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Conserved domains on  [gi|446012281|ref|WP_000090136|]
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MULTISPECIES: glutathione ABC transporter substrate-binding protein GsiB [Enterobacteriaceae]

Protein Classification

glutathione ABC transporter substrate-binding protein( domain architecture ID 11487780)

glutathione ABC transporter substrate-binding protein functions as the primary receptor for the import of extracellular glutathione into the cytoplasm

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
1-512 0e+00

glutathione ABC transporter substrate-binding protein GsiB; Provisional


:

Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 1114.58  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   1 MARAVHRSGLVALGIATALMASCAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
Cdd:PRK15413   1 MARAVHRSWLVALGIATALAASPAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  81 VSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAH 160
Cdd:PRK15413  81 VSDDGLTYTVKLREGVKFQDGTDFNAAAVKANLDRASNPDNHLKRYNLYKNIAKTEAVDPTTVKITLKQPFSAFINILAH 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
Cdd:PRK15413 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 241 AFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAY 320
Cdd:PRK15413 241 AFPIPYEQAALLEKNKNLELVASPSIMQRYISMNVTQKPFDNPKVREALNYAINRQALVKVAFAGYATPATGVVPPSIAY 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 321 AQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
Cdd:PRK15413 321 AQSYKPWPYDPAKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:PRK15413 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDDLAQALKTNDPAEKTRLYKAAQDIIWKESPWIPL 480
                        490       500       510
                 ....*....|....*....|....*....|..
gi 446012281 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
Cdd:PRK15413 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLK 512
 
Name Accession Description Interval E-value
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
1-512 0e+00

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 1114.58  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   1 MARAVHRSGLVALGIATALMASCAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
Cdd:PRK15413   1 MARAVHRSWLVALGIATALAASPAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  81 VSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAH 160
Cdd:PRK15413  81 VSDDGLTYTVKLREGVKFQDGTDFNAAAVKANLDRASNPDNHLKRYNLYKNIAKTEAVDPTTVKITLKQPFSAFINILAH 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
Cdd:PRK15413 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 241 AFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAY 320
Cdd:PRK15413 241 AFPIPYEQAALLEKNKNLELVASPSIMQRYISMNVTQKPFDNPKVREALNYAINRQALVKVAFAGYATPATGVVPPSIAY 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 321 AQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
Cdd:PRK15413 321 AQSYKPWPYDPAKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:PRK15413 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDDLAQALKTNDPAEKTRLYKAAQDIIWKESPWIPL 480
                        490       500       510
                 ....*....|....*....|....*....|..
gi 446012281 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
Cdd:PRK15413 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLK 512
PBP2_Ylib_like cd08499
The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib ...
29-508 0e+00

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: 714.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08499    1 DLVIAVLSDATSLDPHDTNDTPSASVQSNIYEGLVGFDKDMKIVPVLAESWEQSDDGTTWTFKLREGVKFHDGTPFNAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPY 188
Cdd:cd08499   81 VKANLDRVLDPETASPRASLFSMIEEVEVVDDYTVKITLKEPFAPLLAHLAHPGGSIISPKAIEEYGKEISKHPVGTGPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 189 ELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQ 268
Cdd:cd08499  161 KFESWTPGDEVTLVKNDDYWG-GLPKVDTVTFKVVPEDGTRVAMLETGEADIAYPVPPEDVDRLENSPGLNVYRSPSISV 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 269 RYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIA-YAQSYKPWPYDPVKARELLKEAGYPNGF 347
Cdd:cd08499  240 VYIGFNTQKEPFDDVRVRQAINYAIDKEAIIKGILNGYGTPADSPIAPGVFgYSEQVGPYEYDPEKAKELLAEAGYPDGF 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 348 STTLWSSHNHsTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGqkesGVRMFYTGWSASTGEADWALSPLFASQ 427
Cdd:cd08499  320 ETTLWTNDNR-ERIKIAEFIQQQLAQIGIDVEIEVMEWGAYLEETGNGE----EHQMFLLGWSTSTGDADYGLRPLFHSS 394
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 428 NWPPtLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFE 507
Cdd:cd08499  395 NWGA-PGNRAFYSNPEVDALLDEARREADEEERLELYAKAQEIIWEDAPWVFLYHPETLAGVSKEVKGFYIYPSGGFSLK 473

                 .
gi 446012281 508 D 508
Cdd:cd08499  474 D 474
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
41-512 9.93e-174

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


Pssm-ID: 440510 [Multi-domain]  Cd Length: 464  Bit Score: 497.52  E-value: 9.93e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  41 LDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPA 120
Cdd:COG0747    1 MDPALSTDAASANVASLVYEGLVRYDPDGELVPDLAESWEVSDDGKTYTFTLRDGVKFHDGTPLTAEDVVFSLERLLDPD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 121 NHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVK 200
Cdd:COG0747   81 SGSPGAGLLANIESVEAVDDYTVVITLKEPYPPFLYLLASPGAAIVPKHALEKVGDDFNTNPVGTGPYKLVSWVPGQRIV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 201 VKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPF 280
Cdd:COG0747  161 LERNPDYWG-GKPKLDRVVFRVIPDAATRVAALQSGEVDIAEGLPPDDLARLKADPGLKVVTGPGLGTTYLGFNTNKPPF 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 281 DNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSShNHST 359
Cdd:COG0747  240 DDVRVRQALAYAIDREAIIDAVLNGLGTPANGPIPPGSpGYDDDLEPYPYDPEKAKALLAEAGYPDGLELTLLTP-GGPD 318
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 360 AQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEV-EGKGQkesgvrMFYTGWSASTGEADWALSPLFASQNWPPtlFNTAF 438
Cdd:COG0747  319 REDIAEAIQAQLAKIGIKVELETLDWATYLDRLrAGDFD------LALLGWGGDYPDPDNFLSSLFGSDGIGG--SNYSG 390
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446012281 439 YSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
Cdd:COG0747  391 YSNPELDALLDEARAETDPAERKALYAEAQKILAEDAPYIPLYQPPQLYAVRKRVKGVEPNPFGLPDLADVSLA 464
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
70-429 1.17e-108

Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.


Pssm-ID: 425718  Cd Length: 368  Bit Score: 327.83  E-value: 1.17e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   70 KLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKN---IAKTEAIDPTTVKIT 146
Cdd:pfam00496   1 EVVPALAESWEVSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYASLLAYdadIVGVEAVDDYTVRFT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  147 LKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWqPGLPKLDSITWRPVADN 226
Cdd:pfam00496  81 LKKPDPLFLPLLAALAAAPVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYW-GGKPKLDRIVFKVIPDS 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  227 NTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMAS-PSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAG 305
Cdd:pfam00496 160 TARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSgPGGGTYYLAFNTKKPPFDDVRVRQALSYAIDREAIVKAVLGG 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  306 YATPATGVVPPSIA-YAQSYKPWPYDPVKARELLKEAGYPNGF-------STTLWSSHNHSTAQKVLQFTQQQLAQVGIK 377
Cdd:pfam00496 240 YATPANSLVPPGFPgYDDDPKPEYYDPEKAKALLAEAGYKDGDgggrrklKLTLLVYSGNPAAKAIAELIQQQLKKIGIK 319
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446012281  378 AQVTAMDAGQR-AAEVEGKGQkesgvrMFYTGWSASTGEADWALSPLFASQNW 429
Cdd:pfam00496 320 VEIKTVDWATYlERVKDGDFD------MALSGWGADYPDPDNFLYPFLSSTGG 366
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
24-493 1.22e-60

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: 207.35  E-value: 1.22e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   24 AFAAKDVVVAVGSNFTTLDPYDANDtlSQAVAKSF-YQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGT 102
Cdd:TIGR02294   2 KKENKQLTYAWPVDIGPMNPHVYNP--NQMFAQSMvYEPLVRYTADGKIEPWLAKSWTVSEDGKTYTFKLRDDVKFSDGT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  103 DFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHP-ATAMISPAALE-KYGKEIGF 180
Cdd:TIGR02294  80 PFDAEAVKKNFDAVLQNSQRHSWLELSNQLDNVKALDKYTFELVLKEAYYPALQELAMPrPYRFLSPSDFKnDTTKDGVK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  181 HPVGTGPYELDTWNQTDFVKVKKFAGYWQPGlPKLDSITWRPVADNNTRAAMLQTGEAQFAF----PIPYEQATLLEKNK 256
Cdd:TIGR02294 160 KPIGTGPWMLGESKQDEYAVFVRNENYWGEK-PKLKKVTVKVIPDAETRALAFESGEVDLIFgnegSIDLDTFAQLKDDG 238
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  257 NIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQ-SYKPWPYDPVKAR 335
Cdd:TIGR02294 239 DYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPADTLFAKNVPYADiDLKPYKYDVKKAN 318
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  336 ELLKEAGY----------PNGFSTTLWSSHNHSTA-QKVL-QFTQQQLAQVGIKAQVTAMDAGQRAAevegkgQKESGV- 402
Cdd:TIGR02294 319 ALLDEAGWklgkgkdvreKDGKPLELELYYDKTSAlQKSLaEYLQAEWRKIGIKLSLIGEEEDKIAA------RRRDGDf 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  403 -RMFYTGWSASTGEADWALSplFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLV 481
Cdd:TIGR02294 393 dMMFNYTWGAPYDPHSFISA--MRAKGHGDESAQSGLANKDEIDKSIGDALASTDETERQELYKNILTTLHDEAVYIPIS 470
                         490
                  ....*....|..
gi 446012281  482 VEKLVSAHSKNL 493
Cdd:TIGR02294 471 YISMTVVYRKDL 482
 
Name Accession Description Interval E-value
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
1-512 0e+00

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 1114.58  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   1 MARAVHRSGLVALGIATALMASCAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
Cdd:PRK15413   1 MARAVHRSWLVALGIATALAASPAFAAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  81 VSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAH 160
Cdd:PRK15413  81 VSDDGLTYTVKLREGVKFQDGTDFNAAAVKANLDRASNPDNHLKRYNLYKNIAKTEAVDPTTVKITLKQPFSAFINILAH 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
Cdd:PRK15413 161 PATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 241 AFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAY 320
Cdd:PRK15413 241 AFPIPYEQAALLEKNKNLELVASPSIMQRYISMNVTQKPFDNPKVREALNYAINRQALVKVAFAGYATPATGVVPPSIAY 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 321 AQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
Cdd:PRK15413 321 AQSYKPWPYDPAKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKES 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:PRK15413 401 GVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDDLAQALKTNDPAEKTRLYKAAQDIIWKESPWIPL 480
                        490       500       510
                 ....*....|....*....|....*....|..
gi 446012281 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
Cdd:PRK15413 481 VVEKLVSAHSKNLTGFWIMPDTGFSFEDADLK 512
PBP2_Ylib_like cd08499
The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib ...
29-508 0e+00

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: 714.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08499    1 DLVIAVLSDATSLDPHDTNDTPSASVQSNIYEGLVGFDKDMKIVPVLAESWEQSDDGTTWTFKLREGVKFHDGTPFNAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPY 188
Cdd:cd08499   81 VKANLDRVLDPETASPRASLFSMIEEVEVVDDYTVKITLKEPFAPLLAHLAHPGGSIISPKAIEEYGKEISKHPVGTGPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 189 ELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQ 268
Cdd:cd08499  161 KFESWTPGDEVTLVKNDDYWG-GLPKVDTVTFKVVPEDGTRVAMLETGEADIAYPVPPEDVDRLENSPGLNVYRSPSISV 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 269 RYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIA-YAQSYKPWPYDPVKARELLKEAGYPNGF 347
Cdd:cd08499  240 VYIGFNTQKEPFDDVRVRQAINYAIDKEAIIKGILNGYGTPADSPIAPGVFgYSEQVGPYEYDPEKAKELLAEAGYPDGF 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 348 STTLWSSHNHsTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGqkesGVRMFYTGWSASTGEADWALSPLFASQ 427
Cdd:cd08499  320 ETTLWTNDNR-ERIKIAEFIQQQLAQIGIDVEIEVMEWGAYLEETGNGE----EHQMFLLGWSTSTGDADYGLRPLFHSS 394
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 428 NWPPtLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFE 507
Cdd:cd08499  395 NWGA-PGNRAFYSNPEVDALLDEARREADEEERLELYAKAQEIIWEDAPWVFLYHPETLAGVSKEVKGFYIYPSGGFSLK 473

