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Conserved domains on  [gi|2238896597|ref|WP_249230455|]
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ABC transporter substrate-binding protein [Brenneria tiliae]

Protein Classification

ABC transporter substrate-binding protein( domain architecture ID 10170729)

ABC transporter substrate-binding protein functions as the initial receptor in the ABC transport of one or more from a variety of substrates; similar to Escherichia coli DdpA, part of the ABC transporter complex DdpABCDF that is involved in D,D-dipeptide transport

Gene Ontology:  GO:0140359|GO:0042626|GO:0055052
TCDB:  3.A.1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-519 0e+00

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: 526.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  29 PDDQLIVGMNMNnMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGN 108
Cdd:cd08512     1 PKDTLVVATSAD-INTLDPAVAYEVASGEVVQNVYDRLVTYDGEDTGKLVPELAESWEVSDDGKTYTFHLRDGVKFHDGN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 109 AVTAQDFAWSMNRLLHLNMAQATTWKSygfTADNVEKMIRAKDAHTVEIELPKPndPKLVIYSLATlGSGSVLDRQTIMP 188
Cdd:cd08512    80 PVTAEDVKYSFERALKLNKGPAFILTQ---TSLNVPETIKAVDDYTVVFKLDKP--PALFLSTLAA-PVASIVDKKLVKE 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 HEKNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVP 268
Cdd:cd08512   154 HGKDGDWGNAWLSTNSAGSGPYKLKSWDPGEEVVLERNDDYWGGAPKLKRVIIRHVPEAATRRLLLERGDADIARNLPPD 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PG 347
Cdd:cd08512   234 DVAALEGNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLKGQGKPHPGPLPDGLPGGAPDlPP 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 348 YKLDVARAKALLAEAGYPNGFATTLRVLS-DQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGG 426
Cdd:cd08512   314 YKYDLEKAKELLAEAGYPNGFKLTLSYNSgNEPREDIAQLLQASLAQIGIKVEIEPVPWAQLLEAARSREFDIFIGGWGP 393
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 427 GVdPHPHSSlrSVAYNPDNSDAArltnfqGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQM 506
Cdd:cd08512   394 DY-PDPDYF--AATYNSDNGDNA------ANRAWYDNPELDALIDEARAETDPAKRAALYKELQKIVYDDAP-YIPLYQP 463
                         490
                  ....*....|...
gi 2238896597 507 IDSVVLRTDVQGY 519
Cdd:cd08512   464 VEVVAVRKNVKGY 476
 
Name Accession Description Interval E-value
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-519 0e+00

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: 526.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  29 PDDQLIVGMNMNnMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGN 108
Cdd:cd08512     1 PKDTLVVATSAD-INTLDPAVAYEVASGEVVQNVYDRLVTYDGEDTGKLVPELAESWEVSDDGKTYTFHLRDGVKFHDGN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 109 AVTAQDFAWSMNRLLHLNMAQATTWKSygfTADNVEKMIRAKDAHTVEIELPKPndPKLVIYSLATlGSGSVLDRQTIMP 188
Cdd:cd08512    80 PVTAEDVKYSFERALKLNKGPAFILTQ---TSLNVPETIKAVDDYTVVFKLDKP--PALFLSTLAA-PVASIVDKKLVKE 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 HEKNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVP 268
Cdd:cd08512   154 HGKDGDWGNAWLSTNSAGSGPYKLKSWDPGEEVVLERNDDYWGGAPKLKRVIIRHVPEAATRRLLLERGDADIARNLPPD 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PG 347
Cdd:cd08512   234 DVAALEGNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLKGQGKPHPGPLPDGLPGGAPDlPP 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 348 YKLDVARAKALLAEAGYPNGFATTLRVLS-DQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGG 426
Cdd:cd08512   314 YKYDLEKAKELLAEAGYPNGFKLTLSYNSgNEPREDIAQLLQASLAQIGIKVEIEPVPWAQLLEAARSREFDIFIGGWGP 393
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 427 GVdPHPHSSlrSVAYNPDNSDAArltnfqGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQM 506
Cdd:cd08512   394 DY-PDPDYF--AATYNSDNGDNA------ANRAWYDNPELDALIDEARAETDPAKRAALYKELQKIVYDDAP-YIPLYQP 463
                         490
                  ....*....|...
gi 2238896597 507 IDSVVLRTDVQGY 519
Cdd:cd08512   464 VEVVAVRKNVKGY 476
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
45-535 9.08e-129

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


Pssm-ID: 440510 [Multi-domain]  Cd Length: 464  Bit Score: 383.51  E-value: 9.08e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  45 LDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLh 124
Cdd:COG0747     1 MDPALSTDAASANVASLVYEGLVRYDPDG--ELVPDLAESWEVSDDGKTYTFTLRDGVKFHDGTPLTAEDVVFSLERLL- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 125 lNMAQATTWKSYgftADNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGSGsvldrqtIMPHEKNGDWGNgWLTTNA 204
Cdd:COG0747    78 -DPDSGSPGAGL---LANIES-VEAVDDYTVVITLKEPYPP--FLYLLASPGAA-------IVPKHALEKVGD-DFNTNP 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 205 AGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVDEV 284
Cdd:COG0747   143 VGTGPYKLVSWVPGQRIVLERNPDYWGGKPKLDRVVFRVIPDAATRVAALQSGEVDIAEGLPPDDLARLKADPGLKVVTG 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 285 KKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PGYKLDVARAKALLAEAG 363
Cdd:COG0747   223 PGLGTTYLGFNTNKPPFDDVRVRQALAYAIDREAIIDAVLNGLGTPANGPIPPGSPGYDDDlEPYPYDPEKAKALLAEAG 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 364 YPNGFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGGGVdPHPHSSLRSVAynp 443
Cdd:COG0747   303 YPDGLELTLLTPGGPDREDIAEAIQAQLAKIGIKVELETLDWATYLDRLRAGDFDLALLGWGGDY-PDPDNFLSSLF--- 378
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 444 dNSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQMIDSVVLRTDVQGYVPHP 523
Cdd:COG0747   379 -GSDGIGGSNYSGYS----NPELDALLDEARAETDPAERKALYAEAQKILAEDAP-YIPLYQPPQLYAVRKRVKGVEPNP 452
                         490
                  ....*....|..
gi 2238896597 524 SSTTHLREVYKQ 535
Cdd:COG0747   453 FGLPDLADVSLA 464
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
76-447 3.18e-86

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: 270.82  E-value: 3.18e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  76 TVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHLNMAQATTwksYGFTADNVEKMIRAKDAHTV 155
Cdd:pfam00496   1 EVVPALAESWEVSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYA---SLLAYDADIVGVEAVDDYTV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 156 EIELPKPNdPKLVIYSLATLGsgsvldrqtIMPHEKNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAK 235
Cdd:pfam00496  78 RFTLKKPD-PLFLPLLAALAA---------APVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYWGGKPK 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 236 MRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVDEVKKGT-IYYVAMSLKNEHFAKPKVREAVRYLI 314
Cdd:pfam00496 148 LDRIVFKVIPDSTARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSGPGGgTYYLAFNTKKPPFDDVRVRQALSYAI 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 315 DYDGINKTVMTGYGFYHQRPIQKGMD-ATLPNPGYKLDVARAKALLAEAGYPNGFATTLRVLS--------DQPFLNLAT 385
Cdd:pfam00496 228 DREAIVKAVLGGYATPANSLVPPGFPgYDDDPKPEYYDPEKAKALLAEAGYKDGDGGGRRKLKltllvysgNPAAKAIAE 307
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2238896597 386 SVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGrGGGGVDPHPHSSLRSVAYNPDNSD 447
Cdd:pfam00496 308 LIQQQLKKIGIKVEIKTVDWATYLERVKDGDFDMALS-GWGADYPDPDNFLYPFLSSTGGGN 368
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
76-529 2.58e-35

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: 138.40  E-value: 2.58e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  76 TVLPSLAKSWSVSDDGKVITFNLVDNARFHSGN-----AVTAQDFAWSMNRLLHlnmaqatTWKSYGFTADNVEkmirAK 150
Cdd:TIGR02294  47 KIEPWLAKSWTVSEDGKTYTFKLRDDVKFSDGTpfdaeAVKKNFDAVLQNSQRH-------SWLELSNQLDNVK----AL 115
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 151 DAHTVEIELPKPNDPKLviYSLATlgsgsVLDRQTIMPHEKNGDWGNGWLtTNAAGSGPFKLDVWQAKDVLRISRVEGYW 230
Cdd:TIGR02294 116 DKYTFELVLKEAYYPAL--QELAM-----PRPYRFLSPSDFKNDTTKDGV-KKPIGTGPWMLGESKQDEYAVFVRNENYW 187
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 231 RGDAKMRRVIFRHMTESQALRLMIEKGDIDVATG----MSVPDINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKV 306
Cdd:TIGR02294 188 GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGnegsIDLDTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAV 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 307 REAVRYLIDYDGINKTVMTGYGFYHQRPIQKGM-DATLPNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQPFL---- 381
Cdd:TIGR02294 268 RQAINHAVNKQSIAKNILYGTEKPADTLFAKNVpYADIDLKPYKYDVKKANALLDEAGWKLGKGKDVREKDGKPLElely 347
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 382 ---------NLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRG-GGGVDPHPHSSLRSVAYNPDNSDAARL 451
Cdd:TIGR02294 348 ydktsalqkSLAEYLQAEWRKIGIKLSLIGEEEDKIAARRRDGDFDMMFNYTwGAPYDPHSFISAMRAKGHGDESAQSGL 427
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 452 TNfqgwrtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRY--EALYpaiIPVSQMIDSVVLRTDVqGYVPHPSSTTHL 529
Cdd:TIGR02294 428 AN---------KDEIDKSIGDALASTDETERQELYKNILTTLhdEAVY---IPISYISMTVVYRKDL-EKVSFAPSQYEL 494
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
17-492 7.36e-32

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 128.85  E-value: 7.36e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  17 MAAVPAvLSAKtpDDQLIVGmnmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQ-NLSTVLpslAKSWSVSDDGKVIT 95
Cdd:PRK15413   19 LAASPA-FAAK--DVVVAVG---SNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEmKLKNVL---AESYTVSDDGLTYT 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  96 FNLVDNARFHSGNAVTAQDFAWSMNRLL----HLnmaqattwKSYgftadNVEKMI---RAKDAHTVEIELPKP------ 162
Cdd:PRK15413   90 VKLREGVKFQDGTDFNAAAVKANLDRASnpdnHL--------KRY-----NLYKNIaktEAVDPTTVKITLKQPfsafin 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 163 --NDPKLVIYSLATLgsgsvldrqtimphEKNG-DWGngwltTNAAGSGPFKLDVWQAKDVLRISRVEGYWR-GDAKMRR 238
Cdd:PRK15413  157 ilAHPATAMISPAAL--------------EKYGkEIG-----FHPVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDS 217
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 239 VIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVvvDEVKKGTIY--YVAMSLKNEHFAKPKVREAVRYLIDY 316
Cdd:PRK15413  218 ITWRPVADNNTRAAMLQTGEAQFAFPIPYEQAALLEKNKNL--ELVASPSIMqrYISMNVTQKPFDNPKVREALNYAINR 295
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 317 DGINKTVMTGYGFYHQRPIQKGMDATLPNPGYKLDVARAKALLAEAGYPNGFATTL----RVLSDQPFLNLAtsvQSTLA 392
Cdd:PRK15413  296 QALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPAKARELLKEAGYPNGFSTTLwsshNHSTAQKVLQFT---QQQLA 372
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 393 QAGIKARIHSGTGNQVYGAMRDRnfdmlvGRGGGGVdphphsSLRSVAYNPDNSDA----ARLTNFQGW-----RTSFY- 462
Cdd:PRK15413  373 QVGIKAQVTAMDAGQRAAEVEGK------GQKESGV------RMFYTGWSASTGEAdwalSPLFASQNWpptlfNTAFYs 440
                         490       500       510
                  ....*....|....*....|....*....|
gi 2238896597 463 DKQLNELIDRALLEKDPARQKQLYAEVQNR 492
Cdd:PRK15413  441 NKQVDDDLAQALKTNDPAEKTRLYKAAQDI 470
 
Name Accession Description Interval E-value
PBP2_NikA_DppA_OppA_like_7 cd08512
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
29-519 0e+00

