGIVGALFGGQGRPATQLVVPGINGH---NPDLKPWPYDP--EKAKALVAE 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 416 A---GFTADKPLTF----DLLYNTSDLHKklaiAVASIWKKnLGVNVNLENQE---W-----KTFLDTRHQGTFDVARAG 480
Cdd:cd08491   306 AkadGVPVDTEITLigrnGQFPNATEVME----AIQAMLQQ-VGLNVKLRMLEvadWlrylrKPFPEDRGPTLLQSQHDN 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 481 WCADynEPTSFLNTMLSDSSNNTahYKSPAFDKLIADTLKVADDtQRSELYAKAEQQL-DKDSAIVPVYYYVnarlvkpw 559
Cdd:cd08491   381 NSGD--ASFTFPVYYLSEGSQST--FGDPELDALIKAAMAATGD-ERAKLFQEIFAYVhDEIVADIPMFHMV-------- 447

                  ....*....
gi 1109557646 560 vgGYTGKDP 568
Cdd:cd08491   448 --GYTRVSK 454
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
91-549 1.08e-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 [Multi-domain]  Cd Length: 500  Bit Score: 159.97  E-value: 1.08e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  91 LDPHKIEgvPESNVSRDL-FEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAhdfvyswqrladP 168
Cdd:TIGR02294  19 MNPHVYN--PNQMFAQSMvYEPLVRYTADGKIEPWLAKSWTvSEDGKTYTFKLRDDVKFSDGTPFDA------------E 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 169 NTAspyasylqyghiANIDDIIAGKKPATDLG-------VKALDDHTFEVTLSEPV-PYFYKLLVhpsVSPVPKSAVEKF 240
Cdd:TIGR02294  85 AVK------------KNFDAVLQNSQRHSWLElsnqldnVKALDKYTFELVLKEAYyPALQELAM---PRPYRFLSPSDF 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 241 GDKWTQPA--NIVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNN---MPI 315
Cdd:TIGR02294 150 KNDTTKDGvkKPIGTGPWMLGESKQDEYAVFVRNENYW-GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGNegsIDL 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 316 ELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPA---YSYTPPYTDGAkl 392
Cdd:TIGR02294 229 DTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPAdtlFAKNVPYADID-- 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 393 VEPewFKWSQQKrneeAKKLLAEAGFT--ADK--------PLTFDLLY-NTSDLHKKLAIAVASIWKKnLGVNVNLENQE 461
Cdd:TIGR02294 307 LKP--YKYDVKK----ANALLDEAGWKlgKGKdvrekdgkPLELELYYdKTSALQKSLAEYLQAEWRK-IGIKLSLIGEE 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 462 WKTFLDTRHQGTFDVARA-GWCADYnEPTSFLNTMLSDS-SNNTAHYK---SPAFDKLIADTLKVADDTQRSELYAKAEQ 536
Cdd:TIGR02294 380 EDKIAARRRDGDFDMMFNyTWGAPY-DPHSFISAMRAKGhGDESAQSGlanKDEIDKSIGDALASTDETERQELYKNILT 458
                         490
                  ....*....|...
gi 1109557646 537 QLDKDSAIVPVYY 549
Cdd:TIGR02294 459 TLHDEAVYIPISY 471
PBP2_NikA_DppA_OppA_like_14 cd08497
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
90-555 6.54e-42