                 .
gi 446012281 508 D 508
Cdd:cd08499  474 D 474
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
41-512 9.93e-174

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


Pssm-ID: 440510 [Multi-domain]  Cd Length: 464  Bit Score: 497.52  E-value: 9.93e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  41 LDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPA 120
Cdd:COG0747    1 MDPALSTDAASANVASLVYEGLVRYDPDGELVPDLAESWEVSDDGKTYTFTLRDGVKFHDGTPLTAEDVVFSLERLLDPD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 121 NHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVK 200
Cdd:COG0747   81 SGSPGAGLLANIESVEAVDDYTVVITLKEPYPPFLYLLASPGAAIVPKHALEKVGDDFNTNPVGTGPYKLVSWVPGQRIV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 201 VKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPF 280
Cdd:COG0747  161 LERNPDYWG-GKPKLDRVVFRVIPDAATRVAALQSGEVDIAEGLPPDDLARLKADPGLKVVTGPGLGTTYLGFNTNKPPF 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 281 DNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSShNHST 359
Cdd:COG0747  240 DDVRVRQALAYAIDREAIIDAVLNGLGTPANGPIPPGSpGYDDDLEPYPYDPEKAKALLAEAGYPDGLELTLLTP-GGPD 318
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 360 AQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEV-EGKGQkesgvrMFYTGWSASTGEADWALSPLFASQNWPPtlFNTAF 438
Cdd:COG0747  319 REDIAEAIQAQLAKIGIKVELETLDWATYLDRLrAGDFD------LALLGWGGDYPDPDNFLSSLFGSDGIGG--SNYSG 390
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446012281 439 YSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
Cdd:COG0747  391 YSNPELDALLDEARAETDPAERKALYAEAQKILAEDAPYIPLYQPPQLYAVRKRVKGVEPNPFGLPDLADVSLA 464
PBP2_NikA_DppA_OppA_like cd00995
The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains ...
30-496 3.11e-165

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: 476.03  E-value: 3.11e-165
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd00995    2 LTVALGSDPTSLDPAFATDASSGRVLRLIYDGLVRYDPDGELVPDLAESWEVSDDGKTYTFKLRDGVKFHDGTPLTAEDV 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPYE 189
Cdd:cd00995   82 VFSFERLADPKNASPSAGKADEIEGVEVVDDYTVTITLKEPDAPFLALLAYPAASPVPKAAAEKDGKAFGTKPVGTGPYK 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 190 LDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQR 269
Cdd:cd00995  162 LVEWKPGESIVLERNDDYWGPGKPKIDKITFKVIPDASTRVAALQSGEIDIADDVPPSALETLKKNPGIRLVTVPSLGTG 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 270 YISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI--AYAQSYKPWPYDPVKARELLKEAGYPN-- 345
Cdd:cd00995  242 YLGFNTNKPPFDDKRVRQAISYAIDREEIIDAVLGGYGTPATSPLPPGSwgYYDKDLEPYEYDPEKAKELLAEAGYKDgk 321
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 346 GFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKEsgvrMFYTGWSASTGEADWALSPLFA 425
Cdd:cd00995  322 GLELTLLYNSDGPTRKEIAEAIQAQLKEIGIKVEIEPLDFATLLDALDAGDDFD----LFLLGWGADYPDPDNFLSPLFS 397
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446012281 426 SQNWPPtlFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd00995  398 SGASGA--GNYSGYSNPEFDALLDEARAETDPEERKALYQEAQEILAEDAPVIPLYYPNNVYAYSKRVKGF 466
PBP2_DppA_like cd08493
The substrate-binding component of an ABC-type dipeptide import system contains the type 2 ...
31-496 9.97e-143

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: 419.28  E-value: 9.97e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  31 VVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKE-MKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd08493    3 VYCSEGSPESLDPQLATDGESDAVTRQIYEGLVEFKPGtTELEPGLAESWEVSDDGLTYTFHLRKGVKFHDGRPFNADDV 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASDPAN-----------HLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALE-----K 173
Cdd:cd08493   83 VFSFNRWLDPNHpyhkvggggypYFYSMGLGSLIKSVEAVDDYTVKFTLTRPDAPFLANLAMPFASILSPEYADqllaaG 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 174 YGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQF-AFPIPyeQATLL 252
Cdd:cd08493  163 KPEQLDLLPVGTGPFKFVSWQKDDRIRLEANPDYWG-GKAKIDTLVFRIIPDNSVRLAKLLAGECDIvAYPNP--SDLAI 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 253 EKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDP 331
Cdd:cd08493  240 LADAGLQLLERPGLNVGYLAFNTQKPPFDDPKVRQAIAHAINKEAIVDAVYQGTATVAKNPLPPTSwGYNDDVPDYEYDP 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 332 VKARELLKEAGYPNGFSTTLW----SSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQ-RAAEVEGKGQkesgvrMFY 406
Cdd:cd08493  320 EKAKALLAEAGYPDGFELTLWyppvSRPYNPNPKKMAELIQADLAKVGIKVEIVTYEWGEyLERTKAGEHD------LYL 393
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 407 TGWSASTGEADWALSPLFASQNWPPTlFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLV 486
Cdd:cd08493  394 LGWTGDNGDPDNFLRPLLSCDAAPSG-TNRARWCNPEFDELLEKARRTTDQAERAKLYKQAQEIIHEDAPWVPIAHSKRL 472
                        490
                 ....*....|
gi 446012281 487 SAHSKNLTGF 496
Cdd:cd08493  473 LAVRKNVKGF 482
PBP2_NikA_DppA_OppA_like_11 cd08516
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-496 5.56e-138

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: 406.25  E-value: 5.56e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd08516    2 LRFGLSTDPDSLDPHKATAAASEEVLENIYEGLLGPDENGKLVPALAESWEVSDDGLTYTFKLRDGVKFHNGDPVTAADV 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAAlekyGKEIGFHPVGTGPYE 189
Cdd:cd08516   82 KYSFNRIADPDSGAPLRALFQEIESVEAPDDATVVIKLKQPDAPLLSLLASVNSPIIPAAS----GGDLATNPIGTGPFK 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 190 LDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQR 269
Cdd:cd08516  158 FASYEPGVSIVLEKNPDYWGKGLPKLDGITFKIYPDENTRLAALQSGDVDIIEYVPPQQAAQLEEDDGLKLASSPGNSYM 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 270 YISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQ---SYKPWPYDPVKARELLKEAGYPNG 346
Cdd:cd08516  238 YLALNNTREPFDDPKVRQAIAYAIDRDAIVDAAFFGRGTPLGGLPSPAGSPAYdpdDAPCYKYDPEKAKALLAEAGYPNG 317
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 347 FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVeGKGQKESGVrmfyTGWSASTgEADWALSPLFAS 426
Cdd:cd08516  318 FDFTILVTSQYGMHVDTAQVIQAQLAAIGINVEIELVEWATWLDDV-NKGDYDATI----AGTSGNA-DPDGLYNRYFTS 391
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 427 qnwpPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08516  392 ----GGKLNFFNYSNPEVDELLAQGRAETDEAKRKEIYKELQQILAEDVPWVFLYWRSQYYAMNKNVQGF 457
PBP2_NikA_DppA_OppA_like_2 cd08498
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-494 1.56e-123

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: 369.97  E-value: 1.56e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDgITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08498    1 TLRIALAADPTSLDPHFHNEGPTLAVLHNIYDTLVRRDADLKLEPGLATSWEAVDD-TTWRFKLREGVKFHDGSPFTAED 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPANHLKRYNLyKNIAKTEAIDPTTVKITLKQPFSAFINILAHpaTAMISPAALEKYGKE----IGFHPVG 184
Cdd:cd08498   80 VVFSLERARDPPSSPASFYL-RTIKEVEVVDDYTVDIKTKGPNPLLPNDLTN--IFIMSKPWAEAIAKTgdfnAGRNPNG 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 185 TGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASP 264
Cdd:cd08498  157 TGPYKFVSWEPGDRTVLERNDDYWG-GKPNWDEVVFRPIPNDATRVAALLSGEVDVIEDVPPQDIARLKANPGVKVVTGP 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 265 SIMQRYISMNVTQK-----------PFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQS-YKPWPYDPV 332
Cdd:cd08498  236 SLRVIFLGLDQRRDelpagsplgknPLKDPRVRQALSLAIDREAIVDRVMRGLATPAGQLVPPGVFGGEPlDKPPPYDPE 315
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 333 KARELLKEAGYPNGFSTTLWSSHNHST-AQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKgqkesGVRMFYTGWSA 411
Cdd:cd08498  316 KAKKLLAEAGYPDGFELTLHCPNDRYVnDEAIAQAVAGMLARIGIKVNLETMPKSVYFPRATKG-----EADFYLLGWGV 390
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 412 STGEADWALSPLFASQNWPPTL--FNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAH 489
Cdd:cd08498  391 PTGDASSALDALLHTPDPEKGLgaYNRGGYSNPEVDALIEAAASEMDPAKRAALLQEAQEIVADDAAYIPLHQQVLIWAA 470

                 ....*
gi 446012281 490 SKNLT 494
Cdd:cd08498  471 RKGID 475
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
27-496 4.15e-123

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: 368.85  E-value: 4.15e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  27 AKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKE--MKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDF 104
Cdd:cd08512    2 KDTLVVATSADINTLDPAVAYEVASGEVVQNVYDRLVTYDGEdtGKLVPELAESWEVSDDGKTYTFHLRDGVKFHDGNPV 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 105 NAAAVKANLDRA----SDPANHLKRYNLyKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGF 180
Cdd:cd08512   82 TAEDVKYSFERAlklnKGPAFILTQTSL-NVPETIKAVDDYTVVFKLDKPPALFLSTLAAPVASIVDKKLVKEHGKDGDW 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 181 -------HPVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLE 253
Cdd:cd08512  161 gnawlstNSAGSGPYKLKSWDPGEEVVLERNDDYWG-GAPKLKRVIIRHVPEAATRRLLLERGDADIARNLPPDDVAALE 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 254 KNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDPV 332
Cdd:cd08512  240 GNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLKGQGKPHPGPLPDGLpGGAPDLPPYKYDLE 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 333 KARELLKEAGYPNGFSTTL-WSSHNhSTAQKVLQFTQQQLAQVGIKAQVTAMD-AGQRAAEVEGKGQkesgvrMFYTGWS 410
Cdd:cd08512  320 KAKELLAEAGYPNGFKLTLsYNSGN-EPREDIAQLLQASLAQIGIKVEIEPVPwAQLLEAARSREFD------IFIGGWG 392
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 411 ASTGEADWaLSPLFASQNWPPTLfNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHS 490
Cdd:cd08512  393 PDYPDPDY-FAATYNSDNGDNAA-NRAWYDNPELDALIDEARAETDPAKRAALYKELQKIVYDDAPYIPLYQPVEVVAVR 470

                 ....*.
gi 446012281 491 KNLTGF 496
Cdd:cd08512  471 KNVKGY 476
PBP2_NikA_DppA_OppA_like_15 cd08492
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
31-496 5.52e-122

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: 366.17  E-value: 5.52e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  31 VVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVK 110
Cdd:cd08492    5 TYALGQDPTCLDPHTLDFYPNGSVLRQVVDSLVYQDPTGEIVPWLAESWEVSDDGTTYTFHLRDGVTFSDGTPLDAEAVK 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 111 ANLDRASDPANHLKRYNLY-KNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEK-YGKEIGFHPVGTGPY 188
Cdd:cd08492   85 ANFDRILDGSTKSGLAASYlGPYKSTEVVDPYTVKVHFSEPYAPFLQALSTPGLGILSPATLARpGEDGGGENPVGSGPF 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 189 ELDTWNQTDFVKVKKFAGY-WQP------GLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNK--NIE 259
Cdd:cd08492  165 VVESWVRGQSIVLVRNPDYnWAPalakhqGPAYLDKIVFRFIPEASVRVGALQSGQVDVITDIPPQDEKQLAADGgpVIE 244
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 260 LMASPSIMQrYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKP-WPYDPVKARELL 338
Cdd:cd08492  245 TRPTPGVPY-SLYLNTTRPPFDDVRVRQALQLAIDREAIVETVFFGSYPAASSLLSSTTPYYKDLSDaYAYDPEKAKKLL 323
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 339 KEAGY----PNGFST--------TLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKesgvrMFY 406
Cdd:cd08492  324 DEAGWtargADGIRTkdgkrltlTFLYSTGQPQSQSVLQLIQAQLKEVGIDLQLKVLDAGTLTARRASGDYD-----LAL 398
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 407 TGWSASTGEadwALSPLFASQNwPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLV 486
Cdd:cd08492  399 SYYGRADPD---ILRTLFHSAN-RNPPGGYSRFADPELDDLLEKAAATTDPAERAALYADAQKYLIEQAYVVPLYEEPQV 474
                        490
                 ....*....|
gi 446012281 487 SAHSKNLTGF 496
Cdd:cd08492  475 VAAAPNVKGF 484
PBP2_NikA_DppA_OppA_like_5 cd08511
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-501 2.23e-120