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: 526.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  29 PDDQLIVGMNMNnMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGN 108
Cdd:cd08512     1 PKDTLVVATSAD-INTLDPAVAYEVASGEVVQNVYDRLVTYDGEDTGKLVPELAESWEVSDDGKTYTFHLRDGVKFHDGN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 109 AVTAQDFAWSMNRLLHLNMAQATTWKSygfTADNVEKMIRAKDAHTVEIELPKPndPKLVIYSLATlGSGSVLDRQTIMP 188
Cdd:cd08512    80 PVTAEDVKYSFERALKLNKGPAFILTQ---TSLNVPETIKAVDDYTVVFKLDKP--PALFLSTLAA-PVASIVDKKLVKE 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 HEKNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVP 268
Cdd:cd08512   154 HGKDGDWGNAWLSTNSAGSGPYKLKSWDPGEEVVLERNDDYWGGAPKLKRVIIRHVPEAATRRLLLERGDADIARNLPPD 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PG 347
Cdd:cd08512   234 DVAALEGNPGVKVISLPSLTVFYLALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLKGQGKPHPGPLPDGLPGGAPDlPP 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 348 YKLDVARAKALLAEAGYPNGFATTLRVLS-DQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGG 426
Cdd:cd08512   314 YKYDLEKAKELLAEAGYPNGFKLTLSYNSgNEPREDIAQLLQASLAQIGIKVEIEPVPWAQLLEAARSREFDIFIGGWGP 393
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 427 GVdPHPHSSlrSVAYNPDNSDAArltnfqGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQM 506
Cdd:cd08512   394 DY-PDPDYF--AATYNSDNGDNA------ANRAWYDNPELDALIDEARAETDPAKRAALYKELQKIVYDDAP-YIPLYQP 463
                         490
                  ....*....|...
gi 2238896597 507 IDSVVLRTDVQGY 519
Cdd:cd08512   464 VEVVAVRKNVKGY 476
DdpA COG0747
ABC-type transport system, periplasmic component [Amino acid transport and metabolism];
45-535 9.08e-129

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


Pssm-ID: 440510 [Multi-domain]  Cd Length: 464  Bit Score: 383.51  E-value: 9.08e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  45 LDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLh 124
Cdd:COG0747     1 MDPALSTDAASANVASLVYEGLVRYDPDG--ELVPDLAESWEVSDDGKTYTFTLRDGVKFHDGTPLTAEDVVFSLERLL- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 125 lNMAQATTWKSYgftADNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGSGsvldrqtIMPHEKNGDWGNgWLTTNA 204
Cdd:COG0747    78 -DPDSGSPGAGL---LANIES-VEAVDDYTVVITLKEPYPP--FLYLLASPGAA-------IVPKHALEKVGD-DFNTNP 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 205 AGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVDEV 284
Cdd:COG0747   143 VGTGPYKLVSWVPGQRIVLERNPDYWGGKPKLDRVVFRVIPDAATRVAALQSGEVDIAEGLPPDDLARLKADPGLKVVTG 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 285 KKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PGYKLDVARAKALLAEAG 363
Cdd:COG0747   223 PGLGTTYLGFNTNKPPFDDVRVRQALAYAIDREAIIDAVLNGLGTPANGPIPPGSPGYDDDlEPYPYDPEKAKALLAEAG 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 364 YPNGFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGGGVdPHPHSSLRSVAynp 443
Cdd:COG0747   303 YPDGLELTLLTPGGPDREDIAEAIQAQLAKIGIKVELETLDWATYLDRLRAGDFDLALLGWGGDY-PDPDNFLSSLF--- 378
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 444 dNSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQMIDSVVLRTDVQGYVPHP 523
Cdd:COG0747   379 -GSDGIGGSNYSGYS----NPELDALLDEARAETDPAERKALYAEAQKILAEDAP-YIPLYQPPQLYAVRKRVKGVEPNP 452
                         490
                  ....*....|..
gi 2238896597 524 SSTTHLREVYKQ 535
Cdd:COG0747   453 FGLPDLADVSLA 464
PBP2_NikA_DppA_OppA_like cd00995
The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains ...
33-519 4.31e-99

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: 307.70  E-value: 4.31e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  33 LIVGMNmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTA 112
Cdd:cd00995     2 LTVALG-SDPTSLDPAFATDASSGRVLRLIYDGLVRYDPDG--ELVPDLAESWEVSDDGKTYTFKLRDGVKFHDGTPLTA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 113 QDFAWSMNRLLHLNMAQATTWKsygftADNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGSGsvldrqtIMPHEKN 192
Cdd:cd00995    79 EDVVFSFERLADPKNASPSAGK-----ADEIEG-VEVVDDYTVTITLKEPDAP--FLALLAYPAAS-------PVPKAAA 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 193 GDWGNgWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWR-GDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDIN 271
Cdd:cd00995   144 EKDGK-AFGTKPVGTGPYKLVEWKPGESIVLERNDDYWGpGKPKIDKITFKVIPDASTRVAALQSGEIDIADDVPPSALE 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 272 ALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDA--TLPNPGYK 349
Cdd:cd00995   223 TLKKNPGIRLVTVPSLGTGYLGFNTNKPPFDDKRVRQAISYAIDREEIIDAVLGGYGTPATSPLPPGSWGyyDKDLEPYE 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 350 LDVARAKALLAEAGYPN--GFATTLRVLSDQP-FLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGG 426
Cdd:cd00995   303 YDPEKAKELLAEAGYKDgkGLELTLLYNSDGPtRKEIAEAIQAQLKEIGIKVEIEPLDFATLLDALDAGDDFDLFLLGWG 382
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 427 GVDPHPHSSLRSVaYNPDNSDAarltnfqGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQM 506
Cdd:cd00995   383 ADYPDPDNFLSPL-FSSGASGA-------GNYSGYSNPEFDALLDEARAETDPEERKALYQEAQEILAEDAP-VIPLYYP 453
                         490
                  ....*....|...
gi 2238896597 507 IDSVVLRTDVQGY 519
Cdd:cd00995   454 NNVYAYSKRVKGF 466
SBP_bac_5 pfam00496
Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family ...
76-447 3.18e-86

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: 270.82  E-value: 3.18e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  76 TVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHLNMAQATTwksYGFTADNVEKMIRAKDAHTV 155
Cdd:pfam00496   1 EVVPALAESWEVSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERILDPDTASPYA---SLLAYDADIVGVEAVDDYTV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 156 EIELPKPNdPKLVIYSLATLGsgsvldrqtIMPHEKNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAK 235
Cdd:pfam00496  78 RFTLKKPD-PLFLPLLAALAA---------APVKAEKKDDDKKTLPENPIGTGPYKLKSWKPGQKVVLERNPDYWGGKPK 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 236 MRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVDEVKKGT-IYYVAMSLKNEHFAKPKVREAVRYLI 314
Cdd:pfam00496 148 LDRIVFKVIPDSTARAAALQAGEIDDAAEIPPSDIAQLKLDKGLDVKVSGPGGgTYYLAFNTKKPPFDDVRVRQALSYAI 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 315 DYDGINKTVMTGYGFYHQRPIQKGMD-ATLPNPGYKLDVARAKALLAEAGYPNGFATTLRVLS--------DQPFLNLAT 385
Cdd:pfam00496 228 DREAIVKAVLGGYATPANSLVPPGFPgYDDDPKPEYYDPEKAKALLAEAGYKDGDGGGRRKLKltllvysgNPAAKAIAE 307
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2238896597 386 SVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGrGGGGVDPHPHSSLRSVAYNPDNSD 447
Cdd:pfam00496 308 LIQQQLKKIGIKVEIKTVDWATYLERVKDGDFDMALS-GWGADYPDPDNFLYPFLSSTGGGN 368
PBP2_NikA_DppA_OppA_like_11 cd08516
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
32-519 1.54e-83

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: 266.81  E-value: 1.54e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  32 QLIVGMNmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVT 111
Cdd:cd08516     1 TLRFGLS-TDPDSLDPHKATAAASEEVLENIYEGLLGPDENG--KLVPALAESWEVSDDGLTYTFKLRDGVKFHNGDPVT 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 112 AQDFAWSMNRLLHLNMAQATTwksygFTADNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGSGsvldrqtIMPHEK 191
Cdd:cd08516    78 AADVKYSFNRIADPDSGAPLR-----ALFQEIES-VEAPDDATVVIKLKQPDAP--LLSLLASVNSP-------IIPAAS 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 192 NGDwgngwLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWR-GDAKMRRVIFRHMTESQALRLMIEKGDIDVATgmSVP-- 268
Cdd:cd08516   143 GGD-----LATNPIGTGPFKFASYEPGVSIVLEKNPDYWGkGLPKLDGITFKIYPDENTRLAALQSGDVDIIE--YVPpq 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGfyhqRPIQKGMDATL----- 343
Cdd:cd08516   216 QAAQLEEDDGLKLASSPGNSYMYLALNNTREPFDDPKVRQAIAYAIDRDAIVDAAFFGRG----TPLGGLPSPAGspayd 291
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 344 --PNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQPFL-NLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDML 420
Cdd:cd08516   292 pdDAPCYKYDPEKAKALLAEAGYPNGFDFTILVTSQYGMHvDTAQVIQAQLAAIGINVEIELVEWATWLDDVNKGDYDAT 371
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 421 VGRGGGGVDPhphSSLRSVAYNPDNSdaarlTNFQGwrtsFYDKQLNELIDRALLEKDPARQKQLYAEVQNRYeALYPAI 500
Cdd:cd08516   372 IAGTSGNADP---DGLYNRYFTSGGK-----LNFFN----YSNPEVDELLAQGRAETDEAKRKEIYKELQQIL-AEDVPW 438
                         490
                  ....*....|....*....
gi 2238896597 501 IPVSQMIDSVVLRTDVQGY 519
Cdd:cd08516   439 VFLYWRSQYYAMNKNVQGF 457
PBP2_DppA_like cd08493
The substrate-binding component of an ABC-type dipeptide import system contains the type 2 ...
44-519 9.11e-79

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: 255.18  E-value: 9.11e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNLsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLL 123
Cdd:cd08493    12 SLDPQLATDGESDAVTRQIYEGLVEFKPGTT-ELEPGLAESWEVSDDGLTYTFHLRKGVKFHDGRPFNADDVVFSFNRWL 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 124 HLN----MAQATTWKSY--GFTADNVEKmIRAKDAHTVEIELPKPNDPklviySLATLGSG--SVLDRQTIMPHEKNGDW 195
Cdd:cd08493    91 DPNhpyhKVGGGGYPYFysMGLGSLIKS-VEAVDDYTVKFTLTRPDAP-----FLANLAMPfaSILSPEYADQLLAAGKP 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 196 GNgwLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQAlRLM-IEKGDIDVATGMSVPDInALK 274
Cdd:cd08493   165 EQ--LDLLPVGTGPFKFVSWQKDDRIRLEANPDYWGGKAKIDTLVFRIIPDNSV-RLAkLLAGECDIVAYPNPSDL-AIL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 275 QNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-PGYKLDVA 353
Cdd:cd08493   241 ADAGLQLLERPGLNVGYLAFNTQKPPFDDPKVRQAIAHAINKEAIVDAVYQGTATVAKNPLPPTSWGYNDDvPDYEYDPE 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 354 RAKALLAEAGYPNGFATTLRVLSDQPFLN-----LATSVQSTLAQAGIKARIHSgtgnQVYGAMRDR----NFDM-LVGR 423
Cdd:cd08493   321 KAKALLAEAGYPDGFELTLWYPPVSRPYNpnpkkMAELIQADLAKVGIKVEIVT----YEWGEYLERtkagEHDLyLLGW 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 424 GGGGVDPhphSSLRSVAYNPDNSDAArlTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPV 503
Cdd:cd08493   397 TGDNGDP---DNFLRPLLSCDAAPSG--TNRARWC----NPEFDELLEKARRTTDQAERAKLYKQAQEIIHEDAP-WVPI 466
                         490
                  ....*....|....*.
gi 2238896597 504 SQMIDSVVLRTDVQGY 519
Cdd:cd08493   467 AHSKRLLAVRKNVKGF 482
OppA COG4166
ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and ...
1-536 1.72e-78

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


Pssm-ID: 443327 [Multi-domain]  Cd Length: 543  Bit Score: 256.29  E-value: 1.72e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597   1 MKARAILRILLLSTL-----CMAAVPAVLSAKTPDDQLIVGMNMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNls 75
Cdd:COG4166     1 MKKRKALLLLALALAlalaaCGSGGKYPAGDKVNDAKVLRLNNGTEPDSLDPALATGTAAAGVLGLLFEGLVSLDEDG-- 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  76 TVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLlhLNMAQATTWKSY-----GFTADNVEKM---- 146
Cdd:COG4166    79 KPYPGLAESWEVSEDGLTYTFHLRPDAKWSDGTPVTAEDFVYSWKRL--LDPKTASPYAYYladikNAEAINAGKKdpde 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 147 --IRAKDAHTVEIELPKPNdPklviYSLATLGSgsvldrQTIMP-HEKNG-DWGNGWLTT--NAAGSGPFKLDVWQAKDV 220
Cdd:COG4166   157 lgVKALDDHTLEVTLEAPT-P----YFPLLLGF------PAFLPvPKKAVeKYGDDFGTTpeNPVGNGPYKLKEWEHGRS 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 221 LRISRVEGYW-RGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVDEVKKGTIYYVAMSLKNE 299
Cdd:COG4166   226 IVLERNPDYWgADNVNLDKIRFEYYKDATTALEAFKAGELDFTDELPAEQFPALKDDLKEELPTGPYAGTYYLVFNTRRP 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 300 HFAKPKVREAVRYLIDYDGINKTVMTG-----YGFyhqrpIQKGM-------DATLPNPGYKL-----DVARAKALLAEA 362
Cdd:COG4166   306 PFADPRVRKALSLAIDREWINKNVFYGgytpaTSF-----VPPSLagypegeDFLKLPGEFVDgllryNLRKAKKLLAEA 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 363 GYPNGFATTLRVLSDQPFLN--LATSVQSTLAQA-GIKARIHSGTGNQVYGAMRDRNFDMLVGR-GGGGVDPhphSSLRS 438
Cdd:COG4166   381 GYTKGKPLTLELLYNTSEGHkrIAEAVQQQLKKNlGIDVTLRNVDFKQYLDRRRNGDFDMVRAGwGADYPDP---GTFLD 457
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 439 VaYNPDNSdaarlTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLY--AEVQNRYEAlypAIIPVSQMIDSVVLRTDV 516
Cdd:COG4166   458 L-FGSDGS-----NNYAGYS----NPAYDALIEKALAATDREERVAAYraAERILLEDA---PVIPLYYYTNARLVSPYV 524
                         570       580
                  ....*....|....*....|
gi 2238896597 517 QGYVPHPSStTHLREVYKQR 536
Cdd:COG4166   525 KGWVYDPLG-VDFKAAYIEK 543
PBP2_NikA_DppA_OppA_like_13 cd08517
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
39-490 2.68e-78