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 [Multi-domain]  Cd Length: 491  Bit Score: 157.68  E-value: 6.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  90 SLDPHKIEGVPESNVSRDLFEGLLIS--DVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLA 166
Cdd:cd08497    28 SLNPFILKGTAAAGLFLLVYETLMTRspDEPFSLYGLLAESVEyPPDRSWVTFHLRPEARFSDGTPVTAEDVVFSFETLK 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 167 DPNtASPYASYLqyghiANIDDiiagkkpatdlgVKALDDHTFEVTLSEP----VPYFYKLLvhpsvSPVPKSAVEKFGD 242
Cdd:cd08497   108 SKG-PPYYRAYY-----ADVEK------------VEALDDHTVRFTFKEKanreLPLIVGGL-----PVLPKHWYEGRDF 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 243 K-----WTQPaniVTNGAYKLKNWVVNERIVLERNPQYW----------DNAKTVInqVTYlpISSEVTDVNRYRSGEID 307
Cdd:cd08497   165 DkkrynLEPP---PGSGPYVIDSVDPGRSITYERVPDYWgkdlpvnrgrYNFDRIR--YEY--YRDRTVAFEAFKAGEYD 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 308 MTYNNMP--------IELFQK---LKKEIPNEVRVDPylctYYYEINNQKAPFNDVRVRTALKLALDrdiivnkvknqgd 376
Cdd:cd08497   238 FREENSAkrwatgydFPAVDDgrvIKEEFPHGNPQGM----QGFVFNTRRPKFQDIRVREALALAFD------------- 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 377 lpaysytppytdgaklvepewFKWS-------QQKRNE----EAKKLLAEAGFTAD----------KPLTFDLLYNTSDL 435
Cdd:cd08497   301 ---------------------FEWMnknlfygQYTRTRfnlrKALELLAEAGWTVRggdilvnadgEPLSFEILLDSPTF 359
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 436 HKklaiaVASIWKKNL---GVNVNLE---NQEWKTFLDTRHqgtFDVARAGWCADY---NEPTSFLNTMLSD--SSNNTA 504
Cdd:cd08497   360 ER-----VLLPYVRNLkklGIDASLRlvdSAQYQKRLRSFD---FDMITAAWGQSLspgNEQRFHWGSAAADkpGSNNLA 431
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1109557646 505 HYKSPAFDKLIaDTLKVADDtqRSELYAkAEQQLDK----DSAIVPVYYYVNARL 555
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; ...
97-563 7.79e-37

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 [Multi-domain]  Cd Length: 516  Bit Score: 143.56  E-value: 7.79e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  97 EGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASP-Y 174
Cdd:cd08510    24 EDNTDAEIMGFGNEGLFDTDKNYKITDSGAAKFKlDDKAKTVTITIKDGVKWSDGKPVTAKDLEYSYEIIANKDYTGVrY 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 175 ASYLQygHIANIDDIIAGKKPaTDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPA-----N 249
Cdd:cd08510   104 TDSFK--NIVGMEEYHDGKAD-TISGIKKIDDKTVEITFKEMSPSMLQSGNGYFEYAEPKHYLKDVPVKKLESSdqvrkN 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 250 IVTNGAYKLKNWVVNERIVLERNPQYWdNAKTVINQVTYLPISSEvTDVNRYRSGEIDMTyNNMPIELFQKLKKEIPNEV 329
Cdd:cd08510   181 PLGFGPYKVKKIVPGESVEYVPNEYYW-RGKPKLDKIVIKVVSPS-TIVAALKSGKYDIA-ESPPSQWYDQVKDLKNYKF 257
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 330 RVDPYLcTYYY--------------EINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPP----YTDGak 391
Cdd:cd08510   258 LGQPAL-SYSYigfklgkwdkkkgeNVMDPNAKMADKNLRQAMAYAIDNDAVGKKFYNGLRTRANSLIPPvfkdYYDS-- 334
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 392 lvEPEWFKWSQQKrneeAKKLLAEAGF---TAD--------KPLTFDLL-YNTSDLHKKLAIAVASIWKKnLGVNVNLEN 459
Cdd:cd08510   335 --ELKGYTYDPEK----AKKLLDEAGYkdvDGDgfredpdgKPLTINFAaMSGSETAEPIAQYYIQQWKK-IGLNVELTD 407
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 460 ---QEWKTFLDTRHQG--TFDVARAGWCADYN-EPTSFLntmLSDSSNNTAHYKSPAFDKLIA--DTLKVADDTQRSELY 531
Cdd:cd08510   408 grlIEFNSFYDKLQADdpDIDVFQGAWGTGSDpSPSGLY---GENAPFNYSRFVSEENTKLLDaiDSEKAFDEEYRKKAY 484
                         490       500       510
                  ....*....|....*....|....*....|..
gi 1109557646 532 AKAEQQLDKDSAIVPVYYYVNARLVKPWVGGY 563
Cdd:cd08510   485 KEWQKYMNEEAPVIPTLYRYSITPVNKRVKGY 516
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
40-547 6.34e-28