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: 361.60  E-value: 2.23e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08511    2 TLRIGLEADPDRLDPALSRTFVGRQVFAALCDKLVDIDADLKIVPQLATSWEISPDGKTLTLKLRKGVKFHDGTPFDAAA 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPANHLKRYNLyKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPY 188
Cdd:cd08511   82 VKANLERLLTLPGSNRKSEL-ASVESVEVVDPATVRFRLKQPFAPLLAVLSDRAGMMVSPKAAKAAGADFGSAPVGTGPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 189 ELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQ 268
Cdd:cd08511  161 KFVERVQQDRIVLERNPHYWNAGKPHLDRLVYRPIPDATVRLANLRSGDLDIIERLSPSDVAAVKKDPKLKVLPVPGLGY 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 269 RYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWP-YDPVKARELLKEAGYPNgF 347
Cdd:cd08511  241 QGITFNIGNGPFNDPRVRQALALAIDREAINQVVFNGTFKPANQPFPPGSPYYGKSLPVPgRDPAKAKALLAEAGVPT-V 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 348 STTLwSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEgKGQKEsgvrMFYTGWSASTgEADWALSPLFASQ 427
Cdd:cd08511  320 TFEL-TTANTPTGRQLAQVIQAMAAEAGFTVKLRPTEFATLLDRAL-AGDFQ----ATLWGWSGRP-DPDGNIYQFFTSK 392
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446012281 428 NwpptLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPD 501
Cdd:cd08511  393 G----GQNYSRYSNPEVDALLEKARASADPAERKALYNQAAKILADDLPYIYLYHQPYYIAASKKVRGLVPYPD 462
PBP2_NikA_DppA_OppA_like_3 cd08490
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
28-500 7.78e-116

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: 349.98  E-value: 7.78e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  28 KDVVVAVGSNFTTLDPYDANDTLSqaVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDgITYTVKLREGIKFQDGTDFNAA 107
Cdd:cd08490    1 KTLTVGLPFESTSLDPASDDGWLL--SRYGVAETLVKLDDDGKLEPWLAESWEQVDD-TTWEFTLRDGVKFHDGTPLTAE 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVKANLDRASDPANhlkRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEigfHPVGTGP 187
Cdd:cd08490   78 AVKASLERALAKSP---RAKGGALIISVIAVDDYTVTITTKEPYPALPARLADPNTAILDPAAYDDGVDP---APIGTGP 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 188 YELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIM 267
Cdd:cd08490  152 YKVESFEPDQSLTLERNDDYWG-GKPKLDKVTVKFIPDANTRALALQSGEVDIAYGLPPSSVERLEKDDGYKVSSVPTPR 230
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 268 QRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAGYP--- 344
Cdd:cd08490  231 TYFLYLNTEKGPLADVRVRQALSLAIDREGIADSVLEGSAAPAKGPFPPSLPANPKLEPYEYDPEKAKELLAEAGWTdgd 310
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 345 --------NGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGqraaEVEGKGQKESGVRMFYTGWSASTGEA 416
Cdd:cd08490  311 gdgiekdgEPLELTLLTYTSRPELPPIAEAIQAQLKKIGIDVEIRVVEYD----AIEEDLLDGDFDLALYSRNTAPTGDP 386
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 417 DWALSPLFASQNwpptLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08490  387 DYFLNSDYKSDG----SYNYGGYSNPEVDALIEELRTEFDPEERAELAAEIQQIIQDDAPVIPVAHYNQVVAVSKRVKGY 462

                 ....
gi 446012281 497 WIMP 500
Cdd:cd08490  463 KVDP 466
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
70-429 1.17e-108

Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.


Pssm-ID: 425718  Cd Length: 368  Bit Score: 327.83  E-value: 1.17e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   70 KLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKN---IAKTEAIDPTTVKIT 146
Cdd:pfam00496   1 EVVPALAESWEVSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYASLLAYdadIVGVEAVDDYTVRFT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  147 LKQPFSAFINILAHPATAMISPAALEKYGKEIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWqPGLPKLDSITWRPVADN 226
Cdd:pfam00496  81 LKKPDPLFLPLLAALAAAPVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYW-GGKPKLDRIVFKVIPDS 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  227 NTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMAS-PSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAG 305
Cdd:pfam00496 160 TARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSgPGGGTYYLAFNTKKPPFDDVRVRQALSYAIDREAIVKAVLGG 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  306 YATPATGVVPPSIA-YAQSYKPWPYDPVKARELLKEAGYPNGF-------STTLWSSHNHSTAQKVLQFTQQQLAQVGIK 377
Cdd:pfam00496 240 YATPANSLVPPGFPgYDDDPKPEYYDPEKAKALLAEAGYKDGDgggrrklKLTLLVYSGNPAAKAIAELIQQQLKKIGIK 319
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446012281  378 AQVTAMDAGQR-AAEVEGKGQkesgvrMFYTGWSASTGEADWALSPLFASQNW 429
Cdd:pfam00496 320 VEIKTVDWATYlERVKDGDFD------MALSGWGADYPDPDNFLYPFLSSTGG 366
PBP2_NikA_DppA_OppA_like_8 cd08495
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-496 7.34e-108

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: 329.68  E-value: 7.34e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLsQAVAKSFYQGLFGLDKEMKLKN-----VLAESYTVSDDGITYTVKLREGIKFQDGTDF 104
Cdd:cd08495    2 LRIAMDIPLTTLDPDQGAEGL-RFLGLPVYDPLVRWDLSTADRPgeivpGLAESWEVSPDGRRWTFTLRPGVKFHDGTPF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 105 NAAAVKANLDRA-------SDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISP-AALEKYGK 176
Cdd:cd08495   81 DADAVVWNLDRMldpdspqYDPAQAGQVRSRIPSVTSVEAIDDNTVRITTSEPFADLPYVLTTGLASSPSPkEKAGDAWD 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 177 EIGFHPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAfPIPYEQATLLEKNK 256
Cdd:cd08495  161 DFAAHPAGTGPFRITRFVPRERIELVRNDGYWDKRPPKNDKLVLIPMPDANARLAALLSGQVDAI-EAPAPDAIAQLKSA 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 257 NIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDPVKAR 335
Cdd:cd08495  240 GFQLVTNPSPHVWIYQLNMAEGPLSDPRVRQALNLAIDREGLVDLLLGGLAAPATGPVPPGHpGFGKPTFPYKYDPDKAR 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 336 ELLKEAGYPNGFSTTL---WSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEV-EGKGQKESGVRMFYTGWSA 411
Cdd:cd08495  320 ALLKEAGYGPGLTLKLrvsASGSGQMQPLPMNEFIQQNLAEIGIDLDIEVVEWADLYNAWrAGAKDGSRDGANAINMSSA 399
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 412 STgeADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSK 491
Cdd:cd08495  400 MD--PFLALVRFLSSKIDPPVGSNWGGYHNPEFDALIDQARVTFDPAERAALYREAHAIVVDDAPWLFVVHDRNPRALSP 477

                 ....*
gi 446012281 492 NLTGF 496
Cdd:cd08495  478 KVKGF 482
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
7-512 1.57e-106

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


Pssm-ID: 443327 [Multi-domain]  Cd Length: 543  Bit Score: 328.32  E-value: 1.57e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   7 RSGLVALGIATALMASCAFA-----------AKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVL 75
Cdd:COG4166    5 KALLLLALALALALAACGSGgkypagdkvndAKVLRLNNGTEPDSLDPALATGTAAAGVLGLLFEGLVSLDEDGKPYPGL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  76 AESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPAN---------HLKRYNLYKNIAKT------EAIDP 140
Cdd:COG4166   85 AESWEVSEDGLTYTFHLRPDAKWSDGTPVTAEDFVYSWKRLLDPKTaspyayylaDIKNAEAINAGKKDpdelgvKALDD 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 141 TTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFHP---VGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDS 217
Cdd:COG4166  165 HTLEVTLEAPTPYFPLLLGFPAFLPVPKKAVEKYGDDFGTTPenpVGNGPYKLKEWEHGRSIVLERNPDYWGADNVNLDK 244
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 218 ITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASP-SIMQrYISMNVTQKPFDNPKVREALNYAINRP 296
Cdd:COG4166  245 IRFEYYKDATTALEAFKAGELDFTDELPAEQFPALKDDLKEELPTGPyAGTY-YLVFNTRRPPFADPRVRKALSLAIDRE 323
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 297 ALVKVAFAGYATPATGVVPPSIAYAQS----------YKPWP--YDPVKARELLKEAGYPNG--FSTTLWSSHNhSTAQK 362
Cdd:COG4166  324 WINKNVFYGGYTPATSFVPPSLAGYPEgedflklpgeFVDGLlrYNLRKAKKLLAEAGYTKGkpLTLELLYNTS-EGHKR 402
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 363 VLQFTQQQLAQV-GIKAQVTAMDAGQRAAEVEgkgQKESGvrMFYTGWSASTgeadwaLSP-----LFASQNwpptLFNT 436
Cdd:COG4166  403 IAEAVQQQLKKNlGIDVTLRNVDFKQYLDRRR---NGDFD--MVRAGWGADY------PDPgtfldLFGSDG----SNNY 467
                        490       500       510       520       530       540       550
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446012281 437 AFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGfWIMPDTGFSFEDADLQ 512
Cdd:COG4166  468 AGYSNPAYDALIEKALAATDREERVAAYRAAERILLEDAPVIPLYYYTNARLVSPYVKG-WVYDPLGVDFKAAYIE 542
PBP2_NikA_DppA_OppA_like_9 cd08496
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
32-496 3.48e-106

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: 324.68  E-value: 3.48e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  32 VAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKA 111
Cdd:cd08496    4 IATSADPTSWDPAQGGSGADHDYLWLLYDTLIKLDPDGKLEPGLAESWEYNADGTTLTLHLREGLTFSDGTPLDAAAVKA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 112 NLDRASDPANhlKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKeIGFHPVGTGPYELD 191
Cdd:cd08496   84 NLDRGKSTGG--SQVKQLASISSVEVVDDTTVTLTLSQPDPAIPALLSDRAGMIVSPTALEDDGK-LATNPVGAGPYVLT 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 192 TWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELmaSPSIMQRYI 271
Cdd:cd08496  161 EWVPNSKYVFERNEDYWDAANPHLDKLELSVIPDPTARVNALQSGQVDFAQLLAAQVKIARAAGLDVVV--EPTLAATLL 238
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 272 SMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPP-SIAYAQSY-KPWPYDPVKARELLKEAGYPNGFST 349
Cdd:cd08496  239 LLNITGAPFDDPKVRQAINYAIDRKAFVDALLFGLGEPASQPFPPgSWAYDPSLeNTYPYDPEKAKELLAEAGYPNGFSL 318
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 350 TLWSshNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGVRMFYTGWSASTGeadwalsplfASQNW 429
Cdd:cd08496  319 TIPT--GAQNADTLAEIVQQQLAKVGIKVTIKPLTGANAAGEFFAAEKFDLAVSGWVGRPDPSMT----------LSNMF 386
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446012281 430 PPTL-FNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08496  387 GKGGyYNPGKATDPELSALLKEVRATLDDPARKTALRAANKVVVEQAWFVPLFFQPSVYALSKKVSGL 454
PBP2_NikA_DppA_OppA_like_10 cd08515
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-480 1.40e-98