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: 254.01  E-value: 2.68e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  39 MNNMLSLDPAAMTGNevvgvivNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWS 118
Cdd:cd08517    16 NPALKSDGPTQLISG-------KIFEGLLRYDFDL--NPQPDLATSWEVSEDGLTYTFKLRPGVKWHDGKPFTSADVKFS 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 119 MNRLLhlnmaqATTWKSYGFTAdNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGSgsvldrqTIMP-H--EkNGDW 195
Cdd:cd08517    87 IDTLK------EEHPRRRRTFA-NVES-IETPDDLTVVFKLKKPAPA--LLSALSWGES-------PIVPkHiyE-GTDI 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 196 gngwlTTNAA-----GSGPFKLDVWQAKDVLRISRVEGYWRGDA-KMRRVIFRHMTESQALRLMIEKGDIDVATGMSVP- 268
Cdd:cd08517   149 -----LTNPAnnapiGTGPFKFVEWVRGSHIILERNPDYWDKGKpYLDRIVFRIIPDAAARAAAFETGEVDVLPFGPVPl 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 -DINALKQNQGVVVDE---VKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGM----D 340
Cdd:cd08517   224 sDIPRLKALPNLVVTTkgyEYFSPRSYLEFNLRNPPLKDVRVRQAIAHAIDRQFIVDTVFFGYGKPATGPISPSLpffyD 303
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 341 ATLPNpgYKLDVARAKALLAEAGYP---NGFATTLRVL---SDQPFLNLATSVQSTLAQAGIKARIHS---GTGNQ-VYg 410
Cdd:cd08517   304 DDVPT--YPFDVAKAEALLDEAGYPrgaDGIRFKLRLDplpYGEFWKRTAEYVKQALKEVGIDVELRSqdfATWLKrVY- 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 411 amRDRNFDMLVGRGGGGVDPhphSSLRSVAYNPDN-SDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEV 489
Cdd:cd08517   381 --TDRDFDLAMNGGYQGGDP---AVGVQRLYWSGNiKKGVPFSNASGYS----NPEVDALLEKAAVETDPAKRKALYKEF 451

                  .
gi 2238896597 490 Q 490
Cdd:cd08517   452 Q 452
PBP2_NikA_DppA_OppA_like_3 cd08490
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-524 1.86e-75

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: 246.36  E-value: 1.86e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVV--GVivnlYDSLVELDPQnlSTVLPSLAKSWSVSDDgKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08490    13 SLDPASDDGWLLSryGV----AETLVKLDDD--GKLEPWLAESWEQVDD-TTWEFTLRDGVKFHDGTPLTAEAVKASLER 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 LLhlnmAQATTWKSYGFTADnvekmIRAKDAHTVEIELPKPN--------DPKLVIYSLATLGSGSVldrqtimphekng 193
Cdd:cd08490    86 AL----AKSPRAKGGALIIS-----VIAVDDYTVTITTKEPYpalparlaDPNTAILDPAAYDDGVD------------- 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 194 dwgngwltTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINAL 273
Cdd:cd08490   144 --------PAPIGTGPYKVESFEPDQSLTLERNDDYWGGKPKLDKVTVKFIPDANTRALALQSGEVDIAYGLPPSSVERL 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 274 KQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPNPGYKLDVA 353
Cdd:cd08490   216 EKDDGYKVSSVPTPRTYFLYLNTEKGPLADVRVRQALSLAIDREGIADSVLEGSAAPAKGPFPPSLPANPKLEPYEYDPE 295
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 354 RAKALLAEAGYP-----------NGFATTLRVLSDQPFLN-LATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDM-L 420
Cdd:cd08490   296 KAKELLAEAGWTdgdgdgiekdgEPLELTLLTYTSRPELPpIAEAIQAQLKKIGIDVEIRVVEYDAIEEDLLDGDFDLaL 375
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 421 VGRGGGGVdPHPHSSLRSvAYNPDNSDaarltNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNR-YEALypA 499
Cdd:cd08490   376 YSRNTAPT-GDPDYFLNS-DYKSDGSY-----NYGGYS----NPEVDALIEELRTEFDPEERAELAAEIQQIiQDDA--P 442
                         490       500
                  ....*....|....*....|....*
gi 2238896597 500 IIPVSQMIDSVVLRTDVQGYVPHPS 524
Cdd:cd08490   443 VIPVAHYNQVVAVSKRVKGYKVDPT 467
PBP2_OppA cd08504
The substrate-binding component of an ABC-type oligopetide import system contains the type 2 ...
37-533 9.71e-74

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: 242.46  E-value: 9.71e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  37 MNMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFA 116
Cdd:cd08504     6 GIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDKDG--KIVPGLAESWEVSDDGLTYTFHLRKDAKWSNGDPVTAQDFV 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 117 WSMNRLlhLNMAQATTWKSYGFTADNVE-----KM------IRAKDAHTVEIELPKPNDpklviY--SLATLGSGSVLDR 183
Cdd:cd08504    84 YSWRRA--LDPKTASPYAYLLYPIKNAEainagKKppdelgVKALDDYTLEVTLEKPTP-----YflSLLAHPTFFPVNQ 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 184 QTImphEKNGDwgNGWLT-TNAAGSGPFKLDVWQAKDVLRISRVEGYW-RGDAKMRRVIFRHMTESQALRLMIEKGDIDV 261
Cdd:cd08504   157 KFV---EKYGG--KYGTSpENIVYNGPFKLKEWTPNDKIVLVKNPNYWdAKNVKLDKINFLVIKDPNTALNLFEAGELDI 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 262 ATGMSVPDINALKQNQGVVVdeVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTG-------YGFYHqrP 334
Cdd:cd08504   232 AGLPPEQVILKLKNNKDLKS--TPYLGTYYLEFNTKKPPLDNKRVRKALSLAIDREALVEKVLGDaggfvpaGLFVP--P 307
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 335 IQKGMDATLPNPGYKLDVARAKALLAEAGYPNGFAT---TLRVLSDQPFLNLATSVQSTLAQA-GIKARIHSGTGNQVYG 410
Cdd:cd08504   308 GTGGDFRDEAGKLLEYNPEKAKKLLAEAGYELGKNPlklTLLYNTSENHKKIAEAIQQMWKKNlGVKVTLKNVEWKVFLD 387
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 411 AMRDRNFDMlvGRGGGGVD-PHPHSSLRSvaYNPDNSDaarltNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEV 489
Cdd:cd08504   388 RRRKGDFDI--ARSGWGADyNDPSTFLDL--FTSGSGN-----NYGGYS----NPEYDKLLAKAATETDPEKRWELLAKA 454
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....
gi 2238896597 490 QNRYEALYPaIIPVSQMIDSVVLRTDVQGYVPHPSSTTHLREVY 533
Cdd:cd08504   455 EKILLDDAP-IIPLYQYVTAYLVKPKVKGLVYNPLGGYDFKYAY 497
PBP2_NikA_DppA_OppA_like_2 cd08498
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
42-523 1.63e-71

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: 236.30  E-value: 1.63e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  42 MLSLDPAAMTGNEVVGVIVNLYDSLVELDpQNLSTVlPSLAKSWSVSDDgKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08498    10 PTSLDPHFHNEGPTLAVLHNIYDTLVRRD-ADLKLE-PGLATSWEAVDD-TTWRFKLREGVKFHDGSPFTAEDVVFSLER 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 LLHLNMAQAttwksyGFTADNVEKmIRAKDAHTVEIELPKPNdPKLViYSLATLGsgsvldrqtIMPHEKNGDW---GNG 198
Cdd:cd08498    87 ARDPPSSPA------SFYLRTIKE-VEVVDDYTVDIKTKGPN-PLLP-NDLTNIF---------IMSKPWAEAIaktGDF 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 199 WLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESqALRL--MIEkGDIDVATGMSVPDINALKQN 276
Cdd:cd08498   149 NAGRNPNGTGPYKFVSWEPGDRTVLERNDDYWGGKPNWDEVVFRPIPND-ATRVaaLLS-GEVDVIEDVPPQDIARLKAN 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 277 QGVVVDEVKKGTIYYVAMSLKNEH-----------FAKPKVREAVRYLIDYDGINKTVMTGYGfyhqRP----IQKGMDA 341
Cdd:cd08498   227 PGVKVVTGPSLRVIFLGLDQRRDElpagsplgknpLKDPRVRQALSLAIDREAIVDRVMRGLA----TPagqlVPPGVFG 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 342 TLPNPG-YKLDVARAKALLAEAGYPNGFATTL-----RVLSDQpflNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDR 415
Cdd:cd08498   303 GEPLDKpPPYDPEKAKKLLAEAGYPDGFELTLhcpndRYVNDE---AIAQAVAGMLARIGIKVNLETMPKSVYFPRATKG 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 416 NFDM-LVGRGGGGVDphPHSSLRSVAYNPDNSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYE 494
Cdd:cd08498   380 EADFyLLGWGVPTGD--ASSALDALLHTPDPEKGLGAYNRGGYS----NPEVDALIEAAASEMDPAKRAALLQEAQEIVA 453
                         490       500
                  ....*....|....*....|....*....
gi 2238896597 495 ALYPaIIPVSQMIDSVVLRTDVqGYVPHP 523
Cdd:cd08498   454 DDAA-YIPLHQQVLIWAARKGI-DLTPRA 480
PBP2_Ylib_like cd08499
The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib ...
33-524 3.15e-71

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: 235.19  E-value: 3.15e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  33 LIVGMnMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPqNLSTVlPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTA 112
Cdd:cd08499     2 LVIAV-LSDATSLDPHDTNDTPSASVQSNIYEGLVGFDK-DMKIV-PVLAESWEQSDDGTTWTFKLREGVKFHDGTPFNA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 113 QDFAWSMNRLLhlnmAQATTWK-SYGFtaDNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATlGSGSVLDRQTImphEK 191
Cdd:cd08499    79 EAVKANLDRVL----DPETASPrASLF--SMIEE-VEVVDDYTVKITLKEPFAP--LLAHLAH-PGGSIISPKAI---EE 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 192 NGDWgngwLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDIN 271
Cdd:cd08499   146 YGKE----ISKHPVGTGPFKFESWTPGDEVTLVKNDDYWGGLPKVDTVTFKVVPEDGTRVAMLETGEADIAYPVPPEDVD 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 272 ALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPNPG-YKL 350
Cdd:cd08499   222 RLENSPGLNVYRSPSISVVYIGFNTQKEPFDDVRVRQAINYAIDKEAIIKGILNGYGTPADSPIAPGVFGYSEQVGpYEY 301
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 351 DVARAKALLAEAGYPNGFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHS-GTGNQVYGAMRDRNFDMLVGRGG---G 426
Cdd:cd08499   302 DPEKAKELLAEAGYPDGFETTLWTNDNRERIKIAEFIQQQLAQIGIDVEIEVmEWGAYLEETGNGEEHQMFLLGWStstG 381
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 427 GVD----PHPHSSLRSVAYNpdnsdaarltnfqgwrTSFY-DKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaII 501
Cdd:cd08499   382 DADyglrPLFHSSNWGAPGN----------------RAFYsNPEVDALLDEARREADEEERLELYAKAQEIIWEDAP-WV 444
                         490       500
                  ....*....|....*....|...
gi 2238896597 502 PVSQMIDSVVLRTDVQGYVPHPS 524
Cdd:cd08499   445 FLYHPETLAGVSKEVKGFYIYPS 467
PBP2_NikA_DppA_OppA_like_17 cd08503
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-519 7.13e-68