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 117.68  E-value: 6.34e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  40 MSNITKKSLIAAGILTALIAASAATAADVPAGVqladkqtlvrnnGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEG 119
Cdd:PRK15413    2 ARAVHRSWLVALGIATALAASPAFAAKDVVVAV------------GSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEM 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 120 HPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNtaSPYASYLQYGHIANIDdiiagkkpatd 198
Cdd:PRK15413   70 KLKNVLAESYTvSDDGLTYTVKLREGVKFQDGTDFNAAAVKANLDRASNPD--NHLKRYNLYKNIAKTE----------- 136
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 199 lgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFG-DKWTQPaniVTNGAYKLKNWVVNERIVLERNPQYWD 277
Cdd:PRK15413  137 ----AVDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGkEIGFHP---VGTGPYELDTWNQTDFVKVKKFAGYWQ 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 278 NAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYnNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTA 357
Cdd:PRK15413  210 PGLPKLDSITWRPVADNNTRAAMLQTGEAQFAF-PIPYEQAALLEKNKNLELVASPSIMQRYISMNVTQKPFDNPKVREA 288
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 358 LKLALDRDIIVnKVKNQG-DLPAYSYTPPYTDGAKLVEPewfkWSQQKrnEEAKKLLAEAGFTADKPLTFDLLYNTSDLH 436
Cdd:PRK15413  289 LNYAINRQALV-KVAFAGyATPATGVVPPSIAYAQSYKP----WPYDP--AKARELLKEAGYPNGFSTTLWSSHNHSTAQ 361
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 437 KKLAIAVASIWKKNLGVNVN-LENQEWKTFLDTRHQGTFDVAR--AGWCADYNEPTSFLNTMLSDSS-----NNTAHYKS 508
Cdd:PRK15413  362 KVLQFTQQQLAQVGIKAQVTaMDAGQRAAEVEGKGQKESGVRMfyTGWSASTGEADWALSPLFASQNwpptlFNTAFYSN 441
                         490       500       510
                  ....*....|....*....|....*....|....*....
gi 1109557646 509 PAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPV 547
Cdd:PRK15413  442 KQVDDDLAQALKTNDPAEKTRLYKAAQDIIWKESPWIPL 480
PBP2_SgrR_like cd08507
The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related ...
90-548 7.66e-28

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 [Multi-domain]  Cd Length: 448  Bit Score: 116.60  E-value: 7.66e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  90 SLDPHKIEGVPESNVSRDLFEGLLISDVE-GHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLAD 167
Cdd:cd08507    17 TLDPGTPLRRSESHLVRQIFDGLVRYDEEnGEIEPDLAHHWEsNDDLTHWTFYLRKGVRFHNGRELTAEDVVFTLLRLRE 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 168 PNTASPyasylQYGHIANIddiiagkkpatdlgvKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFgDKWTQP 247
Cdd:cd08507    97 LESYSW-----LLSHIEQI---------------ESPSPYTVDIKLSKPDPLFPRLLASANASILPADILFDP-DFARHP 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 248 aniVTNGAYKLKNWvVNERIVLERNPQYWdNAKTVINQVTYLpISSEVTDVNRYRSGEIDMTYNNMPIElFQKlkkeipn 327
Cdd:cd08507   156 ---IGTGPFRVVEN-TDKRLVLEAFDDYF-GERPLLDEVEIW-VVPELYENLVYPPQSTYLQYEESDSD-EQQ------- 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 328 EVRVDPylCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKN---QGDLPAYSYTPPYTDgaklvepewfkwsqqk 404
Cdd:cd08507   222 ESRLEE--GCYFLLFNQRKPGAQDPAFRRALSELLDPEALIQHLGGerqRGWFPAYGLLPEWPR---------------- 283
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 405 rnEEAKKLLAEAGFtADKPLTfdLLYNTSDLHKKLAIAVASIWKKnlgVNVNLENQEWktFLDTRHQGTFDVARAGWCA- 483
Cdd:cd08507   284 --EKIRRLLKESEY-PGEELT--LATYNQHPHREDAKWIQQRLAK---HGIRLEIHIL--SYEELLEGDADSMADLWLGs 353
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1109557646 484 ---DYNEPTSFLNTMLsDSSNNTAHYKSPAFDKLIADTLKvadDTQRSELYAKAEQQLDKDSAIVPVY 548
Cdd:cd08507   354 anfADDLEFSLFAWLL-DKPLLRHGCILEDLDALLAQWRN---EELAQAPLEEIEEQLVDEAWLLPLF 417
PRK15109 PRK15109
antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
123-549 5.48e-18

antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional


Pssm-ID: 185064  Cd Length: 547  Bit Score: 87.06  E-value: 5.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 123 PGVAEKWENKDF-KVWTFHLREN-----AKWSDGT-PVTAHDFVYSWQRLADPN--------TASPYASYLQYGhianiD 187
Cdd:PRK15109   81 PELAESWEVLDNgATYRFHLRRDvpfqkTDWFTPTrKMNADDVVFSFQRIFDRNhpwhnvngGNYPYFDSLQFA-----D 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 188 DIiagkkpatdLGVKALDDHTFEVTLSEPVPYF-YKLLVH--PSVSPVPKSAVEKFGDK----WtQPaniVTNGAYKLKN 260
Cdd:PRK15109  156 NV---------KSVRKLDNYTVEFRLAQPDASFlWHLATHyaSVLSAEYAAKLTKEDRQeqldR-QP---VGTGPFQLSE 222
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 261 WVVNERIVLERNPQYWdNAKTVINQVtylpisseVTDV--------NRYRSGEID-MTY---NNMPIelfqklkkeipne 328
Cdd:PRK15109  223 YRAGQFIRLQRHDDYW-RGKPLMPQV--------VVDLgsggtgrlSKLLTGECDvLAYpaaSQLSI------------- 280
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 329 VRVDPYL--------CTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTP----PYTDGAKLVE-- 394
Cdd:PRK15109  281 LRDDPRLrltlrpgmNIAYLAFNTRKPPLNNPAVRHALALAINNQRLMQSIYYGTAETAASILPraswAYDNEAKITEyn 360
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 395 PEwfkwsqqkrneEAKKLLAEAGFTAdkpLTFDLL-------YNTSDLhKKLAIAVASIwkKNLGVNVNLENQEWKtFLD 467
Cdd:PRK15109  361 PE-----------KSREQLKALGLEN---LTLKLWvptasqaWNPSPL-KTAELIQADL--AQVGVKVVIVPVEGR-FQE 422
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 468 TR-HQGTFDVARAGWCADYNEPTSFLNTMLS----DSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDS 542
Cdd:PRK15109  423 ARlMDMNHDLTLSGWATDSNDPDSFFRPLLScaaiRSQTNYAHWCDPAFDSVLRKALSSQQLASRIEAYDEAQSILAQEL 502

                  ....*..
gi 1109557646 543 AIVPVYY 549
Cdd:PRK15109  503 PILPLAS 509
SgrR COG4533
DNA-binding transcriptional regulator SgrR of sgrS sRNA, contains a MarR-type HTH domain and ...
87-275 1.41e-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: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646  87 EVQSLDPHKIEGVPESNVSRDLFEGLLISD-VEGHPSPGVAEKWE-NKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQR 164
Cdd:COG4533   130 PLEPLDPGQALRRSEQHLARQIFSGLTRYDeEKGELEPDLAHHWQqSDDGLRWRFYLRPGVLFHNGRELDASDVIASLLR 209
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109557646 165 LADPNTASPyasylQYGHIANIDdiiagkkpatdlgvkALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVekfgdkw 244
Cdd:COG4533   210 LLQLPALAW-----LFSHIKTIT---------------SPHPYTLEIHLHRPDPWLPLLLASVPAMILPRDVP------- 262
                         170       180       190
                  ....*....|....*....|....*....|...
gi 1109557646 245 TQPANIVTNGAYKlknWVVN--ERIVLERNPQY 275
Cdd:COG4533   263 TDPDHPIGTGPFK---VQENtdNRLVLEAFDHY 292
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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