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: 305.29  E-value: 1.40e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKE-MKLKNVLAESYTVSDDgITYTVKLREGIKFQDGTDFNAA 107
Cdd:cd08515    3 TLVIAVQKEPPTLDPYYNTSREGVIISRNIFDTLIYRDPDtGELVPGLATSWKWIDD-TTLEFTLREGVKFHDGSPMTAE 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVKANLDRASDPANHLKRY-NLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEiGFH--PVG 184
Cdd:cd08515   82 DVVFTFNRVRDPDSKAPRGrQNFNWLDKVEKVDPYTVRIVTKKPDPAALERLAGLVGPIVPKAYYEKVGPE-GFAlkPVG 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 185 TGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELmASP 264
Cdd:cd08515  161 TGPYKVTEFVPGERVVLEAFDDYWG-GKPPIEKITFRVIPDVSTRVAELLSGGVDIITNVPPDQAERLKSSPGLTV-VGG 238
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 265 SIMQ-RYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYAT-PATGVVPPSIAYAQSYKP-WPYDPVKARELLKEA 341
Cdd:cd08515  239 PTMRiGFITFDAAGPPLKDVRVRQALNHAIDRQAIVKALWGGRAKvPNTACQPPQFGCEFDVDTkYPYDPEKAKALLAEA 318
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 342 GYPNGFSTTLWSSHNHSTAQK-VLQFTQQQLAQVGIKAQVTaMDAGQRAAEVEGKGQKEsgVRMFYTGWSASTGeadwaL 420
Cdd:cd08515  319 GYPDGFEIDYYAYRGYYPNDRpVAEAIVGMWKAVGINAELN-VLSKYRALRAWSKGGLF--VPAFFYTWGSNGI-----N 390
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 421 SPLFASQNWpptlfntAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:cd08515  391 DASASTSTW-------FKARDAEFDELLEKAETTTDPAKRKAAYKKALKIIAEEAYWTPL 443
PBP2_NikA_DppA_OppA_like_17 cd08503
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-496 1.65e-98

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: 304.88  E-value: 1.65e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd08503    9 VAVPGGSTADTLDPHTADSSADYVRGFALYEYLVEIDPDGTLVPDLAESWEPNDDATTWTFKLRKGVTFHDGKPLTADDV 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPatamISPAALEKYGKEIGFHPVGTGPYE 189
Cdd:cd08503   89 VASLNRHRDPASGSPAKTGLLDVGAIEAVDDHTVRFTLKRPNADFPYLLSDY----HFPIVPAGDGGDDFKNPIGTGPFK 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 190 LDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQR 269
Cdd:cd08503  165 LESFEPGVRAVLERNPDYWKPGRPYLDRIEFIDIPDPAARVNALLSGQVDVINQVDPKTADLLKRNPGVRVLRSPTGTHY 244
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 270 YISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGV-VPPSIAYAQSYKPWPYDPVKARELLKEAGYPNgFS 348
Cdd:cd08503  245 TFVMRTDTAPFDDPRVRRALKLAVDREALVETVLLGYGTVGNDHpVAPIPPYYADLPQREYDPDKAKALLAEAGLPD-LE 323
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 349 TTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQkesgvrmFYTGWSASTGEADWALSPLFASQ- 427
Cdd:cd08503  324 VELVTSDAAPGAVDAAVLFAEQAAQAGININVKRVPADGYWSDVWMKKP-------FSATYWGGRPTGDQMLSLAYRSGa 396
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 428 NWpptlfNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESP-WIPlVVEKLVSAHSKNLTGF 496
Cdd:cd08503  397 PW-----NETHWANPEFDALLDAARAELDEAKRKELYAEMQQILHDEGGiIIP-YFRSYLDAHSDKVKGY 460
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
28-509 8.78e-97

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: 301.78  E-value: 8.78e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  28 KDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTdfnaa 107
Cdd:cd08504    1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDGKIVPGLAESWEVSDDGLTYTFHLRKDAKWSNGD----- 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVKAN-----LDRASDPANHLKRYNLYKNIAKTE---------------AIDPTTVKITLKQPFSAFINILAHPATAMIS 167
Cdd:cd08504   76 PVTAQdfvysWRRALDPKTASPYAYLLYPIKNAEainagkkppdelgvkALDDYTLEVTLEKPTPYFLSLLAHPTFFPVN 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 168 PAALEKYGKEIGFHP---VGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPI 244
Cdd:cd08504  156 QKFVEKYGGKYGTSPeniVYNGPFKLKEWTPNDKIVLVKNPNYWDAKNVKLDKINFLVIKDPNTALNLFEAGELDIAGLP 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 245 PYEQATLLEKNKNIELMASPSIMqrYISMNVTQKPFDNPKVREALNYAINRPALVK--VAFAGYATPATGVVPPSIA--- 319
Cdd:cd08504  236 PEQVILKLKNNKDLKSTPYLGTY--YLEFNTKKPPLDNKRVRKALSLAIDREALVEkvLGDAGGFVPAGLFVPPGTGgdf 313
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 320 YAQSYKPWPYDPVKARELLKEAGYPNGFST---TLWSShNHSTAQKVLQFTQQQLAQV-GIKAQVTAMDAGQRAAEVEgK 395
Cdd:cd08504  314 RDEAGKLLEYNPEKAKKLLAEAGYELGKNPlklTLLYN-TSENHKKIAEAIQQMWKKNlGVKVTLKNVEWKVFLDRRR-K 391
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 396 GQKEsgvrMFYTGWSastgeADWA-----LSpLFASQNWpptlFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDI 470
Cdd:cd08504  392 GDFD----IARSGWG-----ADYNdpstfLD-LFTSGSG----NNYGGYSNPEYDKLLAKAATETDPEKRWELLAKAEKI 457
                        490       500       510
                 ....*....|....*....|....*....|....*....
gi 446012281 471 IWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFEDA 509
Cdd:cd08504  458 LLDDAPIIPLYQYVTAYLVKPKVKGLVYNPLGGYDFKYA 496
PBP2_NikA_DppA_OppA_like_13 cd08517
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-493 2.29e-95

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: 297.54  E-value: 2.29e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd08517    4 LNVVVQPEPPSLNPALKSDGPTQLISGKIFEGLLRYDFDLNPQPDLATSWEVSEDGLTYTFKLRPGVKWHDGKPFTSADV 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASdpANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAhPATAMISPAALekY-GKEI-----GFHPV 183
Cdd:cd08517   84 KFSIDTLK--EEHPRRRRTFANVESIETPDDLTVVFKLKKPAPALLSALS-WGESPIVPKHI--YeGTDIltnpaNNAPI 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 184 GTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFA--FPIPYEQATLLEKNKNI--- 258
Cdd:cd08517  159 GTGPFKFVEWVRGSHIILERNPDYWDKGKPYLDRIVFRIIPDAAARAAAFETGEVDVLpfGPVPLSDIPRLKALPNLvvt 238
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 259 ----ELMASPSimqrYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIA--YAQSYKPWPYDPV 332
Cdd:cd08517  239 tkgyEYFSPRS----YLEFNLRNPPLKDVRVRQAIAHAIDRQFIVDTVFFGYGKPATGPISPSLPffYDDDVPTYPFDVA 314
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 333 KARELLKEAGYPNG-----FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGqraaevegkgqkesgvrmfyt 407
Cdd:cd08517  315 KAEALLDEAGYPRGadgirFKLRLDPLPYGEFWKRTAEYVKQALKEVGIDVELRSQDFA--------------------- 373
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 408 GWSASTGE-ADWALSPLFASQNWPPTL-----------------FNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQD 469
Cdd:cd08517  374 TWLKRVYTdRDFDLAMNGGYQGGDPAVgvqrlywsgnikkgvpfSNASGYSNPEVDALLEKAAVETDPAKRKALYKEFQK 453
                        490       500
                 ....*....|....*....|....
gi 446012281 470 IIWQESPWIPLVVEKLVSAHSKNL 493
Cdd:cd08517  454 ILAEDLPIIPLVELGFPTVYRKRV 477
PBP2_NikA_DppA_OppA_like_16 cd08502
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-496 8.84e-95

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: 295.64  E-value: 8.84e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08502    1 TLRVVPQADLRTLDPIVTTAYITRNHGYMIYDTLFGMDANGEPQPQMAESWEVSDDGKTYTFTLRDGLKFHDGSPVTAAD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDR--ASDPANHlkryNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPAT--AMISPAAL-EKYGKEIGFHPV 183
Cdd:cd08502   81 VVASLKRwaKRDAMGQ----ALMAAVESLEAVDDKTVVITLKEPFGLLLDALAKPSSqpAFIMPKRIaATPPDKQITEYI 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 184 GTGPYELDTWNQTDFVKVKKFAGYwQP------GL-----PKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLL 252
Cdd:cd08502  157 GSGPFKFVEWEPDQYVVYEKFADY-VPrkeppsGLaggkvVYVDRVEFIVVPDANTAVAALQSGEIDFAEQPPADLLPTL 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 253 EKNKNIELmaSPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAF--AGYATPATGVVPPSIAY---AQSYKPW 327
Cdd:cd08502  236 KADPVVVL--KPLGGQGVLRFNHLQPPFDNPKIRRAVLAALDQEDLLAAAVgdPDFYKVCGSMFPCGTPWyseAGKEGYN 313
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 328 PYDPVKARELLKEAGYpNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAgqrAAEVEGKGQKESGVRMFYT 407
Cdd:cd08502  314 KPDLEKAKKLLKEAGY-DGEPIVILTPTDYAYLYNAALVAAQQLKAAGFNVDLQVMDW---ATLVQRRAKPDGGWNIFIT 389
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 408 GWSASTGEADWALSPLFASQNWPptlfntAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVS 487
Cdd:cd08502  390 SWSGLDLLNPLLNTGLNAGKAWF------GWPDDPEIEALRAAFIAATDPAERKALAAEIQKRAYEDVPYIPLGQFTQPT 463

                 ....*....
gi 446012281 488 AHSKNLTGF 496
Cdd:cd08502  464 AYRSKLEGL 472
PBP2_NikA_DppA_OppA_like_6 cd08494
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-496 1.36e-92

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: 289.14  E-value: 1.36e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPY-DANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAA 107
Cdd:cd08494    1 TLTIGLTLEPTSLDITtTAGAAIDQVLLGNVYETLVRRDEDGKVQPGLAESWTISDDGLTYTFTLRSGVTFHDGTPFDAA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKeigfHPVGTGP 187
Cdd:cd08494   81 DVKFSLQRARAPDSTNADKALLAAIASVEAPDAHTVVVTLKHPDPSLLFNLGGRAGVVVDPASAADLAT----KPVGTGP 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 188 YELDTWNQTDFVKVKKFAGYWQPGlPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIM 267
Cdd:cd08494  157 FTVAAWARGSSITLVRNDDYWGAK-PKLDKVTFRYFSDPTALTNALLAGDIDAAPPFDAPELEQFADDPRFTVLVGTTTG 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 268 QRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATG-VVPPSIAYAQSYKPWPYDPVKARELLKEAGYPNG 346
Cdd:cd08494  236 KVLLAMNNARAPFDDVRVRQAIRYAIDRKALIDAAWDGYGTPIGGpISPLDPGYVDLTGLYPYDPDKARQLLAEAGAAYG 315
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 347 FSTTLwSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQkesgvrmfYTGWSASTGEADwaLSPLFAS 426
Cdd:cd08494  316 LTLTL-TLPPLPYARRIGEIIASQLAEVGITVKIEVVEPATWLQRVYKGKD--------YDLTLIAHVEPD--DIGIFAD 384
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 427 qnwPPTLFNtafYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08494  385 ---PDYYFG---YDNPEFQELYAQALAATDADERAELLKQAQRTLAEDAAADWLYTRPNIVVARKGVTGY 448
PBP2_thermophilic_Hb8_like cd08513
The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like ...
30-496 2.04e-92