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173868 [Multi-domain]  Cd Length: 460  Bit Score: 225.91  E-value: 7.13e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLL 123
Cdd:cd08503    19 TLDPHTADSSADYVRGFALYEYLVEIDPDG--TLVPDLAESWEPNDDATTWTFKLRKGVTFHDGKPLTADDVVASLNRHR 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 124 HLNMAqattwkSYGFTADNVEKMIRAKDAHTVEIELPKPNdpklviYSLATLGSGSVLdrqTIMPHEKNGDwgngwLTTN 203
Cdd:cd08503    97 DPASG------SPAKTGLLDVGAIEAVDDHTVRFTLKRPN------ADFPYLLSDYHF---PIVPAGDGGD-----DFKN 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 204 AAGSGPFKLDVWQAKDVLRISRVEGYWR-GDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVVVD 282
Cdd:cd08503   157 PIGTGPFKLESFEPGVRAVLERNPDYWKpGRPYLDRIEFIDIPDPAARVNALLSGQVDVINQVDPKTADLLKRNPGVRVL 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 283 EVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGF----YHQRPIQKgMDATLPNPGYklDVARAKAL 358
Cdd:cd08503   237 RSPTGTHYTFVMRTDTAPFDDPRVRRALKLAVDREALVETVLLGYGTvgndHPVAPIPP-YYADLPQREY--DPDKAKAL 313
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 359 LAEAGYPNgFATTLRVLSDQP-FLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDR-NFDMlvgrGGGGVDPHPHSSL 436
Cdd:cd08503   314 LAEAGLPD-LEVELVTSDAAPgAVDAAVLFAEQAAQAGININVKRVPADGYWSDVWMKkPFSA----TYWGGRPTGDQML 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 437 rSVAYnpdNSDAArlTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRyeaLY---PAIIPV-SQMIDSVvl 512
Cdd:cd08503   389 -SLAY---RSGAP--WNETHWA----NPEFDALLDAARAELDEAKRKELYAEMQQI---LHdegGIIIPYfRSYLDAH-- 453

                  ....*..
gi 2238896597 513 RTDVQGY 519
Cdd:cd08503   454 SDKVKGY 460
PBP2_thermophilic_Hb8_like cd08513
The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like ...
32-519 1.84e-67

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: 225.63  E-value: 1.84e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  32 QLIVGMNmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVT 111
Cdd:cd08513     1 TLVIGLS-QEPTTLNPLLASGATDAEAAQLLFEPLARIDPDG--SLVPVLAEEIPTSENGLSVTFTLRPGVKWSDGTPVT 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 112 AQDFAWSMNrllhLNMAQATTWkSYGFTADNVEKmIRAKDAHTVEIELPKPNDPklviyslATLGSGSVldrqTIMP-HE 190
Cdd:cd08513    78 ADDVVFTWE----LIKAPGVSA-AYAAGYDNIAS-VEAVDDYTVTVTLKKPTPY-------APFLFLTF----PILPaHL 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 191 KNGDWGNGWLTTNAA----GSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMS 266
Cdd:cd08513   141 LEGYSGAAARQANFNlapvGTGPYKLEEFVPGDSIELVRNPNYWGGKPYIDRVVLKGVPDTDAARAALRSGEIDLAWLPG 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 267 VPDIN-ALKQNQGVVVDEVKKGTIYYVAMSLKNeH--FAKPKVREAVRYLIDYDGINKTVMTGYG---FYHQRPIQKGMD 340
Cdd:cd08513   221 AKDLQqEALLSPGYNVVVAPGSGYEYLAFNLTN-HpiLADVRVRQALAYAIDRDAIVKTLYGGKAtpaPTPVPPGSWADD 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 341 AtlPNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQP--FLNLATS-----------VQSTLAQAGIKARIHSGTGNQ 407
Cdd:cd08513   300 P--LVPAYEYDPEKAKQLLDEAGWKLGPDGGIREKDGTPlsFTLLTTSgnavrervaelIQQQLAKIGIDVEIENVPASV 377
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 408 VYGA-MRDRNFDMLVGRGGGGVDPHPhSSLRSVAYNPDNSDAARltNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLY 486
Cdd:cd08513   378 FFSDdPGNRKFDLALFGWGLGSDPDL-SPLFHSCASPANGWGGQ--NFGGYS----NPEADELLDAARTELDPEERKALY 450
                         490       500       510
                  ....*....|....*....|....*....|...
gi 2238896597 487 AEVQNRYEALYPAiIPVSQMIDSVVLRTDVQGY 519
Cdd:cd08513   451 IRYQDLLAEDLPV-IPLYFRNQVSAYKKNLKGV 482
PBP2_NikA_DppA_OppA_like_15 cd08492
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-518 1.29e-65

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173857 [Multi-domain]  Cd Length: 484  Bit Score: 220.56  E-value: 1.29e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLL 123
Cdd:cd08492    14 CLDPHTLDFYPNGSVLRQVVDSLVYQDPTG--EIVPWLAESWEVSDDGTTYTFHLRDGVTFSDGTPLDAEAVKANFDRIL 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 124 HLNmaqatTWKSYGFTADNVEKMIRAKDAHTVEIELPKPNDPklVIYSLATLGSGsVLDRQTImphEKNGDWGNGwltTN 203
Cdd:cd08492    92 DGS-----TKSGLAASYLGPYKSTEVVDPYTVKVHFSEPYAP--FLQALSTPGLG-ILSPATL---ARPGEDGGG---EN 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 204 AAGSGPFKLDVWQAKDVLRISRVEGY-W-------RGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQ 275
Cdd:cd08492   158 PVGSGPFVVESWVRGQSIVLVRNPDYnWapalakhQGPAYLDKIVFRFIPEASVRVGALQSGQVDVITDIPPQDEKQLAA 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 276 NQGVVVDE-VKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQK--GMDATLPNpGYKLDV 352
Cdd:cd08492   238 DGGPVIETrPTPGVPYSLYLNTTRPPFDDVRVRQALQLAIDREAIVETVFFGSYPAASSLLSSttPYYKDLSD-AYAYDP 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 353 ARAKALLAEAGY----PNGFAT------TLRVLSDQPFLN---LATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDm 419
Cdd:cd08492   317 EKAKKLLDEAGWtargADGIRTkdgkrlTLTFLYSTGQPQsqsVLQLIQAQLKEVGIDLQLKVLDAGTLTARRASGDYD- 395
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 420 LVGRGGGGVDPHPHSSLrsvaYNPDNSDAArltnfqGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRY--EALy 497
Cdd:cd08492   396 LALSYYGRADPDILRTL----FHSANRNPP------GGYSRFADPELDDLLEKAAATTDPAERAALYADAQKYLieQAY- 464
                         490       500
                  ....*....|....*....|.
gi 2238896597 498 paIIPVSQMIDSVVLRTDVQG 518
Cdd:cd08492   465 --VVPLYEEPQVVAAAPNVKG 483
PBP2_NikA_DppA_OppA_like_6 cd08494
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-519 2.92e-65

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173859 [Multi-domain]  Cd Length: 448  Bit Score: 218.65  E-value: 2.92e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAmTGNEVVGVIV--NLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08494    12 SLDITT-TAGAAIDQVLlgNVYETLVRRDEDG--KVQPGLAESWTISDDGLTYTFTLRSGVTFHDGTPFDAADVKFSLQR 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 llhlnmAQATTWKSYGFTA-DNVEKmIRAKDAHTVEIELPKPnDPKLviysLATLGSGSVLdrqtIMPHEKNGDwgngwL 200
Cdd:cd08494    89 ------ARAPDSTNADKALlAAIAS-VEAPDAHTVVVTLKHP-DPSL----LFNLGGRAGV----VVDPASAAD-----L 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 201 TTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVV 280
Cdd:cd08494   148 ATKPVGTGPFTVAAWARGSSITLVRNDDYWGAKPKLDKVTFRYFSDPTALTNALLAGDIDAAPPFDAPELEQFADDPRFT 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 281 VDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIqkgmdaTLPNPGY-KL------DVA 353
Cdd:cd08494   228 VLVGTTTGKVLLAMNNARAPFDDVRVRQAIRYAIDRKALIDAAWDGYGTPIGGPI------SPLDPGYvDLtglypyDPD 301
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 354 RAKALLAEAGYPNGFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYG-AMRDRNFDM-LVGRggggVDPH 431
Cdd:cd08494   302 KARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKIEVVEPATWLQrVYKGKDYDLtLIAH----VEPD 377
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 432 phsslrsvaynpdnsDAARLTNfqgwrTSFY----DKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPAIIpVSQMI 507
Cdd:cd08494   378 ---------------DIGIFAD-----PDYYfgydNPEFQELYAQALAATDADERAELLKQAQRTLAEDAAADW-LYTRP 436
                         490
                  ....*....|..
gi 2238896597 508 DSVVLRTDVQGY 519
Cdd:cd08494   437 NIVVARKGVTGY 448
PBP2_AppA_like cd08514
The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus ...
38-490 1.01e-60

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: 207.86  E-value: 1.01e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  38 NMNNMLSLDpaaMTGNEVVGvivNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAW 117
Cdd:cd08514    12 NLNPILSTD---SASSEVAG---LIYEGLLKYDKDL--NFEPDLAESWEVSDDGKTYTFKLRKDVKWHDGEPLTADDVKF 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 118 SMNRLLHLNMAqatTWKSyGFTADNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGsgsvldrqtIMP-----HEKN 192
Cdd:cd08514    84 TYKAIADPKYA---GPRA-SGDYDEIKG-VEVPDDYTVVFHYKEPYAP--ALESWALNG---------ILPkhlleDVPI 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 193 GDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVatgMSVPDINA 272
Cdd:cd08514   148 ADFRHSPFNRNPVGTGPYKLKEWKRGQYIVLEANPDYFLGRPYIDKIVFRIIPDPTTALLELKAGELDI---VELPPPQY 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 273 LKQNQGvvVDEVKKGTIY--------YVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYG---FYHQRPIQKGMDA 341
Cdd:cd08514   225 DRQTED--KAFDKKINIYeypsfsytYLGWNLKRPLFQDKRVRQAITYAIDREEIIDGLLLGLGevaNGPFSPGTWAYNP 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 342 TLPNPGYklDVARAKALLAEAGYPNGFATTLRVLSDQPF-------------LNLATSVQSTLAQAGIKARIHSGTGNQV 408
Cdd:cd08514   303 DLKPYPY--DPDKAKELLAEAGWVDGDDDGILDKDGKPFsftlltnqgnpvrEQAATIIQQQLKEIGIDVKIRVLEWAAF 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 409 YGAMRDRNFDMLVGRGGGGVDPHPHSSLRSVAYNPDNSdaarltNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAE 488
Cdd:cd08514   381 LEKVDDKDFDAVLLGWSLGPDPDPYDIWHSSGAKPGGF------NFVGYK----NPEVDKLIEKARSTLDREKRAEIYHE 450

                  ..
gi 2238896597 489 VQ 490
Cdd:cd08514   451 WQ 452
PBP2_NikA_DppA_OppA_like_10 cd08515
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
30-517 9.46e-59