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 [Multi-domain]  Cd Length: 482  Bit Score: 289.95  E-value: 2.04e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAV 109
Cdd:cd08513    2 LVIGLSQEPTTLNPLLASGATDAEAAQLLFEPLARIDPDGSLVPVLAEEIPTSENGLSVTFTLRPGVKWSDGTPVTADDV 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 110 KANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQP--FSAFINIlahpaTAMISPA-ALEKY-GKEIG-----F 180
Cdd:cd08513   82 VFTWELIKAPGVSAAYAAGYDNIASVEAVDDYTVTVTLKKPtpYAPFLFL-----TFPILPAhLLEGYsGAAARqanfnL 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 181 HPVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPY---EQATLLEKNKN 257
Cdd:cd08513  157 APVGTGPYKLEEFVPGDSIELVRNPNYWG-GKPYIDRVVLKGVPDTDAARAALRSGEIDLAWLPGAkdlQQEALLSPGYN 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 258 IELMASPSImqRYISMNVT-QKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPP-SIAYAQSYKPWPYDPVKAR 335
Cdd:cd08513  236 VVVAPGSGY--EYLAFNLTnHPILADVRVRQALAYAIDRDAIVKTLYGGKATPAPTPVPPgSWADDPLVPAYEYDPEKAK 313
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 336 ELLKEAGY---PNG---------FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKEsgvr 403
Cdd:cd08513  314 QLLDEAGWklgPDGgirekdgtpLSFTLLTTSGNAVRERVAELIQQQLAKIGIDVEIENVPASVFFSDDPGNRKFD---- 389
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 404 MFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVE 483
Cdd:cd08513  390 LALFGWGLGSDPDLSPLFHSCASPANGWGGQNFGGYSNPEADELLDAARTELDPEERKALYIRYQDLLAEDLPVIPLYFR 469
                        490
                 ....*....|...
gi 446012281 484 KLVSAHSKNLTGF 496
Cdd:cd08513  470 NQVSAYKKNLKGV 482
PBP2_NikA cd08489
The substrate-binding component of an ABC-type nickel import system contains the type 2 ...
30-496 2.76e-91

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: 287.20  E-value: 2.76e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANdtlSQAVAKS-FYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08489    2 LTYAWPKDIGDLNPHLYS---NQMFAQNmVYEPLVKYGEDGKIEPWLAESWEISEDGKTYTFHLRKGVKFSDGTPFNAEA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRAsdPANhLKRYN---LYKNIAKTEAIDPTTVKITLKQPFSAFINILAHP-ATAMISPAALEKYGKEIGF-HPV 183
Cdd:cd08489   79 VKKNFDAV--LAN-RDRHSwleLVNKIDSVEVVDEYTVRLHLKEPYYPTLNELALVrPFRFLSPKAFPDGGTKGGVkKPI 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 184 GTGPYELDTWNQTDFVKVKKFAGYWQPGlPKLDSITWRPVADNNTRAAMLQTGEAQFAF---PIPYEQATLLEKNKNIEL 260
Cdd:cd08489  156 GTGPWVLAEYKKGEYAVFVRNPNYWGEK-PKIDKITVKVIPDAQTRLLALQSGEIDLIYgadGISADAFKQLKKDKGYGT 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 261 MASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQ-SYKPWPYDPVKARELLK 339
Cdd:cd08489  235 AVSEPTSTRFLALNTASEPLSDLKVREAINYAIDKEAISKGILYGLEKPADTLFAPNVPYADiDLKPYSYDPEKANALLD 314
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 340 EAGY--PNG----------------FSTTlwsshnhSTAQKVL-QFTQQQLAQVGIKAQVTAMD-AGQRAAEVEGKGQke 399
Cdd:cd08489  315 EAGWtlNEGdgirekdgkplslelvYQTD-------NALQKSIaEYLQSELKKIGIDLNIIGEEeQAYYDRQKDGDFD-- 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 400 sgvRMFYTGWSASTGEADWaLSPLFASQNWPPtlFNTAFYSNK-QVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWI 478
Cdd:cd08489  386 ---LIFYRTWGAPYDPHSF-LSSMRVPSHADY--QAQVGLANKaELDALINEVLATTDEEKRQELYDEILTTLHDQAVYI 459
                        490
                 ....*....|....*...
gi 446012281 479 PLVVEKLVSAHSKNLTGF 496
Cdd:cd08489  460 PLTYPRNKAVYNPKVKGV 477
PBP2_AppA_like cd08514
The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus ...
29-496 1.06e-89

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: 282.97  E-value: 1.06e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08514    1 TLVLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDKDLNFEPDLAESWEVSDDGKTYTFKLRKDVKWHDGEPLTADD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPAN---HLKRYnlYKNIAKTEAIDPTTVKITLKQPFSAFINILAHpatAMISPAALEKYGKEIGFH---- 181
Cdd:cd08514   81 VKFTYKAIADPKYagpRASGD--YDEIKGVEVPDDYTVVFHYKEPYAPALESWAL---NGILPKHLLEDVPIADFRhspf 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 182 ---PVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGE---AQFAFPIPYEQATLLEKN 255
Cdd:cd08514  156 nrnPVGTGPYKLKEWKRGQYIVLEANPDYFL-GRPYIDKIVFRIIPDPTTALLELKAGEldiVELPPPQYDRQTEDKAFD 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 256 KNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPP-SIAYAQSYKPWPYDPVKA 334
Cdd:cd08514  235 KKINIYEYPSFSYTYLGWNLKRPLFQDKRVRQAITYAIDREEIIDGLLLGLGEVANGPFSPgTWAYNPDLKPYPYDPDKA 314
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 335 RELLKEAGY----------PNG--FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKgQKEsgv 402
Cdd:cd08514  315 KELLAEAGWvdgdddgildKDGkpFSFTLLTNQGNPVREQAATIIQQQLKEIGIDVKIRVLEWAAFLEKVDDK-DFD--- 390
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 403 rMFYTGWSASTgEADwaLSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVV 482
Cdd:cd08514  391 -AVLLGWSLGP-DPD--PYDIWHSSGAKPGGFNFVGYKNPEVDKLIEKARSTLDREKRAEIYHEWQEILAEDQPYTFLYA 466
                        490
                 ....*....|....
gi 446012281 483 EKLVSAHSKNLTGF 496
Cdd:cd08514  467 PNSLYAVNKRLKGI 480
PBP2_NikA_DppA_OppA_like_19 cd08518
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-495 1.24e-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: 173883 [Multi-domain]  Cd Length: 464  Bit Score: 279.47  E-value: 1.24e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTT-LDPYDANDTLSQAVaksFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAA 108
Cdd:cd08518    3 LVLAVGSEPETgFNPLLGWGEHGEPL---IFSGLLKRDENLNLVPDLATSYKVSDDGLTWTFTLRDDVKFSDGEPLTAED 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 109 VKANLDRASDPANHLKRYNLYKNIaktEAIDPTTVKITLKQPFSAFINILAHPAtamISPAALEKYGKEIGFHPVGTGPY 188
Cdd:cd08518   80 VAFTYNTAKDPGSASDILSNLEDV---EAVDDYTVKFTLKKPDSTFLDKLASLG---IVPKHAYENTDTYNQNPIGTGPY 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 189 ELDTWNQTDFVKVKKFAGYWqPGLPKLDSITWRPVADnNTRAAMLQTGEAQFAFpIPYEQATllEKNKNIELMASPSIMQ 268
Cdd:cd08518  154 KLVQWDKGQQVIFEANPDYY-GGKPKFKKLTFLFLPD-DAAAAALKSGEVDLAL-IPPSLAK--QGVDGYKLYSIKSADY 228
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 269 RYISMNV---TQKPFDN-----PKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKE 340
Cdd:cd08518  229 RGISLPFvpaTGKKIGNnvtsdPAIRKALNYAIDRQAIVDGVLNGYGTPAYSPPDGLPWGNPDAAIYDYDPEKAKKILEE 308
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 341 AG---------YPNG--FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDagqrAAEVEGKGQKESgvrmFYTGW 409
Cdd:cd08518  309 AGwkdgddggrEKDGqkAEFTLYYPSGDQVRQDLAVAVASQAKKLGIEVKLEGKS----WDEIDPRMHDNA----VLLGW 380
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 410 -SASTGEADWALSPLFASQNWpptlFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSA 488
Cdd:cd08518  381 gSPDDTELYSLYHSSLAGGGY----NNPGHYSNPEVDAYLDKARTSTDPEERKKYWKKAQWDGAEDPPWLWLVNIDHLYV 456

                 ....*..
gi 446012281 489 HSKNLTG 495
Cdd:cd08518  457 VNDGLDG 463
PBP2_NikA_DppA_OppA_like_20 cd08519
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-495 1.31e-85

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: 271.80  E-value: 1.31e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEM-KLKNVLAESY-TVSDDGITYTVKLREGIKFQDGTDFNAA 107
Cdd:cd08519    2 IVVGTTDKVRTLDPAGAYDLGSWQLLSNLGDTLYTYEPGTtELVPDLATSLpFVSDDGLTYTIPLRQGVKFHDGTPFTAK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVKANLDR----ASDPAnhlkrYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKY-GKEIGFHP 182
Cdd:cd08519   82 AVKFSLDRfikiGGGPA-----SLLADRVESVEAPDDYTVTFRLKKPFATFPALLATPALTPVSPKAYPADaDLFLPNTF 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 183 VGTGPYELDTWnQTDFVKVKKFAGYWqpGL-PKLDSITWRPVADNNTRAAMLQTGEAQFAFP--IPYEQATL-LEKNKNI 258
Cdd:cd08519  157 VGTGPYKLKSF-RSESIRLEPNPDYW--GEkPKNDGVDIRFYSDSSNLFLALQTGEIDVAYRslSPEDIADLlLAKDGDL 233
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 259 ELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAyaqSYKPWP------YDPV 332
Cdd:cd08519  234 QVVEGPGGEIRYIVFNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYGTAEPLYSLVPTGFW---GHKPVFkekygdPNVE 310
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 333 KARELLKEAGY--PNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVG-IKAQVTAMDAGQ-RAAEVEGKGQkesgvrMFYTG 408
Cdd:cd08519  311 KARQLLQQAGYsaENPLKLELWYRSNHPADKLEAATLKAQLEADGlFKVNLKSVEWTTyYKQLSKGAYP------VYLLG 384
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 409 WSASTGEADWALSPLFASQNwppTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSA 488
Cdd:cd08519  385 WYPDYPDPDNYLTPFLSCGN---GVFLGSFYSNPKVNQLIDKSRTELDPAARLKILAEIQDILAEDVPYIPLWQGKQYAV 461

                 ....*..
gi 446012281 489 HSKNLTG 495
Cdd:cd08519  462 AQKNVKG 468
PBP2_clavulanate_OppA2 cd08506
The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis ...
30-496 6.50e-76