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: 201.68  E-value: 9.46e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  30 DDQLIVGMNmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQNLSTVlPSLAKSWSVSDDgKVITFNLVDNARFHSGNA 109
Cdd:cd08515     1 RDTLVIAVQ-KEPPTLDPYYNTSREGVIISRNIFDTLIYRDPDTGELV-PGLATSWKWIDD-TTLEFTLREGVKFHDGSP 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 110 VTAQDFAWSMNRLLhlnmAQATTWKSYGFTADNVEKmIRAKDAHTVEIELPKPnDPKLVIYsLATLGSgsvldrqTIMPH 189
Cdd:cd08515    78 MTAEDVVFTFNRVR----DPDSKAPRGRQNFNWLDK-VEKVDPYTVRIVTKKP-DPAALER-LAGLVG-------PIVPK 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 190 ---EKNGDWGngwLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATgmS 266
Cdd:cd08515   144 ayyEKVGPEG---FALKPVGTGPYKVTEFVPGERVVLEAFDDYWGGKPPIEKITFRVIPDVSTRVAELLSGGVDIIT--N 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 267 VP--DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYG----FYHQrPIQKGmD 340
Cdd:cd08515   219 VPpdQAERLKSSPGLTVVGGPTMRIGFITFDAAGPPLKDVRVRQALNHAIDRQAIVKALWGGRAkvpnTACQ-PPQFG-C 296
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 341 ATLPNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQPFLNLATS--VQSTLAQAGIKARIHSGTGnqvYGAMRDRNFD 418
Cdd:cd08515   297 EFDVDTKYPYDPEKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAeaIVGMWKAVGINAELNVLSK---YRALRAWSKG 373
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 419 MLVGRggggvdphphSSLRSVAYNPDNSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYEAlYP 498
Cdd:cd08515   374 GLFVP----------AFFYTWGSNGINDASASTSTWFKAR----DAEFDELLEKAETTTDPAKRKAAYKKALKIIAE-EA 438
                         490
                  ....*....|....*....
gi 2238896597 499 AIIPVSQMIDSVVLRTDVQ 517
Cdd:cd08515   439 YWTPLYQYSQNYGYSKDLN 457
PBP2_NikA_DppA_OppA_like_8 cd08495
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
52-492 4.71e-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: 173860 [Multi-domain]  Cd Length: 482  Bit Score: 195.25  E-value: 4.71e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  52 GNEVVGVIVnlYDSLVELD---PQNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHLNMA 128
Cdd:cd08495    21 GLRFLGLPV--YDPLVRWDlstADRPGEIVPGLAESWEVSPDGRRWTFTLRPGVKFHDGTPFDADAVVWNLDRMLDPDSP 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 129 QATTWKSyGFTADNVEKM--IRAKDAHTVEIELPKPNDPKLviYSLATLGSGSVldrqtiMPHEKNGDWGNGwLTTNAAG 206
Cdd:cd08495    99 QYDPAQA-GQVRSRIPSVtsVEAIDDNTVRITTSEPFADLP--YVLTTGLASSP------SPKEKAGDAWDD-FAAHPAG 168
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 207 SGPFKLDVWQAKDVLRISRVEGYWRGD-AKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQnQGVVVDEVK 285
Cdd:cd08495   169 TGPFRITRFVPRERIELVRNDGYWDKRpPKNDKLVLIPMPDANARLAALLSGQVDAIEAPAPDAIAQLKS-AGFQLVTNP 247
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 286 KGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDA-TLPNPGYKLDVARAKALLAEAGY 364
Cdd:cd08495   248 SPHVWIYQLNMAEGPLSDPRVRQALNLAIDREGLVDLLLGGLAAPATGPVPPGHPGfGKPTFPYKYDPDKARALLKEAGY 327
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 365 PNGFATTLRVLSDQPF----LNLATSVQSTLAQAGIKARIHSGTGNQVYGAMR---DRNFDMLVGRGGGGVDPHPHSSLR 437
Cdd:cd08495   328 GPGLTLKLRVSASGSGqmqpLPMNEFIQQNLAEIGIDLDIEVVEWADLYNAWRagaKDGSRDGANAINMSSAMDPFLALV 407
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2238896597 438 SVAYNPdnSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNR 492
Cdd:cd08495   408 RFLSSK--IDPPVGSNWGGYH----NPEFDALIDQARVTFDPAERAALYREAHAI 456
PBP2_NikA_DppA_OppA_like_5 cd08511
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-523 2.37e-54

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: 190.18  E-value: 2.37e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAamTGNEVVGVIV--NLYDSLVELDPqNLSTVlPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08511    13 RLDPA--LSRTFVGRQVfaALCDKLVDIDA-DLKIV-PQLATSWEISPDGKTLTLKLRKGVKFHDGTPFDAAAVKANLER 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 LLHLnmaQATTWKSYGFTADNVEKMirakDAHTVEIELPKPNDPklviySLATLGsgsvlDRQTIMPHEK-----NGDWG 196
Cdd:cd08511    89 LLTL---PGSNRKSELASVESVEVV----DPATVRFRLKQPFAP-----LLAVLS-----DRAGMMVSPKaakaaGADFG 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 197 NgwlttNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDA-KMRRVIFRHMTESQaLRLM-IEKGDIDVATGMSVPDINALK 274
Cdd:cd08511   152 S-----APVGTGPFKFVERVQQDRIVLERNPHYWNAGKpHLDRLVYRPIPDAT-VRLAnLRSGDLDIIERLSPSDVAAVK 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 275 QNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKG---MDATLPNPGYklD 351
Cdd:cd08511   226 KDPKLKVLPVPGLGYQGITFNIGNGPFNDPRVRQALALAIDREAINQVVFNGTFKPANQPFPPGspyYGKSLPVPGR--D 303
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 352 VARAKALLAEAGYPNgFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRGGGGVDPH 431
Cdd:cd08511   304 PAKAKALLAEAGVPT-VTFELTTANTPTGRQLAQVIQAMAAEAGFTVKLRPTEFATLLDRALAGDFQATLWGWSGRPDPD 382
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 432 P--HSSLRSVAYNpdnsdaarltNFQGWRTsfydKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQMIDS 509
Cdd:cd08511   383 GniYQFFTSKGGQ----------NYSRYSN----PEVDALLEKARASADPAERKALYNQAAKILADDLP-YIYLYHQPYY 447
                         490
                  ....*....|....
gi 2238896597 510 VVLRTDVQGYVPHP 523
Cdd:cd08511   448 IAASKKVRGLVPYP 461
PBP2_NikA_DppA_OppA_like_16 cd08502
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-519 4.91e-54

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173867 [Multi-domain]  Cd Length: 472  Bit Score: 189.32  E-value: 4.91e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLL 123
Cdd:cd08502    12 TLDPIVTTAYITRNHGYMIYDTLFGMDANG--EPQPQMAESWEVSDDGKTYTFTLRDGLKFHDGSPVTAADVVASLKRWA 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 124 HLN-MAQAttwkSYGFTADnvekmIRAKDAHTVEIELPKPNDPklVIYSLATLGSGSVLdrqtIMPHEKNGDWGNGWLTT 202
Cdd:cd08502    90 KRDaMGQA----LMAAVES-----LEAVDDKTVVITLKEPFGL--LLDALAKPSSQPAF----IMPKRIAATPPDKQITE 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 203 nAAGSGPFKLDVWQAKDVLRISRVEGY--------WRGDAK---MRRVIFRHMTESQ----ALRlmieKGDIDVATGMSV 267
Cdd:cd08502   155 -YIGSGPFKFVEWEPDQYVVYEKFADYvprkeppsGLAGGKvvyVDRVEFIVVPDANtavaALQ----SGEIDFAEQPPA 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 268 PDINALKQNQGVVVDEVkkGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRP--IQKG--MDATL 343
Cdd:cd08502   230 DLLPTLKADPVVVLKPL--GGQGVLRFNHLQPPFDNPKIRRAVLAALDQEDLLAAAVGDPDFYKVCGsmFPCGtpWYSEA 307
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 344 PNPGY-KLDVARAKALLAEAGYpNGfaTTLRVL--SDQPFL-NLATSVQSTLAQAGIKARIHS---GTGNQvYGAMRDRN 416
Cdd:cd08502   308 GKEGYnKPDLEKAKKLLKEAGY-DG--EPIVILtpTDYAYLyNAALVAAQQLKAAGFNVDLQVmdwATLVQ-RRAKPDGG 383
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 417 FDMLVGRGGGGVDPHPhsslrsVAYNPDNSDAARLtnfqGWRTsfyDKQLNELIDRALLEKDPARQKQLYAEVQNR-YEa 495
Cdd:cd08502   384 WNIFITSWSGLDLLNP------LLNTGLNAGKAWF----GWPD---DPEIEALRAAFIAATDPAERKALAAEIQKRaYE- 449
                         490       500
                  ....*....|....*....|....
gi 2238896597 496 lYPAIIPVSQMIDSVVLRTDVQGY 519
Cdd:cd08502   450 -DVPYIPLGQFTQPTAYRSKLEGL 472
PBP2_NikA cd08489
The substrate-binding component of an ABC-type nickel import system contains the type 2 ...
62-526 1.89e-51

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: 182.81  E-value: 1.89e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  62 LYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLlhLNMAQATTWKSYGFTAD 141
Cdd:cd08489    28 VYEPLVKYGEDG--KIEPWLAESWEISEDGKTYTFHLRKGVKFSDGTPFNAEAVKKNFDAV--LANRDRHSWLELVNKID 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 142 NVEkmirAKDAHTVEIELPKPNDPKLVIYSLAT----LGSGSVldrqtimpheKNGDWGNGwlTTNAAGSGPFKLDVWQA 217
Cdd:cd08489   104 SVE----VVDEYTVRLHLKEPYYPTLNELALVRpfrfLSPKAF----------PDGGTKGG--VKKPIGTGPWVLAEYKK 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 218 KDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDV---ATGMSVPDINALKQNQGVVVDEVKKGTIYYVAM 294
Cdd:cd08489   168 GEYAVFVRNPNYWGEKPKIDKITVKVIPDAQTRLLALQSGEIDLiygADGISADAFKQLKKDKGYGTAVSEPTSTRFLAL 247
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 295 SLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYG------FYHQRPiqkgmDATLPNPGYKLDVARAKALLAEAGYPNGF 368
Cdd:cd08489   248 NTASEPLSDLKVREAINYAIDKEAISKGILYGLEkpadtlFAPNVP-----YADIDLKPYSYDPEKANALLDEAGWTLNE 322
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 369 ATTLRVLSDQPF-LNL------------ATSVQSTLAQAGIKARIhSGTGNQVYGA-MRDRNFDMLVGRGGGgvDPH-PH 433
Cdd:cd08489   323 GDGIREKDGKPLsLELvyqtdnalqksiAEYLQSELKKIGIDLNI-IGEEEQAYYDrQKDGDFDLIFYRTWG--APYdPH 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 434 SSLRSVAYnPDNSDaarltnFQGWRTSFYDKQLNELIDRALLEKDPARQKQLYAEVQNRY--EALYpaiIPVSQMIDSVV 511
Cdd:cd08489   400 SFLSSMRV-PSHAD------YQAQVGLANKAELDALINEVLATTDEEKRQELYDEILTTLhdQAVY---IPLTYPRNKAV 469
                         490
                  ....*....|....*
gi 2238896597 512 LRTDVQGYVPHPSST 526
Cdd:cd08489   470 YNPKVKGVTFSPTQY 484
PBP2_NikA_DppA_OppA_like_20 cd08519
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
43-518 1.54e-50

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: 180.12  E-value: 1.54e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  43 LSLDPAAMTGNEVVGVIVNLYDSLVELDPQNlSTVLPSLAKSWS-VSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08519    11 RTLDPAGAYDLGSWQLLSNLGDTLYTYEPGT-TELVPDLATSLPfVSDDGLTYTIPLRQGVKFHDGTPFTAKAVKFSLDR 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 LLHLNMAQAttwksYGFtADNVEKmIRAKDAHTVEIELPKPNDPklvIYSLATLGSGSVLDRQTIMPHEkngdwgNGWLT 201
Cdd:cd08519    90 FIKIGGGPA-----SLL-ADRVES-VEAPDDYTVTFRLKKPFAT---FPALLATPALTPVSPKAYPADA------DLFLP 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 202 TNAAGSGPFKLDVWQaKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVAT-GMSVPDI--NALKQNQG 278
Cdd:cd08519   154 NTFVGTGPYKLKSFR-SESIRLEPNPDYWGEKPKNDGVDIRFYSDSSNLFLALQTGEIDVAYrSLSPEDIadLLLAKDGD 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 279 VVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVmtgygFYHQRP-----IQKGMDATLPNP--GY-KL 350
Cdd:cd08519   233 LQVVEGPGGEIRYIVFNVNQPPLDNLAVRQALAYLIDRDLIVNRV-----YYGTAEplyslVPTGFWGHKPVFkeKYgDP 307
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 351 DVARAKALLAEAGYPNG------FATTLRVLSDQPflnLATSVQSTL-AQAGIKARIHSGTGNQVYGAMRDRNFDM-LVG 422
Cdd:cd08519   308 NVEKARQLLQQAGYSAEnplkleLWYRSNHPADKL---EAATLKAQLeADGLFKVNLKSVEWTTYYKQLSKGAYPVyLLG 384
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 423 rggggvdphphsslrsvaYNPDNSDA-ARLTNFQG-----WRTSFYD-KQLNELIDRALLEKDPARQKQLYAEVQnRYEA 495
Cdd:cd08519   385 ------------------WYPDYPDPdNYLTPFLScgngvFLGSFYSnPKVNQLIDKSRTELDPAARLKILAEIQ-DILA 445
                         490       500
                  ....*....|....*....|...
gi 2238896597 496 LYPAIIPVSQMIDSVVLRTDVQG 518
Cdd:cd08519   446 EDVPYIPLWQGKQYAVAQKNVKG 468
PBP2_NikA_DppA_OppA_like_1 cd08508
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
33-500 1.22e-49

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 173873  Cd Length: 470  Bit Score: 177.57  E-value: 1.22e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  33 LIVGMNMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDP--QNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSG-NA 109
Cdd:cd08508     2 LRIGSAADDIRTLDPHFATGTTDKGVISWVFNGLVRFPPgsADPYEIEPDLAESWESSDDPLTWTFKLRKGVMFHGGyGE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 110 VTAQDFAWSMNRllhlnmaqATTWKSYGFTAD-NVEKMIRAKDAHTVEIELPKPnDPKLvIYSLATLGSGSVLDRQTImp 188
Cdd:cd08508    82 VTAEDVVFSLER--------AADPKRSSFSADfAALKEVEAHDPYTVRITLSRP-VPSF-LGLVSNYHSGLIVSKKAV-- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 hEKNGDWgngwLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVP 268
Cdd:cd08508   150 -EKLGEQ----FGRKPVGTGPFEVEEHSPQQGVTLVANDGYFRGAPKLERINYRFIPNDASRELAFESGEIDMTQGKRDQ 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 269 -DINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGInktVMTGYGFYHQR------PIQKGMDA 341
Cdd:cd08508   225 rWVQRREANDGVVVDVFEPAEFRTLGLNITKPPLDDLKVRQAIAAAVNVDEV---VEFVGAGVAQPgnsvipPGLLGEDA 301
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 342 tlPNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLV 421
Cdd:cd08508   302 --DAPVYPYDPAKAKALLAEAGFPNGLTLTFLVSPAAGQQSIMQVVQAQLAEAGINLEIDVVEHATFHAQIRKDLSAIVL 379
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2238896597 422 grGGGGVDPHPHSSLRSVaYNPDNSDAARLTNFQGWRTSFYDKQlnelIDRALLEKDPARQKQLYAEVQNRYEALYPAI 500
Cdd:cd08508   380 --YGAARFPIADSYLTEF-YDSASIIGAPTAVTNFSHCPVADKR----IEAARVEPDPESRSALWKEAQKKIDEDVCAI 451
PBP2_NikA_DppA_OppA_like_9 cd08496
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
39-519 4.45e-48

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA 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: 172.91  E-value: 4.45e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  39 MNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQnlSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWS 118
Cdd:cd08496     7 SADPTSWDPAQGGSGADHDYLWLLYDTLIKLDPD--GKLEPGLAESWEYNADGTTLTLHLREGLTFSDGTPLDAAAVKAN 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 119 MNRLLHL---NMAQATTWKSygftadnVEkmirAKDAHTVEIELPKPnDPKLvIYSLAtlgsgsvlDRQTIMPHEKNGDW 195
Cdd:cd08496    85 LDRGKSTggsQVKQLASISS-------VE----VVDDTTVTLTLSQP-DPAI-PALLS--------DRAGMIVSPTALED 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 196 GnGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDA-KMRRVIFRHMTESQALRLMIEKGDIDVATGMSvPDINALK 274
Cdd:cd08496   144 D-GKLATNPVGAGPYVLTEWVPNSKYVFERNEDYWDAANpHLDKLELSVIPDPTARVNALQSGQVDFAQLLA-AQVKIAR 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 275 QNQGVVVDEVKKGTIyYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLP--NPGYKLDV 352
Cdd:cd08496   222 AAGLDVVVEPTLAAT-LLLLNITGAPFDDPKVRQAINYAIDRKAFVDALLFGLGEPASQPFPPGSWAYDPslENTYPYDP 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 353 ARAKALLAEAGYPNGFATTLRVLSdQPFLNLATSVQSTLAQAGIKARIHSGTG----NQVYGAmrdRNFDMLVGRGGGGV 428
Cdd:cd08496   301 EKAKELLAEAGYPNGFSLTIPTGA-QNADTLAEIVQQQLAKVGIKVTIKPLTGanaaGEFFAA---EKFDLAVSGWVGRP 376
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 429 DPhphsslRSVAYNPDNSDAARLTNfqgwrtSFYDKQLNELIDRALLEKDPARQKQLYAEVqNRY---EALYpaiIPVSQ 505
Cdd:cd08496   377 DP------SMTLSNMFGKGGYYNPG------KATDPELSALLKEVRATLDDPARKTALRAA-NKVvveQAWF---VPLFF 440
                         490
                  ....*....|....
gi 2238896597 506 MIDSVVLRTDVQGY 519
Cdd:cd08496   441 QPSVYALSKKVSGL 454
PBP2_NikA_DppA_OppA_like_19 cd08518
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
31-500 1.15e-46

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: 169.31  E-value: 1.15e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  31 DQLIVGMNMNNMLSLDPaaMTGNEVVGVIvNLYDSLVELDPQNlsTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAV 110
Cdd:cd08518     1 DELVLAVGSEPETGFNP--LLGWGEHGEP-LIFSGLLKRDENL--NLVPDLATSYKVSDDGLTWTFTLRDDVKFSDGEPL 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 111 TAQDFAWSmnrllhLNMAQATTWKSYGFTadNVEKmIRAKDAHTVEIELPKPNDPklVIYSLATLGsgsvldrqtIMP-- 188
Cdd:cd08518    76 TAEDVAFT------YNTAKDPGSASDILS--NLED-VEAVDDYTVKFTLKKPDST--FLDKLASLG---------IVPkh 135
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 -HEKNGDWGngwltTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRlMIEKGDIDVAT---- 263
Cdd:cd08518   136 aYENTDTYN-----QNPIGTGPYKLVQWDKGQQVIFEANPDYYGGKPKFKKLTFLFLPDDAAAA-ALKSGEVDLALipps 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 264 -------GMSVPDINALkQNQGVVVDEVKKGTiyyvaMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQ 336
Cdd:cd08518   210 lakqgvdGYKLYSIKSA-DYRGISLPFVPATG-----KKIGNNVTSDPAIRKALNYAIDRQAIVDGVLNGYGTPAYSPPD 283
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 337 KgmdatLP--NPG---YKLDVARAKALLAEAG---------YPNG--FATTLRVLSDQPF-LNLATSVQSTLAQAGIKAR 399
Cdd:cd08518   284 G-----LPwgNPDaaiYDYDPEKAKKILEEAGwkdgddggrEKDGqkAEFTLYYPSGDQVrQDLAVAVASQAKKLGIEVK 358
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 400 IHSGTGNQVYGAMRDRNFDMlvgrGGGGVDPHP-----HSSLRSVAYNpdNSdaarltnfqgwrtSFY-DKQLNELIDRA 473
Cdd:cd08518   359 LEGKSWDEIDPRMHDNAVLL----GWGSPDDTElyslyHSSLAGGGYN--NP-------------GHYsNPEVDAYLDKA 419
                         490       500
                  ....*....|....*....|....*..
gi 2238896597 474 LLEKDPARQKQLYAEVQNRYEALYPAI 500
Cdd:cd08518   420 RTSTDPEERKKYWKKAQWDGAEDPPWL 446
PBP2_NikA_DppA_OppA_like_21 cd08520
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
62-500 4.80e-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: 173885 [Multi-domain]  Cd Length: 468  Bit Score: 165.19  E-value: 4.80e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  62 LYDSLVELDPQNlstVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLlhlnmaQATTWKSYGFTAD 141
Cdd:cd08520    32 IFDSLVWKDEKG---FIPWLAESWEVSEDGLTYTFHLREGAKWHDGEPLTAEDVAFTFDYM------KKHPYVWVDIELS 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 142 NVEKmIRAKDAHTVEIELPKPNDPKLviYSLATLgsgsvldrQTIMP-H--EKNGDwGNGWLTTNAA-GSGPFKL-DVWQ 216
Cdd:cd08520   103 IIER-VEALDDYTVKITLKRPYAPFL--EKIATT--------VPILPkHiwEKVED-PEKFTGPEAAiGSGPYKLvDYNK 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 217 AKDVLRISRVEGYWRGDAKMRRVIFRHMTES-QALrlmiEKGDIDVaTGMSVPDINALKQNQGVVVDEVKKGTIYYVAMS 295
Cdd:cd08520   171 EQGTYLYEANEDYWGGKPKVKRLEFVPVSDAlLAL----ENGEVDA-ISILPDTLAALENNKGFKVIEGPGFWVYRLMFN 245
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 296 LKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGF-----YhqrpIQKGMDATLPN-PGYKLDVARAKALLAEAGY----- 364
Cdd:cd08520   246 HDKNPFSDKEFRQAIAYAIDRQELVEKAARGAAAlgspgY----LPPDSPWYNPNvPKYPYDPEKAKELLKGLGYtdngg 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 365 ---PNGFATTLRVL--SDQPFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLV-GRGGGGVDPhphSSLRS 438
Cdd:cd08520   322 dgeKDGEPLSLELLtsSSGDEVRVAELIKEQLERVGIKVNVKSLESKTLDSAVKDGDYDLAIsGHGGIGGDP---DILRE 398
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2238896597 439 VaYNPDNSDAARltnfqGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPAI 500
Cdd:cd08520   399 V-YSSNTKKSAR-----GYD----NEELNALLRQQLQEMDPEKRKELVFEIQELYAEELPMI 450
PBP2_TmCBP_oligosaccharides_like cd08509
The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains ...
47-500 2.13e-44

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: 164.03  E-value: 2.13e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  47 PAAMTGNEVVGVIVNLYDSLVELDPQNlSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSmnrllhLN 126
Cdd:cd08509    18 PYAPGGASTAGLVQLIYEPLAIYNPLT-GEFIPWLAESWTWSDDFTTLTVTLRKGVKWSDGEPFTADDVVFT------FE 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 127 MAQATTWKSYGFTADNVEKmIRAKDAHTVEIELPKPNdPKLVIYSLATLGsgsvldRQTIMP-H--EKNGDWGNGWLTTN 203
Cdd:cd08509    91 LLKKYPALDYSGFWYYVES-VEAVDDYTVVFTFKKPS-PTEAFYFLYTLG------LVPIVPkHvwEKVDDPLITFTNEP 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 204 AAGSGPFKLDVWQAKDVLrISRVEGYWRGDAKMR--RVIFRHMTESQALRLMIEKGDIDVAtGMSVPDI--NALKQNQGV 279
Cdd:cd08509   163 PVGTGPYTLKSFSPQWIV-LERNPNYWGAFGKPKpdYVVYPAYSSNDQALLALANGEVDWA-GLFIPDIqkTVLKDPENN 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 280 VVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGMDATLPN-----------PGY 348
Cdd:cd08509   241 KYWYFPYGGTVGLYFNTKKYPFNDPEVRKALALAIDRTAIVKIAGYGYATPAPLPGPPYKVPLDPSgiakyfgsfglGWY 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 349 KLDVARAKALLAEAGY----------PNGFATTLRVL-----SDqpFLNLATSVQSTLAQAGIKARIHSGTGNQVYGAMR 413
Cdd:cd08509   321 KYDPDKAKKLLESAGFkkdkdgkwytPDGTPLKFTIIvpsgwTD--WMAAAQIIAEQLKEFGIDVTVKTPDFGTYWAALT 398
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 414 DRNFDM-LVGRGGGGVDPHPHSSLRSvAYNPDNSDAARLTNFQGWRtsFYDKQLNELIDRALLEKDPARQKQLYAEVQNR 492
Cdd:cd08509   399 KGDFDTfDAATPWGGPGPTPLGYYNS-AFDPPNGGPGGSAAGNFGR--WKNPELDELIDELNKTTDEAEQKELGNELQKI 475

                  ....*...
gi 2238896597 493 YEALYPAI 500
Cdd:cd08509   476 FAEEMPVI 483
PBP2_clavulanate_OppA2 cd08506
The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis ...
44-489 1.09e-41

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: 155.88  E-value: 1.09e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNLS---TVLPSLAKSW-SVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSM 119
Cdd:cd08506    12 HLDPARTYYADGWQVLRLIYRQLTTYKPAPGAegtEVVPDLATDTgTVSDDGKTWTYTLRDGLKFEDGTPITAKDVKYGI 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 120 NRLLHlnmaqattwksygftadnvekmIRAKDAHTVEIELPKPnDPKLViySLATLGSGSVLdrqtimPHEKnGDWGNGw 199
Cdd:cd08506    92 ERSFA----------------------IETPDDKTIVFHLNRP-DSDFP--YLLALPAAAPV------PAEK-DTKADY- 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 200 lTTNAAGSGPFKLDVWQAKDVLRISRVEgYWR------GDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINAl 273
Cdd:cd08506   139 -GRAPVSSGPYKIESYDPGKGLVLVRNP-HWDaetdpiRDAYPDKIVVTFGLDPETIDQRLQAGDADLALDGDGVPRAP- 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 274 kqnQGVVVDEVKK-------GTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTV-MTGYGFYHQRPIQKGMDA---- 341
Cdd:cd08506   216 ---AAELVEELKArlhnvpgGGVYYLAINTNVPPFDDVKVRQAVAYAVDRAALVRAFgGPAGGEPATTILPPGIPGyedy 292
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 342 -TLPNPGYKLDVARAKALLAEAGYPnGFATTLRVLSDQPFLNLATSVQSTLAQAGIKAR---IHSGTGNQVYGAMRDRNF 417
Cdd:cd08506   293 dPYPTKGPKGDPDKAKELLAEAGVP-GLKLTLAYRDTAVDKKIAEALQASLARAGIDVTlkpIDSATYYDTIANPDGAAY 371
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2238896597 418 DMLVgRGGGGVDPHPHSSLRSVaYNPDNSDAARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQLYAEV 489
Cdd:cd08506   372 DLFI-TGWGPDWPSASTFLPPL-FDGDAIGPGGNSNYSGYD----DPEVNALIDEALATTDPAEAAALWAEL 437
MbnE-like cd08497
Methanobactin MbnE, a periplasmic binding protein of the TonB-dependent transport system, and ...
44-480 1.31e-39