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: 246.40  E-value: 6.50e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFG-----LDKEMKLKNVLAESY-TVSDDGITYTVKLREGIKFQDGTD 103
Cdd:cd08506    2 LRLLSSADFDHLDPARTYYADGWQVLRLIYRQLTTykpapGAEGTEVVPDLATDTgTVSDDGKTWTYTLRDGLKFEDGTP 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 104 FNAAAVKANLDRasdpanhlkrynlyknIAKTEAIDPTTVKITLKQPFSAFINILAHPATamiSPAALEK-YGKEIGFHP 182
Cdd:cd08506   82 ITAKDVKYGIER----------------SFAIETPDDKTIVFHLNRPDSDFPYLLALPAA---APVPAEKdTKADYGRAP 142
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 183 VGTGPYEL---DTWNQTDFVKVKkfagYWQP-----GLPKLDSITWRPVADNNTRAAMLQTGEAQFAF---PIPYEQATL 251
Cdd:cd08506  143 VSSGPYKIesyDPGKGLVLVRNP----HWDAetdpiRDAYPDKIVVTFGLDPETIDQRLQAGDADLALdgdGVPRAPAAE 218
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 252 LEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKvAFAG--YATPATGVVPPSIAYAQSYKPWP- 328
Cdd:cd08506  219 LVEELKARLHNVPGGGVYYLAINTNVPPFDDVKVRQAVAYAVDRAALVR-AFGGpaGGEPATTILPPGIPGYEDYDPYPt 297
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 329 ----YDPVKARELLKEAGYPnGFSTTLWSShNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGvrM 404
Cdd:cd08506  298 kgpkGDPDKAKELLAEAGVP-GLKLTLAYR-DTAVDKKIAEALQASLARAGIDVTLKPIDSATYYDTIANPDGAAYD--L 373
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 405 FYTGWSAstgeaDWA-----LSPLFASQNWPPTL-FNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWI 478
Cdd:cd08506  374 FITGWGP-----DWPsastfLPPLFDGDAIGPGGnSNYSGYDDPEVNALIDEALATTDPAEAAALWAELDRQIMEDAPIV 448
                        490
                 ....*....|....*...
gi 446012281 479 PLVVEKLVSAHSKNLTGF 496
Cdd:cd08506  449 PLVYPKALDLRSSRVTNY 466
PBP2_NikA_DppA_OppA_like_1 cd08508
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
39-493 2.92e-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: 173873  Cd Length: 470  Bit Score: 242.29  E-value: 2.92e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  39 TTLDPYDANDTLSQAVAKSFYQGLF----GLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGT-DFNAAAVKANL 113
Cdd:cd08508   12 RTLDPHFATGTTDKGVISWVFNGLVrfppGSADPYEIEPDLAESWESSDDPLTWTFKLRKGVMFHGGYgEVTAEDVVFSL 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 114 DRASDPANHLKRyNLYKNIAKTEAIDPTTVKITLKQPFSAFINILA-HPATAMISPAALEKYGKEIGFHPVGTGPYELDT 192
Cdd:cd08508   92 ERAADPKRSSFS-ADFAALKEVEAHDPYTVRITLSRPVPSFLGLVSnYHSGLIVSKKAVEKLGEQFGRKPVGTGPFEVEE 170
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 193 WNQTDFVKVKKFAGYWQpGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFpIPYEQATLLEKNKNIELMASPSIMQRYI- 271
Cdd:cd08508  171 HSPQQGVTLVANDGYFR-GAPKLERINYRFIPNDASRELAFESGEIDMTQ-GKRDQRWVQRREANDGVVVDVFEPAEFRt 248
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 272 -SMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIA-YAQSYKPWPYDPVKARELLKEAGYPNGFST 349
Cdd:cd08508  249 lGLNITKPPLDDLKVRQAIAAAVNVDEVVEFVGAGVAQPGNSVIPPGLLgEDADAPVYPYDPAKAKALLAEAGFPNGLTL 328
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 350 TLWSSHNhSTAQKVLQFTQQQLAQVGIKAQVTAMDagqrAAEVEGKGQKESGVRMFYTgwSASTGEADWALSPLF--ASQ 427
Cdd:cd08508  329 TFLVSPA-AGQQSIMQVVQAQLAEAGINLEIDVVE----HATFHAQIRKDLSAIVLYG--AARFPIADSYLTEFYdsASI 401
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446012281 428 NWPPTlFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNL 493
Cdd:cd08508  402 IGAPT-AVTNFSHCPVADKRIEAARVEPDPESRSALWKEAQKKIDEDVCAIPLTNLVQAWARKPAL 466
PBP2_TmCBP_oligosaccharides_like cd08509
The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains ...
43-481 1.45e-67

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: 226.05  E-value: 1.45e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  43 PYDANDTLSQAVAKSFYQGLFGLD-KEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLD-RASDPA 120
Cdd:cd08509   18 PYAPGGASTAGLVQLIYEPLAIYNpLTGEFIPWLAESWTWSDDFTTLTVTLRKGVKWSDGEPFTADDVVFTFElLKKYPA 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 121 nhLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFI-NILAHPATAMISP-----AALEKYGKEIGFHPVGTGPYELDTWN 194
Cdd:cd08509   98 --LDYSGFWYYVESVEAVDDYTVVFTFKKPSPTEAfYFLYTLGLVPIVPkhvweKVDDPLITFTNEPPVGTGPYTLKSFS 175
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 195 QTDFVkVKKFAGYWQP-GLPKLDSITWRPVADNNTRAAMLQTGEAQFAFP-IPYEQATLLEKNKNIELMASPSIMQRYIS 272
Cdd:cd08509  176 PQWIV-LERNPNYWGAfGKPKPDYVVYPAYSSNDQALLALANGEVDWAGLfIPDIQKTVLKDPENNKYWYFPYGGTVGLY 254
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 273 MNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPP-----------SIAYAQSYKPWPYDPVKARELLKEA 341
Cdd:cd08509  255 FNTKKYPFNDPEVRKALALAIDRTAIVKIAGYGYATPAPLPGPPykvpldpsgiaKYFGSFGLGWYKYDPDKAKKLLESA 334
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 342 GY----------PNG--FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGVrmfYTGW 409
Cdd:cd08509  335 GFkkdkdgkwytPDGtpLKFTIIVPSGWTDWMAAAQIIAEQLKEFGIDVTVKTPDFGTYWAALTKGDFDTFDA---ATPW 411
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446012281 410 SASTGEADWALSPLFAS---QNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLV 481
Cdd:cd08509  412 GGPGPTPLGYYNSAFDPpngGPGGSAAGNFGRWKNPELDELIDELNKTTDEAEQKELGNELQKIFAEEMPVIPLF 486
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
24-493 1.22e-60

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: 207.35  E-value: 1.22e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   24 AFAAKDVVVAVGSNFTTLDPYDANDtlSQAVAKSF-YQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGT 102
Cdd:TIGR02294   2 KKENKQLTYAWPVDIGPMNPHVYNP--NQMFAQSMvYEPLVRYTADGKIEPWLAKSWTVSEDGKTYTFKLRDDVKFSDGT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  103 DFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHP-ATAMISPAALE-KYGKEIGF 180
Cdd:TIGR02294  80 PFDAEAVKKNFDAVLQNSQRHSWLELSNQLDNVKALDKYTFELVLKEAYYPALQELAMPrPYRFLSPSDFKnDTTKDGVK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  181 HPVGTGPYELDTWNQTDFVKVKKFAGYWQPGlPKLDSITWRPVADNNTRAAMLQTGEAQFAF----PIPYEQATLLEKNK 256
Cdd:TIGR02294 160 KPIGTGPWMLGESKQDEYAVFVRNENYWGEK-PKLKKVTVKVIPDAETRALAFESGEVDLIFgnegSIDLDTFAQLKDDG 238
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  257 NIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQ-SYKPWPYDPVKAR 335
Cdd:TIGR02294 239 DYQTALSQPMNTRMLLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPADTLFAKNVPYADiDLKPYKYDVKKAN 318
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  336 ELLKEAGY----------PNGFSTTLWSSHNHSTA-QKVL-QFTQQQLAQVGIKAQVTAMDAGQRAAevegkgQKESGV- 402
Cdd:TIGR02294 319 ALLDEAGWklgkgkdvreKDGKPLELELYYDKTSAlQKSLaEYLQAEWRKIGIKLSLIGEEEDKIAA------RRRDGDf 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  403 -RMFYTGWSASTGEADWALSplFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLV 481
Cdd:TIGR02294 393 dMMFNYTWGAPYDPHSFISA--MRAKGHGDESAQSGLANKDEIDKSIGDALASTDETERQELYKNILTTLHDEAVYIPIS 470
                         490
                  ....*....|..
gi 446012281  482 VEKLVSAHSKNL 493
Cdd:TIGR02294 471 YISMTVVYRKDL 482
PBP2_NikA_DppA_OppA_like_12 cd08491
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-467 4.05e-56

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: 194.52  E-value: 4.05e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDT-LSQAVAKSFYQGLFGLDKEM-KLKNVLAESYTVSDDgITYTVKLREGIKFQDGTDFNA 106
Cdd:cd08491    1 DVTIVLPEEPDSLEPCDSSRTaVGRVIRSNVTEPLTEIDPESgTVGPRLATEWEQVDD-NTWRFKLRPGVKFHDGTPFDA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 107 AAVKANLDRASDPANHLKRYNLYKNIAK--TEAIDPTTVKITLKQPfsafINIL-AHPATAMISPAALEKygKEIGFHPV 183
Cdd:cd08491   80 EAVAFSIERSMNGKLTCETRGYYFGDAKltVKAVDDYTVEIKTDEP----DPILpLLLSYVDVVSPNTPT--DKKVRDPI 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 184 GTGPYELDTWNQTDFVKVKKFAGYW--QPGLPKLDSItWRpvADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNknielM 261
Cdd:cd08491  154 GTGPYKFDSWEPGQSIVLSRFDGYWgeKPEVTKATYV-WR--SESSVRAAMVETGEADLAPSIAVQDATNPDTD-----F 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 262 ASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSI-AYAQSYKPWPYDPVKARELLKE 340
Cdd:cd08491  226 AYLNSETTALRIDAQIPPLDDVRVRKALNLAIDRDGIVGALFGGQGRPATQLVVPGInGHNPDLKPWPYDPEKAKALVAE 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 341 A---GYPNGFSTTLWS-SHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAG-----QRAAEVEGkgqkeSGVRMFYTGWSA 411
Cdd:cd08491  306 AkadGVPVDTEITLIGrNGQFPNATEVMEAIQAMLQQVGLNVKLRMLEVAdwlryLRKPFPED-----RGPTLLQSQHDN 380
                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446012281 412 STGEADWALsPLFASQNWPPTLFNtafysNKQVDDFLAQALKTNDpAEKTRLYKAA 467
Cdd:cd08491  381 NSGDASFTF-PVYYLSEGSQSTFG-----DPELDALIKAAMAATG-DERAKLFQEI 429
PBP2_NikA_DppA_OppA_like_21 cd08520
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
75-496 4.95e-56