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: 150.36  E-value: 1.31e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPQNLSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLl 123
Cdd:cd08497    28 SLNPFILKGTAAAGLFLLVYETLMTRSPDEPFSLYGLLAESVEYPPDRSWVTFHLRPEARFSDGTPVTAEDVVFSFETL- 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 124 hlnMAQATTWKSYgFTADnVEKmIRAKDAHTVEIELPKPNDPKLvIYSLATLgsgsvldrqTIMPHE--KNGDWGNGWLT 201
Cdd:cd08497   107 ---KSKGPPYYRA-YYAD-VEK-VEALDDHTVRFTFKEKANREL-PLIVGGL---------PVLPKHwyEGRDFDKKRYN 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 202 TNAA-GSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRR-------VIFRHMTESQALRLMIEKGDIDV---------ATG 264
Cdd:cd08497   171 LEPPpGSGPYVIDSVDPGRSITYERVPDYWGKDLPVNRgrynfdrIRYEYYRDRTVAFEAFKAGEYDFreensakrwATG 250
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 265 MsvpDINALKQNqgvvvdEVKKGTIYY--------VAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMtgYGFYhQRpiq 336
Cdd:cd08497   251 Y---DFPAVDDG------RVIKEEFPHgnpqgmqgFVFNTRRPKFQDIRVREALALAFDFEWMNKNLF--YGQY-TR--- 315
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 337 kgmdatlpnpgYKLDVARAKALLAEAGY----------PNGFATTLRVLSDQP-FLNLATSVQSTLAQAGIKARIHSGTG 405
Cdd:cd08497   316 -----------TRFNLRKALELLAEAGWtvrggdilvnADGEPLSFEILLDSPtFERVLLPYVRNLKKLGIDASLRLVDS 384
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2238896597 406 NQVYGAMRDRNFDMLVGRGGGGVDPHPHSSLRSvaynpdNSDAARLT---NFQGWRtsfyDKQLNELIDRALLEKDPA 480
Cdd:cd08497   385 AQYQKRLRSFDFDMITAAWGQSLSPGNEQRFHW------GSAAADKPgsnNLAGIK----DPAVDALIEAVLAADDRE 452
PBP2_NikA_DppA_OppA_like_4 cd08500
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
45-519 9.57e-39

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: 148.16  E-value: 9.57e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  45 LDPAAMTGNEVVGVIVNLYDSLVELDPQNlSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLh 124
Cdd:cd08500    20 LNPALADEWGSRDIIGLGYAGLVRYDPDT-GELVPNLAESWEVSEDGREFTFKLREGLKWSDGQPFTADDVVFTYEDIY- 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 125 LNmAQATTWKSYGFTADNVEKMIRAKDAHTVEIELPKPNDPklVIYSLATlgsgsvldrqTIMPhekngdwgngwlttna 204
Cdd:cd08500    98 LN-PEIPPSAPDTLLVGGKPPKVEKVDDYTVRFTLPAPNPL--FLAYLAP----------PDIP---------------- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 205 aGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMR------RVIFRHMTESQALRLMIEKGDIDV-ATGMSVPDINALKQNQ 277
Cdd:cd08500   149 -TLGPWKLESYTPGERVVLERNPYYWKVDTEGNqlpyidRIVYQIVEDAEAQLLKFLAGEIDLqGRHPEDLDYPLLKENE 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 278 gvvvdEVKKGTIY---------YVAMSL------KNEHFAKPKVREAVRYLIDYDGINKTVMTGYGFYHQ---RPIQKGM 339
Cdd:cd08500   228 -----EKGGYTVYnlgpatstlFINFNLndkdpvKRKLFRDVRFRQALSLAINREEIIETVYFGLGEPQQgpvSPGSPYY 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 340 DATLPNPGYKLDVARAKALLAEAGY----PNGFattlRVLSD--------------QPFLNLATSVQSTLAQAGIKARIH 401
Cdd:cd08500   303 YPEWELKYYEYDPDKANKLLDEAGLkkkdADGF----RLDPDgkpveftlitnagnSIREDIAELIKDDWRKIGIKVNLQ 378
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 402 SGTGNQVYG-AMRDRNFD-MLVGRGGGGVDPH-----PHSSLRSVAYNPDNSDAARLtnfQGWRTSFYDKQLNELIDRAL 474
Cdd:cd08500   379 PIDFNLLVTrLSANEDWDaILLGLTGGGPDPAlgapvWRSGGSLHLWNQPYPGGGPP---GGPEPPPWEKKIDDLYDKGA 455
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 2238896597 475 LEKDPARQKQLYAEVQnRYEALYPAIIPVSQMIDSVVLRTDVQGY 519
Cdd:cd08500   456 VELDQEKRKALYAEIQ-KIAAENLPVIGTVGPLAPVAVKNRLGNV 499
nickel_nikA TIGR02294
nickel ABC transporter, nickel/metallophore periplasmic binding protein; Members of this ...
76-529 2.58e-35

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: 138.40  E-value: 2.58e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  76 TVLPSLAKSWSVSDDGKVITFNLVDNARFHSGN-----AVTAQDFAWSMNRLLHlnmaqatTWKSYGFTADNVEkmirAK 150
Cdd:TIGR02294  47 KIEPWLAKSWTVSEDGKTYTFKLRDDVKFSDGTpfdaeAVKKNFDAVLQNSQRH-------SWLELSNQLDNVK----AL 115
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 151 DAHTVEIELPKPNDPKLviYSLATlgsgsVLDRQTIMPHEKNGDWGNGWLtTNAAGSGPFKLDVWQAKDVLRISRVEGYW 230
Cdd:TIGR02294 116 DKYTFELVLKEAYYPAL--QELAM-----PRPYRFLSPSDFKNDTTKDGV-KKPIGTGPWMLGESKQDEYAVFVRNENYW 187
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 231 RGDAKMRRVIFRHMTESQALRLMIEKGDIDVATG----MSVPDINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKV 306
Cdd:TIGR02294 188 GEKPKLKKVTVKVIPDAETRALAFESGEVDLIFGnegsIDLDTFAQLKDDGDYQTALSQPMNTRMLLLNTGKNATSDLAV 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 307 REAVRYLIDYDGINKTVMTGYGFYHQRPIQKGM-DATLPNPGYKLDVARAKALLAEAGYPNGFATTLRVLSDQPFL---- 381
Cdd:TIGR02294 268 RQAINHAVNKQSIAKNILYGTEKPADTLFAKNVpYADIDLKPYKYDVKKANALLDEAGWKLGKGKDVREKDGKPLElely 347
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 382 ---------NLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDMLVGRG-GGGVDPHPHSSLRSVAYNPDNSDAARL 451
Cdd:TIGR02294 348 ydktsalqkSLAEYLQAEWRKIGIKLSLIGEEEDKIAARRRDGDFDMMFNYTwGAPYDPHSFISAMRAKGHGDESAQSGL 427
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 452 TNfqgwrtsfyDKQLNELIDRALLEKDPARQKQLYAEVQNRY--EALYpaiIPVSQMIDSVVLRTDVqGYVPHPSSTTHL 529
Cdd:TIGR02294 428 AN---------KDEIDKSIGDALASTDETERQELYKNILTTLhdEAVY---IPISYISMTVVYRKDL-EKVSFAPSQYEL 494
PBP2_NikA_DppA_OppA_like_12 cd08491
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-530 1.42e-32

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: 130.19  E-value: 1.42e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAaMTGNEVVGVIV--NLYDSLVELDPQNlSTVLPSLAKSWSVSDDgKVITFNLVDNARFHSGNAVTAQDFAWSMNR 121
Cdd:cd08491    12 SLEPC-DSSRTAVGRVIrsNVTEPLTEIDPES-GTVGPRLATEWEQVDD-NTWRFKLRPGVKFHDGTPFDAEAVAFSIER 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 122 llhlNMAQATTWKSYGFTADNVEKMIRAKDAHTVEIELPKPnDPKL-VIYSLATLGSgsvldrqTIMPHEKngdwgngwL 200
Cdd:cd08491    89 ----SMNGKLTCETRGYYFGDAKLTVKAVDDYTVEIKTDEP-DPILpLLLSYVDVVS-------PNTPTDK--------K 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 201 TTNAAGSGPFKLDVWQAKDVLRISRVEGYWRGDAKMRRVIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVV 280
Cdd:cd08491   149 VRDPIGTGPYKFDSWEPGQSIVLSRFDGYWGEKPEVTKATYVWRSESSVRAAMVETGEADLAPSIAVQDATNPDTDFAYL 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 281 VDEvkkgtIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTGYG---FYHQRPIQKGMDATLpnPGYKLDVARAKA 357
Cdd:cd08491   229 NSE-----TTALRIDAQIPPLDDVRVRKALNLAIDRDGIVGALFGGQGrpaTQLVVPGINGHNPDL--KPWPYDPEKAKA 301
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 358 LLAEA---GYPNGFATTLRVLSDQpFLNLATSV---QSTLAQAGIKARIHSGTGNQVYGAMRdRNFDMlvGRGgggvdph 431
Cdd:cd08491   302 LVAEAkadGVPVDTEITLIGRNGQ-FPNATEVMeaiQAMLQQVGLNVKLRMLEVADWLRYLR-KPFPE--DRG------- 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 432 phSSLRSVAYNPDNSDAArLTNFQ-----GWRTSFYDKQLNELIDRALLEKDPARQKqLYAEV-QNRYEALYPaIIPVSQ 505
Cdd:cd08491   371 --PTLLQSQHDNNSGDAS-FTFPVyylseGSQSTFGDPELDALIKAAMAATGDERAK-LFQEIfAYVHDEIVA-DIPMFH 445
                         490       500
                  ....*....|....*....|....*
gi 2238896597 506 MIdSVVLRTDVQGYVPHPSSTTHLR 530
Cdd:cd08491   446 MV-GYTRVSKRLDYKPDIATNSELR 469
PRK15413 PRK15413
glutathione ABC transporter substrate-binding protein GsiB; Provisional
17-492 7.36e-32

glutathione ABC transporter substrate-binding protein GsiB; Provisional


Pssm-ID: 185311 [Multi-domain]  Cd Length: 512  Bit Score: 128.85  E-value: 7.36e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  17 MAAVPAvLSAKtpDDQLIVGmnmNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQ-NLSTVLpslAKSWSVSDDGKVIT 95
Cdd:PRK15413   19 LAASPA-FAAK--DVVVAVG---SNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEmKLKNVL---AESYTVSDDGLTYT 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  96 FNLVDNARFHSGNAVTAQDFAWSMNRLL----HLnmaqattwKSYgftadNVEKMI---RAKDAHTVEIELPKP------ 162
Cdd:PRK15413   90 VKLREGVKFQDGTDFNAAAVKANLDRASnpdnHL--------KRY-----NLYKNIaktEAVDPTTVKITLKQPfsafin 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 163 --NDPKLVIYSLATLgsgsvldrqtimphEKNG-DWGngwltTNAAGSGPFKLDVWQAKDVLRISRVEGYWR-GDAKMRR 238
Cdd:PRK15413  157 ilAHPATAMISPAAL--------------EKYGkEIG-----FHPVGTGPYELDTWNQTDFVKVKKFAGYWQpGLPKLDS 217
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 239 VIFRHMTESQALRLMIEKGDIDVATGMSVPDINALKQNQGVvvDEVKKGTIY--YVAMSLKNEHFAKPKVREAVRYLIDY 316
Cdd:PRK15413  218 ITWRPVADNNTRAAMLQTGEAQFAFPIPYEQAALLEKNKNL--ELVASPSIMqrYISMNVTQKPFDNPKVREALNYAINR 295
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 317 DGINKTVMTGYGFYHQRPIQKGMDATLPNPGYKLDVARAKALLAEAGYPNGFATTL----RVLSDQPFLNLAtsvQSTLA 392
Cdd:PRK15413  296 QALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPAKARELLKEAGYPNGFSTTLwsshNHSTAQKVLQFT---QQQLA 372
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 393 QAGIKARIHSGTGNQVYGAMRDRnfdmlvGRGGGGVdphphsSLRSVAYNPDNSDA----ARLTNFQGW-----RTSFY- 462
Cdd:PRK15413  373 QVGIKAQVTAMDAGQRAAEVEGK------GQKESGV------RMFYTGWSASTGEAdwalSPLFASQNWpptlfNTAFYs 440
                         490       500       510
                  ....*....|....*....|....*....|
gi 2238896597 463 DKQLNELIDRALLEKDPARQKQLYAEVQNR 492
Cdd:PRK15413  441 NKQVDDDLAQALKTNDPAEKTRLYKAAQDI 470
PBP2_Lpqw cd08501
The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic ...
41-519 8.11e-29