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: 194.08  E-value: 4.95e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  75 LAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLyKNIAKTEAIDPTTVKITLKQPFSAF 154
Cdd:cd08520   48 LAESWEVSEDGLTYTFHLREGAKWHDGEPLTAEDVAFTFDYMKKHPYVWVDIEL-SIIERVEALDDYTVKITLKRPYAPF 126
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 155 INILAhpATAMISP-------AALEKYGKEIGFhpVGTGPYELdtwnqTDFVKVK------KFAGYWQPGlPKLDSITWR 221
Cdd:cd08520  127 LEKIA--TTVPILPkhiwekvEDPEKFTGPEAA--IGSGPYKL-----VDYNKEQgtylyeANEDYWGGK-PKVKRLEFV 196
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 222 PVADNntrAAMLQTGEAQFAfPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKV 301
Cdd:cd08520  197 PVSDA---LLALENGEVDAI-SILPDTLAALENNKGFKVIEGPGFWVYRLMFNHDKNPFSDKEFRQAIAYAIDRQELVEK 272
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 302 AFAGYATPA-TGVVPP-SIAYAQSYKPWPYDPVKARELLKEAGY----PNGFSTTLWSSHNHSTAQ-----KVLQFTQQQ 370
Cdd:cd08520  273 AARGAAALGsPGYLPPdSPWYNPNVPKYPYDPEKAKELLKGLGYtdngGDGEKDGEPLSLELLTSSsgdevRVAELIKEQ 352
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 371 LAQVGIKAQVTAMDAGQRAAEVegkgqKESGVRMFYTGWSASTGEADwALSPLFASQnwppTLFNTAFYSNKQVDDFLAQ 450
Cdd:cd08520  353 LERVGIKVNVKSLESKTLDSAV-----KDGDYDLAISGHGGIGGDPD-ILREVYSSN----TKKSARGYDNEELNALLRQ 422
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 446012281 451 ALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08520  423 QLQEMDPEKRKELVFEIQELYAEELPMIPLYYPTMYTVHRGKYDGW 468
PBP2_NikA_DppA_OppA_like_4 cd08500
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-496 3.25e-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: 192.84  E-value: 3.25e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  29 DVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKE-MKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAA 107
Cdd:cd08500    8 TPYESVGQYGGTLNPALADEWGSRDIIGLGYAGLVRYDPDtGELVPNLAESWEVSEDGREFTFKLREGLKWSDGQPFTAD 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 108 AVK-------ANLDRASDPANHLKRYNlyKNIaKTEAIDPTTVKITLKQPFSAFInilahpatAMISPAALekygkeigf 180
Cdd:cd08500   88 DVVftyediyLNPEIPPSAPDTLLVGG--KPP-KVEKVDDYTVRFTLPAPNPLFL--------AYLAPPDI--------- 147
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 181 hpVGTGPYELDTWNQTDFVKVKKFAGYWQ-----PGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFP-IPYEQATLLEK 254
Cdd:cd08500  148 --PTLGPWKLESYTPGERVVLERNPYYWKvdtegNQLPYIDRIVYQIVEDAEAQLLKFLAGEIDLQGRhPEDLDYPLLKE 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 255 N---KNIELM-ASPSIMQRYISMNVTQKP------FDNPKVREALNYAINRPALVKVAFAGYATP-ATGVVPPSIAY-AQ 322
Cdd:cd08500  226 NeekGGYTVYnLGPATSTLFINFNLNDKDpvkrklFRDVRFRQALSLAINREEIIETVYFGLGEPqQGPVSPGSPYYyPE 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 323 SYKPW-PYDPVKARELLKEAGY-----------PNG--FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQR 388
Cdd:cd08500  306 WELKYyEYDPDKANKLLDEAGLkkkdadgfrldPDGkpVEFTLITNAGNSIREDIAELIKDDWRKIGIKVNLQPIDFNLL 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 389 AAEVEGKGQKESGV----------RMFYTGWSASTGEADWALsplfASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPA 458
Cdd:cd08500  386 VTRLSANEDWDAILlgltgggpdpALGAPVWRSGGSLHLWNQ----PYPGGGPPGGPEPPPWEKKIDDLYDKGAVELDQE 461
                        490       500       510
                 ....*....|....*....|....*....|....*...
gi 446012281 459 EKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08500  462 KRKALYAEIQKIAAENLPVIGTVGPLAPVAVKNRLGNV 499
PBP2_Lpqw cd08501
The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic ...
30-496 2.41e-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: 174.07  E-value: 2.41e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  30 VVVAVGSNFTTLDPY--DANDTLSQAVAKSFYQGLFGLDKEMKLK---NVLAESYTVSDDGITYTVKLREGIKFQDGTDF 104
Cdd:cd08501    2 LTVAIDELGPGFNPHsaAGNSTYTSALASLVLPSAFRYDPDGTDVpnpDYVGSVEVTSDDPQTVTYTINPEAQWSDGTPI 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 105 NAAA----VKANLDR--ASDPANHlKRYNLYKNIAKTEaiDPTTVKITLKQPF----SAFINILahPATAMISPAALEKY 174
Cdd:cd08501   82 TAADfeylWKAMSGEpgTYDPAST-DGYDLIESVEKGD--GGKTVVVTFKQPYadwrALFSNLL--PAHLVADEAGFFGT 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 175 GKEIGfHPVGTGPYELDTWN-QTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATL-L 252
Cdd:cd08501  157 GLDDH-PPWSAGPYKVESVDrGRGEVTLVRNDRWWGDKPPKLDKITFRAMEDPDAQINALRNGEIDAADVGPTEDTLEaL 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 253 EKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGV-----VPPSIAYAQ-SYKP 326
Cdd:cd08501  236 GLLPGVEVRTGDGPRYLHLTLNTKSPALADVAVRKAFLKAIDRDTIARIAFGGLPPEAEPPgshllLPGQAGYEDnSSAY 315
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 327 WPYDPVKARELLKEAGYPNGFST----------TLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKG 396
Cdd:cd08501  316 GKYDPEAAKKLLDDAGYTLGGDGiekdgkpltlRIAYDGDDPTAVAAAELIQDMLAKAGIKVTVVSVPSNDFSKTLLSGG 395
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 397 QkesgVRMFYTGWSASTGeadwalsPLFASQNW--PPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQE 474
Cdd:cd08501  396 D----YDAVLFGWQGTPG-------VANAGQIYgsCSESSNFSGFCDPEIDELIAEALTTTDPDEQAELLNEADKLLWEQ 464
                        490       500
                 ....*....|....*....|..
gi 446012281 475 SPWIPLVVEKLVSAHSKNLTGF 496
Cdd:cd08501  465 AYTLPLYQGPGLVAVKKGLANV 486
PRK15109 PRK15109
antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
3-480 1.63e-46

antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional


Pssm-ID: 185064  Cd Length: 547  Bit Score: 170.26  E-value: 1.63e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281   3 RAVHRSGLVALGI--ATALMASCAFAAKDV-----VVAVGSNFTTLDPYDAN-----DTLsqavAKSFYQGLFGLDK-EM 69
Cdd:PRK15109   2 RLVLSSLLVIAGLlsGQAIAAPESPPHADIrqsgfVYCVSGQVNTFNPQKASsglivDTL----AAQLYDRLLDVDPyTY 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  70 KLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDF------NAAAVKANLDRASDPANHLKRYN-----------LYKNI 132
Cdd:PRK15109  78 RLMPELAESWEVLDNGATYRFHLRRDVPFQKTDWFtptrkmNADDVVFSFQRIFDRNHPWHNVNggnypyfdslqFADNV 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 133 AKTEAIDPTTVKITLKQPFSAFINILA-HPATAMISPAA--LEKYGKE--IGFHPVGTGPYELDTWNQTDFVKVKKFAGY 207
Cdd:PRK15109 158 KSVRKLDNYTVEFRLAQPDASFLWHLAtHYASVLSAEYAakLTKEDRQeqLDRQPVGTGPFQLSEYRAGQFIRLQRHDDY 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 208 WQpGLPKLDSITWRPVADNNTRAAMLQTGEAQ-FAFPiPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVR 286
Cdd:PRK15109 238 WR-GKPLMPQVVVDLGSGGTGRLSKLLTGECDvLAYP-AASQLSILRDDPRLRLTLRPGMNIAYLAFNTRKPPLNNPAVR 315
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 287 EALNYAINRPALVKVAFAGYATPATGVVP-PSIAYAQSYKPWPYDPVKARELLKEAGYpNGFSTTLW-----SSHNHSTA 360
Cdd:PRK15109 316 HALALAINNQRLMQSIYYGTAETAASILPrASWAYDNEAKITEYNPEKSREQLKALGL-ENLTLKLWvptasQAWNPSPL 394
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 361 qKVLQFTQQQLAQVGIKaqVTAMdagqraaEVEGKGQKESGVRMFY----TGWSASTGEADWALSPLF-----ASQNwpp 431
Cdd:PRK15109 395 -KTAELIQADLAQVGVK--VVIV-------PVEGRFQEARLMDMNHdltlSGWATDSNDPDSFFRPLLscaaiRSQT--- 461
                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*....
gi 446012281 432 tlfNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:PRK15109 462 ---NYAHWCDPAFDSVLRKALSSQQLASRIEAYDEAQSILAQELPILPL 507
PBP2_NikA_DppA_OppA_like_18 cd08505
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
39-489 3.20e-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: 173870 [Multi-domain]  Cd Length: 528  Bit Score: 166.30  E-value: 3.20e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  39 TTLDPYDANDTLSQAVAKSFYQGLFG---LDKEMKLK-NVLAESYTVSD---DGITYTVKLREGIKFQDGTDFNAaaVKA 111
Cdd:cd08505   11 KGLDPAQSYDSYSAEIIEQIYEPLLQyhyLKRPYELVpNTAAAMPEVSYldvDGSVYTIRIKPGIYFQPDPAFPK--GKT 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 112 NLDRASDPANHLKRYnLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYG--------KEIGFHPV 183
Cdd:cd08505   89 RELTAEDYVYSIKRL-ADPPLEGVEAVDRYTLRIRLTGPYPQFLYWLAMPFFAPVPWEAVEFYGqpgmaeknLTLDWHPV 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 184 GTGPYELDTWNQTDFVKVKK---FAGYWQPG------------------LPKLDSITWRPVADNNTRAAMLQTGEAQF-- 240
Cdd:cd08505  168 GTGPYMLTENNPNSRMVLVRnpnYRGEVYPFegsadddqaglladagkrLPFIDRIVFSLEKEAQPRWLKFLQGYYDVsg 247
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 241 ----AFPI-----PYEQATLLE--KNKNIEL--MASPSIMqrYISMNV-------TQKpfDNPKVREALNYAINRPALVK 300
Cdd:cd08505  248 issdAFDQalrvsAGGEPELTPelAKKGIRLsrAVEPSIF--YIGFNMldpvvggYSK--EKRKLRQAISIAFDWEEYIS 323
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 301 VAFAGYATPATGVVPPSIA-YAQSY--KPWPYDPVKARELLKEAGYPNGFSTTL-------WSSHNHSTAQKVLQFTQQQ 370
Cdd:cd08505  324 IFRNGRAVPAQGPIPPGIFgYRPGEdgKPVRYDLELAKALLAEAGYPDGRDGPTgkplvlnYDTQATPDDKQRLEWWRKQ 403
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 371 LAQVGIKAQVTAMDAGQRAAEVE-GKGQkesgvrMFYTGWSASTGEADWALSpLFASQNWPPTLFNTAFYSNKQVDDFLA 449
Cdd:cd08505  404 FAKLGIQLNVRATDYNRFQDKLRkGNAQ------LFSWGWNADYPDPENFLF-LLYGPNAKSGGENAANYSNPEFDRLFE 476
                        490       500       510       520
                 ....*....|....*....|....*....|....*....|
gi 446012281 450 QALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAH 489
Cdd:cd08505  477 QMKTMPDGPERQALIDQMNRILREDAPWIFGFHPKSNGLA 516
PBP2_Lactococcal_OppA_like cd08510
The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; ...
58-496 1.90e-39

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: 150.11  E-value: 1.90e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  58 FYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRY-NLYKNI---- 132
Cdd:cd08510   35 GNEGLFDTDKNYKITDSGAAKFKLDDKAKTVTITIKDGVKWSDGKPVTAKDLEYSYEIIANKDYTGVRYtDSFKNIvgme 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 133 ------AKT----EAIDPTTVKITLKQPFSAFINILAHPatamISPAALEKYGKEIGF-----------HPVGTGPYELD 191
Cdd:cd08510  115 eyhdgkADTisgiKKIDDKTVEITFKEMSPSMLQSGNGY----FEYAEPKHYLKDVPVkklessdqvrkNPLGFGPYKVK 190
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 192 TWNQTDFVKVKKFAGYWQpGLPKLDSITWRpVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQRYI 271
Cdd:cd08510  191 KIVPGESVEYVPNEYYWR-GKPKLDKIVIK-VVSPSTIVAALKSGKYDIAESPPSQWYDQVKDLKNYKFLGQPALSYSYI 268
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 272 SMNV-------------TQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIA--YAQSYKPWPYDPVKARE 336
Cdd:cd08510  269 GFKLgkwdkkkgenvmdPNAKMADKNLRQAMAYAIDNDAVGKKFYNGLRTRANSLIPPVFKdyYDSELKGYTYDPEKAKK 348
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 337 LLKEAGY-----------PNG--FSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTamdaGQRAAE----VEGKGQKE 399
Cdd:cd08510  349 LLDEAGYkdvdgdgfredPDGkpLTINFAAMSGSETAEPIAQYYIQQWKKIGLNVELT----DGRLIEfnsfYDKLQADD 424
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 400 SGVRMFYTGWSASTgeaDWALSPLFaSQNWPptlFNTAFYSNKQVDDFLAQAL--KTNDPAEKTRLYKAAQDIIWQESPW 477
Cdd:cd08510  425 PDIDVFQGAWGTGS---DPSPSGLY-GENAP---FNYSRFVSEENTKLLDAIDseKAFDEEYRKKAYKEWQKYMNEEAPV 497
                        490
                 ....*....|....*....
gi 446012281 478 IPLVVEKLVSAHSKNLTGF 496
Cdd:cd08510  498 IPTLYRYSITPVNKRVKGY 516
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
10-495 4.95e-31

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059 [Multi-domain]  Cd Length: 543  Bit Score: 126.43  E-value: 4.95e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  10 LVALGIATALMASCAFAAKDVVVAV------------GSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAE 77
Cdd:PRK15104   9 LIAAGVLAALMAGNVALAADVPAGVqlaekqtlvrnnGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPDGHPAPGVAE 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  78 SYTvSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDP--ANHLKRYNLYKNIAKTE---------------AIDP 140
Cdd:PRK15104  89 SWD-NKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLADPktASPYASYLQYGHIANIDdiiagkkpptdlgvkAIDD 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 141 TTVKITLKQPFSAFINILAHPATAMISPAALEKYGkEIGFHP---VGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDS 217
Cdd:PRK15104 168 HTLEVTLSEPVPYFYKLLVHPSMSPVPKAAVEKFG-EKWTQPaniVTNGAYKLKDWVVNERIVLERNPTYWDNAKTVINQ 246
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 218 ITWRPVADNNTRAAMLQTGEAQFAFP-IPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRP 296
Cdd:PRK15104 247 VTYLPISSEVTDVNRYRSGEIDMTYNnMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGLDRD 326
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 297 ALV-KVAFAGyATPATGVVPPSIAYAQSYKP----WPYDP--VKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLqftqq 369
Cdd:PRK15104 327 IIVnKVKNQG-DLPAYGYTPPYTDGAKLTQPewfgWSQEKrnEEAKKLLAEAGYTADKPLTFNLLYNTSDLHKKL----- 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 370 QLAQVGIKAQVTAMDAGQRAAE----VEGKGQKESGVRMfyTGWSASTGEADWALSPLFA-SQNwpptlfNTAFYSNKQV 444
Cdd:PRK15104 401 AIAAASIWKKNLGVNVKLENQEwktfLDTRHQGTFDVAR--AGWCADYNEPTSFLNTMLSnSSN------NTAHYKSPAF 472
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446012281 445 DDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL---VVEKLVSAHSKNLTG 495
Cdd:PRK15104 473 DKLMAETLKVKDEAQRAALYQKAEQQLDKDSAIVPVyyyVNARLVKPWVGGYTG 526
PRK09755 PRK09755
ABC transporter substrate-binding protein;
40-496 3.02e-30

ABC transporter substrate-binding protein;


Pssm-ID: 182060  Cd Length: 535  Bit Score: 124.10  E-value: 3.02e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  40 TLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDP 119
Cdd:PRK09755  45 TLDPQKVEENTAAQIVLDLFEGLVWMDGEGQVQPAQAERWEILDGGKRYIFHLRSGLQWSDGQPLTAEDFVLGWQRAVDP 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 120 ------ANHLKRYNLYKNIA-----------KTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGF-- 180
Cdd:PRK09755 125 ktaspfAGYLAQAHINNAAAivagkadvtslGVKATDDRTLEVTLEQPVPWFTTMLAWPTLFPVPHHVIAKHGDSWSKpe 204
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 181 HPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFpIPYEQATLLEKNKNIEL 260
Cdd:PRK09755 205 NMVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQVEYLALDNSVTGYNRYRAGEVDLTW-VPAQQIPAIEKSLPGEL 283
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 261 MASPSIMQRYISMNVTQKPFDNPKVREALNYAINRpALVKVAFAGYATPATGVVPPSI------AYAQSYKPWPYDPVKA 334
Cdd:PRK09755 284 RIIPRLNSEYYNFNLEKPPFNDVRVRRALYLTVDR-QLIAQKVLGLRTPATTLTPPEVkgfsatTFDELQKPMSERVAMA 362
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 335 RELLKEAGY----PNGFST--TLWSSHNHSTAQKVLQFTQQQLAQVGIKAQ--VTAMDAgQRAAEVEGKGQKesgvrmfy 406
Cdd:PRK09755 363 KALLKQAGYdashPLRFELfyNKYDLHEKTAIALSSEWKKWLGAQVTLRTMewKTYLDA-RRAGDFMLSRQS-------- 433
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 407 tgWSASTGEADWALSPLFASQNWpptlfNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLV 486
Cdd:PRK09755 434 --WDATYNDASSFLNTLKSDSEE-----NVGHWKNAQYDALLNQATQITDATKRNALYQQAEVIINQQAPLIPIYYQPLI 506
                        490
                 ....*....|
gi 446012281 487 SAHSKNLTGF 496
Cdd:PRK09755 507 KLLKPYVGGF 516
MbnE-like cd08497
Methanobactin MbnE, a periplasmic binding protein of the TonB-dependent transport system, and ...
75-480 5.49e-27

Methanobactin MbnE, a periplasmic binding protein of the TonB-dependent transport system, and similar proteins; Methanobactin MbnE is a periplasmic binding protein that is involved in the TonB-dependent transport system in bacteria. The function of MbnE is to bind to methanobactin and transport it across the periplasmic space to the TonB receptor on the outer membrane of the cell. The binding of MbnE to methanobactin allows the bacteria to scavenge iron from the environment, which is essential for many biological processes. The evolutionary relationship between MbnE and the ABC transport system is not clear, as they are distinct systems that have evolved separately. However, it is possible that there have been some functional convergences between these systems in terms of nutrient uptake and transport.


Pssm-ID: 173862 [Multi-domain]  Cd Length: 491  Bit Score: 113.77  E-value: 5.49e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  75 LAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLD-RASDPANHLKRYnlYKNIAKTEAIDPTTVKITLKQPFSA 153
Cdd:cd08497   65 LAESVEYPPDRSWVTFHLRPEARFSDGTPVTAEDVVFSFEtLKSKGPPYYRAY--YADVEKVEALDDHTVRFTFKEKANR 142
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 154 -FINILAhpaTAMISPaalEKYGKEIGFH--------PVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPK------LDSI 218
Cdd:cd08497  143 eLPLIVG---GLPVLP---KHWYEGRDFDkkrynlepPPGSGPYVIDSVDPGRSITYERVPDYWGKDLPVnrgrynFDRI 216
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 219 TWRPVADNNTRAAMLQTGEAQF-AFPIPYEQATLLE----KNKNIELMA----SPSIMQRYIsMNVTQKPFDNPKVREAL 289
Cdd:cd08497  217 RYEYYRDRTVAFEAFKAGEYDFrEENSAKRWATGYDfpavDDGRVIKEEfphgNPQGMQGFV-FNTRRPKFQDIRVREAL 295
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 290 NYAINRPALVKVAFAGyatpatgvvppsiayaqSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSH----------NHST 359
Cdd:cd08497  296 ALAFDFEWMNKNLFYG-----------------QYTRTRFNLRKALELLAEAGWTVRGGDILVNADgeplsfeillDSPT 358
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 360 AQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKesgvrMFYTGWSASTGEADWALSpLFASQNWP-PTLFNTAF 438
Cdd:cd08497  359 FERVLLPYVRNLKKLGIDASLRLVDSAQYQKRLRSFDFD-----MITAAWGQSLSPGNEQRF-HWGSAAADkPGSNNLAG 432
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 446012281 439 YSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPL 480
Cdd:cd08497  433 IKDPAVDALIEAVLAADDREELVAAVRALDRVLRAGHYVIPQ 474
PBP2_SgrR_like cd08507
The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related ...
38-376 5.23e-25

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: 107.36  E-value: 5.23e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  38 FTTLDPYDANDTLSQAVAKSFYQGLFGLDKEM-KLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRA 116
Cdd:cd08507   15 LPTLDPGTPLRRSESHLVRQIFDGLVRYDEENgEIEPDLAHHWESNDDLTHWTFYLRKGVRFHNGRELTAEDVVFTLLRL 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 117 SDPANHlkrYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPAtAMISPAALEKygkEIGF--HPVGTGPYELDTWN 194
Cdd:cd08507   95 RELESY---SWLLSHIEQIESPSPYTVDIKLSKPDPLFPRLLASAN-ASILPADILF---DPDFarHPIGTGPFRVVENT 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 195 QTDFvKVKKFAGYWQpGLPKLDSIT-WRpvadnntraamlqtgeaqfaFPIPYEQATLLEKNKNIELMASPSIMQR---- 269
Cdd:cd08507  168 DKRL-VLEAFDDYFG-ERPLLDEVEiWV--------------------VPELYENLVYPPQSTYLQYEESDSDEQQesrl 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 270 -----YISMNVTQKPFDNPKVREALNYAINRPALVKVAfAGYATPatGVVPpsiayAQSYKPWPYDPvKARELLKEAGYP 344
Cdd:cd08507  226 eegcyFLLFNQRKPGAQDPAFRRALSELLDPEALIQHL-GGERQR--GWFP-----AYGLLPEWPRE-KIRRLLKESEYP 296
                        330       340       350
                 ....*....|....*....|....*....|..
gi 446012281 345 nGFSTTLwSSHNHSTAQKVLQFTQQQLAQVGI 376
Cdd:cd08507  297 -GEELTL-ATYNQHPHREDAKWIQQRLAKHGI 326
COG3889 COG3889
Extracellular solute-binding protein, contains Ig-fold domain [General function prediction ...
209-507 2.36e-13

Extracellular solute-binding protein, contains Ig-fold domain [General function prediction only];


Pssm-ID: 443097 [Multi-domain]  Cd Length: 878  Bit Score: 72.75  E-value: 2.36e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 209 QPGlPKLDSITWRPVADNNTRAAMLQTGEAQ-FAFPIPYEQATLLEKNKNIELMASPS-----IMQRYISMNVTQKPFDN 282
Cdd:COG3889   33 EKG-PAVDKVIFIVYSDEEQALEEVESGDIDlYFFGIPPSLAQKLKSRPGLDVYSAPGgsydlLLNPAPPGNGKFNPFAI 111
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 283 PKVREALNYAINRPALVKVAFAGYATP----ATGVVPPSIAYAQ---SYKPWPYDPVKAREL----LKEAG--YPNGFst 349
Cdd:COG3889  112 KEIRFAMNYLIDRDYIVNEILGGYGVPmytpYGPYDPDYLRYADviaKFELFRYNPEYANEIiteaMTKAGaeKIDGK-- 189
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 350 tlWSSHNHSTAQKVL------------QFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGVRMFYTGWSASTGEAD 417
Cdd:COG3889  190 --WYYNGKPVTIKFFirvddpvrkqigDYIASQLEKLGFTVERIYGDLAKAIPIVYGSDPADLQWHIYTEGWGAGAFVRY 267
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 418 WAL------SPLFASQnwpPTLFNTAF--YSNKQVDDfLAQALKTND---PAEKTRLYKAAQDIIWQESPWIPLVVEKLV 486
Cdd:COG3889  268 DSSnlaqmyAPWFGNM---PGWQEPGFwnYENDEIDE-LTQRLATGNftsLEERWELYRKALELGIQESVRIWLVDQLDP 343
                        330       340
                 ....*....|....*....|.
gi 446012281 487 SAHSKNLTGfwIMPDTGFSFE 507
Cdd:COG3889  344 YVANSNVKG--VANDLGAGLR 362
SgrR COG4533
DNA-binding transcriptional regulator SgrR of sgrS sRNA, contains a MarR-type HTH domain and a ...
75-380 6.30e-09

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


Pssm-ID: 443600 [Multi-domain]  Cd Length: 574  Bit Score: 58.36  E-value: 6.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  75 LAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASdpanHLKRYN-LYKNIAKTEAIDPTTVKITLKQPFSA 153
Cdd:COG4533  169 LAHHWQQLSPGLHWRFYLRPALHFHNGRELTAEDVISSLERLR----ALPALRpLFSHIARITSPHPLCLDITLHQPDYW 244
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 154 FINILAHPAtAMISPAALEKYgKEIGFHPVGTGPYELDTwNQTDFVKVKKFAGYWqpGL-PKLDSIT-W---RPVADNNT 228
Cdd:COG4533  245 LAHLLASVC-AMILPPEWQTL-PDFARPPIGTGPFRVVE-NSPNLLRLEAFDDYF--GYrALLDEVEiWilpELFEQLLS 319
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281 229 RAAMLQTGEAQFAFPIPYEQATLLEKNKNielmaspsimqrYISMNVTQKPFDNPKVREALNYAINRPALVKVA---FAG 305
Cdd:COG4533  320 CQHPVQLGQDETELASLRPVESRLEEGCY------------YLLFNQRSGRLSDAQARRWLSQLIHPIALLQHLpleYQR 387
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446012281 306 YATPATGVVPpsiayaqsykPWP---YDPVKARELLKeagypngfSTTLwSSHNHSTAQKVLQFTQQQLAQVGIKAQV 380
Cdd:COG4533  388 FWTPAYGLLP----------GWHhplPAPEKPVPLPT--------KLTL-AYYEHVELHAIAQALQELLAQQGVELEI 446
PRK13626 PRK13626
HTH-type transcriptional regulator SgrR;
92-207 1.23e-05

HTH-type transcriptional regulator SgrR;


Pssm-ID: 184188 [Multi-domain]  Cd Length: 552  Bit Score: 47.71  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446012281  92 LREGIKFQDGTDFNAAAVKANLDRasdpanhLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPaTAMISPAAL 171
Cdd:PRK13626 184 LRPAIHFHHGRELEMEDVIASLKR-------LNTLPLYSHIAKIVSPTPWTLDIHLSQPDRWLPWLLGSV-PAMILPQEW 255
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446012281 172 EKYgKEIGFHPVGTGPYELdTWNQTDFVKVKKFAGY 207
Cdd:PRK13626 256 ETL-PNFASHPIGTGPYAV-IRNTTNQLKIQAFDDY 289
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
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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