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: 119.37  E-value: 8.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  41 NMLSLDpaamTGNEVVGVIVNLY---------DSLVELDPQNLSTVLPslakswsVSDDGKVITFNLVDNARFHSGNAVT 111
Cdd:cd08501    14 NPHSAA----GNSTYTSALASLVlpsafrydpDGTDVPNPDYVGSVEV-------TSDDPQTVTYTINPEAQWSDGTPIT 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 112 AQDF--AWSMNrllhlNMAQATTWKSYGFTADNVEKMIRAKDAHTVEIELPKPNDPklviY-SLATLGSGSVLDRqtimp 188
Cdd:cd08501    83 AADFeyLWKAM-----SGEPGTYDPASTDGYDLIESVEKGDGGKTVVVTFKQPYAD----WrALFSNLLPAHLVA----- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 hEKNGDWGNGWLTTNAAGSGPFKLD-VWQAKDVLRISRVEGYWrGD--AKMRRVIFRHMTESQALRLMIEKGDIDVA-TG 264
Cdd:cd08501   149 -DEAGFFGTGLDDHPPWSAGPYKVEsVDRGRGEVTLVRNDRWW-GDkpPKLDKITFRAMEDPDAQINALRNGEIDAAdVG 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 265 MSVPDINALKQNQGVVVDEVKKGTIYYVAMSLKNEHFAKPKVREAVRYLIDYDGINKTVMTG-------YGFYHQRPIQK 337
Cdd:cd08501   227 PTEDTLEALGLLPGVEVRTGDGPRYLHLTLNTKSPALADVAVRKAFLKAIDRDTIARIAFGGlppeaepPGSHLLLPGQA 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 338 GMDATLPNPGyKLDVARAKALLAEAGYPNGFAT--------TLRVL---SDQPFLNLATSVQSTLAQAGIKARIHSGTGN 406
Cdd:cd08501   307 GYEDNSSAYG-KYDPEAAKKLLDDAGYTLGGDGiekdgkplTLRIAydgDDPTAVAAAELIQDMLAKAGIKVTVVSVPSN 385
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 407 QVYGAMRDR-NFDMLVGRGGGGVdphphsslrSVAYNPDNSDA-ARLTNFQGWRtsfyDKQLNELIDRALLEKDPARQKQ 484
Cdd:cd08501   386 DFSKTLLSGgDYDAVLFGWQGTP---------GVANAGQIYGScSESSNFSGFC----DPEIDELIAEALTTTDPDEQAE 452
                         490       500       510
                  ....*....|....*....|....*....|....*
gi 2238896597 485 LYAEVQNRYEALYpAIIPVSQMIDSVVLRTDVQGY 519
Cdd:cd08501   453 LLNEADKLLWEQA-YTLPLYQGPGLVAVKKGLANV 486
PBP2_Lactococcal_OppA_like cd08510
The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; ...
79-519 2.03e-26

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: 112.75  E-value: 2.03e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  79 PSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHlnmaQATTWKSYGFTADNVEKMIRAKDAHTVEIE 158
Cdd:cd08510    50 DSGAAKFKLDDKAKTVTITIKDGVKWSDGKPVTAKDLEYSYEIIAN----KDYTGVRYTDSFKNIVGMEEYHDGKADTIS 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 159 -LPKPNDPKLVIY------SLATLGSGSVldrQTIMPHEKNGDWGNGWL------TTNAAGSGPFKLDVWQAKDVLRISR 225
Cdd:cd08510   126 gIKKIDDKTVEITfkemspSMLQSGNGYF---EYAEPKHYLKDVPVKKLessdqvRKNPLGFGPYKVKKIVPGESVEYVP 202
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 226 VEGYWRGDAKMRRVIFRHMTESQALRLMiEKGDIDVATGMSVPDINALKQNQGVVVdeVKKGTIYYVAMSLKNEHF---- 301
Cdd:cd08510   203 NEYYWRGKPKLDKIVIKVVSPSTIVAAL-KSGKYDIAESPPSQWYDQVKDLKNYKF--LGQPALSYSYIGFKLGKWdkkk 279
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 302 -----------AKPKVREAVRYLIDYDGINKTVMTGYGFYHQRPI----QKGMDATLpnPGYKLDVARAKALLAEAGY-- 364
Cdd:cd08510   280 genvmdpnakmADKNLRQAMAYAIDNDAVGKKFYNGLRTRANSLIppvfKDYYDSEL--KGYTYDPEKAKKLLDEAGYkd 357
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 365 ---------PNGfattlrvlsdQPF-LNLA----TSVQSTLAQA--------GIKARIHSGT---GNQVYGAMR--DRNF 417
Cdd:cd08510   358 vdgdgfredPDG----------KPLtINFAamsgSETAEPIAQYyiqqwkkiGLNVELTDGRlieFNSFYDKLQadDPDI 427
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 418 DMLVGRGGGGVDPHPhSSLRSvaynpdnSDAArlTNFQGWRTSFYDKQLNELIDRALLekDPARQKQLYAEVQN-RYEAL 496
Cdd:cd08510   428 DVFQGAWGTGSDPSP-SGLYG-------ENAP--FNYSRFVSEENTKLLDAIDSEKAF--DEEYRKKAYKEWQKyMNEEA 495
                         490       500
                  ....*....|....*....|...
gi 2238896597 497 YpaIIPVSQMIDSVVLRTDVQGY 519
Cdd:cd08510   496 P--VIPTLYRYSITPVNKRVKGY 516
PRK15104 PRK15104
oligopeptide ABC transporter substrate-binding protein OppA; Provisional
3-533 1.96e-23

oligopeptide ABC transporter substrate-binding protein OppA; Provisional


Pssm-ID: 185059 [Multi-domain]  Cd Length: 543  Bit Score: 103.71  E-value: 1.96e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597   3 ARAILRILLLSTLCMAA-VPAvlSAKTPDDQLIVGMNMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQnlSTVLPSL 81
Cdd:PRK15104   11 AAGVLAALMAGNVALAAdVPA--GVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDPD--GHPAPGV 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  82 AKSWSvSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHLNMAQA-TTWKSYGFTAdNVEKMIRAK---------- 150
Cdd:PRK15104   87 AESWD-NKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLADPKTASPyASYLQYGHIA-NIDDIIAGKkpptdlgvka 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 151 -DAHTVEIEL--PKPNDPKLVIYSlatlgSGSVLDRQTImphEKNGDwgnGW-LTTNAAGSGPFKLDVWQAKDVLRISRV 226
Cdd:PRK15104  165 iDDHTLEVTLsePVPYFYKLLVHP-----SMSPVPKAAV---EKFGE---KWtQPANIVTNGAYKLKDWVVNERIVLERN 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 227 EGYWrGDAK--MRRVIF----RHMTESQALRlmieKGDIDVA-TGMSVPDINALKQNqgvVVDEVKKG---TIYYVAMSL 296
Cdd:PRK15104  234 PTYW-DNAKtvINQVTYlpisSEVTDVNRYR----SGEIDMTyNNMPIELFQKLKKE---IPDEVHVDpylCTYYYEINN 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 297 KNEHFAKPKVREAVRYLIDYDGI-NKTVMTG----YGFyhQRPIQKGMDATLPN----PGYKLDvARAKALLAEAGYPNG 367
Cdd:PRK15104  306 QKPPFNDVRVRTALKLGLDRDIIvNKVKNQGdlpaYGY--TPPYTDGAKLTQPEwfgwSQEKRN-EEAKKLLAEAGYTAD 382
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 368 FATTLRVLSDQPFLN--LATSVQSTLAQ-AGIKARIHsgtgNQVYGAMRDR----NFDmlVGRGGGGVD-PHPHSSLRSV 439
Cdd:PRK15104  383 KPLTFNLLYNTSDLHkkLAIAAASIWKKnLGVNVKLE----NQEWKTFLDTrhqgTFD--VARAGWCADyNEPTSFLNTM 456
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 440 AYNPDNSdaarltnfqgwrTSFY-DKQLNELIDRALLEKDPARQKQLY--AEVQNRYEAlypAIIPVSQMIDSVVLRTDV 516
Cdd:PRK15104  457 LSNSSNN------------TAHYkSPAFDKLMAETLKVKDEAQRAALYqkAEQQLDKDS---AIVPVYYYVNARLVKPWV 521
                         570
                  ....*....|....*...
gi 2238896597 517 QGYV-PHPSSTTHLREVY 533
Cdd:PRK15104  522 GGYTgKDPLDNIYVKNLY 539
PBP2_NikA_DppA_OppA_like_18 cd08505
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide ...
44-419 1.59e-21

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: 97.73  E-value: 1.59e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  44 SLDPAAMTGNEVVGVIVNLYDSLVELDPqnLS---TVLPSLAKSW----SVSDDGKVITFNLVDNARFH--------SGN 108
Cdd:cd08505    12 GLDPAQSYDSYSAEIIEQIYEPLLQYHY--LKrpyELVPNTAAAMpevsYLDVDGSVYTIRIKPGIYFQpdpafpkgKTR 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 109 AVTAQDFAWSMNRLLHLNMAqattwksyGftadnvekmIRAKDAHTVEIELPKPnDPKLvIYSLATLGSGSVldrqtimP 188
Cdd:cd08505    90 ELTAEDYVYSIKRLADPPLE--------G---------VEAVDRYTLRIRLTGP-YPQF-LYWLAMPFFAPV-------P 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 189 HE-------KNGDWGNGWLTTNAAGSGPFKLDVWQAKDVLRISRVEGYwRG------------------DAKMR-----R 238
Cdd:cd08505   144 WEavefygqPGMAEKNLTLDWHPVGTGPYMLTENNPNSRMVLVRNPNY-RGevypfegsadddqagllaDAGKRlpfidR 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 239 VIFRHMTESQALRLMIEKGDIDV----------ATGMSVPDINALK---QNQGVVVDEVKKGTIYYVAMSLKNEHFA--- 302
Cdd:cd08505   223 IVFSLEKEAQPRWLKFLQGYYDVsgissdafdqALRVSAGGEPELTpelAKKGIRLSRAVEPSIFYIGFNMLDPVVGgys 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 303 --KPKVREAVRYLIDYDGINKTVMTGYGFYHQRPIQKGM---DATLPNPGYKLDVARAKALLAEAGYPNG-FATTLRVL- 375
Cdd:cd08505   303 keKRKLRQAISIAFDWEEYISIFRNGRAVPAQGPIPPGIfgyRPGEDGKPVRYDLELAKALLAEAGYPDGrDGPTGKPLv 382
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2238896597 376 ---------SDQPFLNLatsVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDM 419
Cdd:cd08505   383 lnydtqatpDDKQRLEW---WRKQFAKLGIQLNVRATDYNRFQDKLRKGNAQL 432
PRK15109 PRK15109
antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
1-535 6.68e-19

antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional


Pssm-ID: 185064  Cd Length: 547  Bit Score: 89.75  E-value: 6.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597   1 MKARAILRILLLSTLCMAAVPAVLSAKTPD--DQLIVGMNMNNMLSLDPAAMTGnevvGVIVN-----LYDSLVELDPQN 73
Cdd:PRK15109    1 MRLVLSSLLVIAGLLSGQAIAAPESPPHADirQSGFVYCVSGQVNTFNPQKASS----GLIVDtlaaqLYDRLLDVDPYT 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  74 LSTVlPSLAKSWSVSDDGKVITFNLVDNARFHSGN------AVTAQDFAWSMNRLL-------HLNMAQATTWKSYGFtA 140
Cdd:PRK15109   77 YRLM-PELAESWEVLDNGATYRFHLRRDVPFQKTDwftptrKMNADDVVFSFQRIFdrnhpwhNVNGGNYPYFDSLQF-A 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 141 DNVeKMIRAKDAHTVEIELPKPNDPKLviYSLAT----LGSGSVLDRQTIMPHEKNGDWgngwlttNAAGSGPFKLDVWQ 216
Cdd:PRK15109  155 DNV-KSVRKLDNYTVEFRLAQPDASFL--WHLAThyasVLSAEYAAKLTKEDRQEQLDR-------QPVGTGPFQLSEYR 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 217 AKDVLRISRVEGYWRGDAKMRRVIFrHMTESQALRL-MIEKGDIDVatgMSVPDINALKqnqgVVVDE------VKKG-T 288
Cdd:PRK15109  225 AGQFIRLQRHDDYWRGKPLMPQVVV-DLGSGGTGRLsKLLTGECDV---LAYPAASQLS----ILRDDprlrltLRPGmN 296
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 289 IYYVAMSLKNEHFAKPKVREAVRYLIDydgiNKTVMTGygfyhqrpIQKGMDAT----LPNPGYKLDV---------ARA 355
Cdd:PRK15109  297 IAYLAFNTRKPPLNNPAVRHALALAIN----NQRLMQS--------IYYGTAETaasiLPRASWAYDNeakiteynpEKS 364
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 356 KALLAEAGYpNGFATTLRV-LSDQPF----LNLATSVQSTLAQAGIKARIHSGTGNQVYGAMRDRNFDM-LVGRGGGGVD 429
Cdd:PRK15109  365 REQLKALGL-ENLTLKLWVpTASQAWnpspLKTAELIQADLAQVGVKVVIVPVEGRFQEARLMDMNHDLtLSGWATDSND 443
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 430 phPHSSLRsvaynPDNSDAA--RLTNFQGWrtsfYDKQLNELIDRALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQMI 507
Cdd:PRK15109  444 --PDSFFR-----PLLSCAAirSQTNYAHW----CDPAFDSVLRKALSSQQLASRIEAYDEAQSILAQELP-ILPLASSL 511
                         570       580
                  ....*....|....*....|....*...
gi 2238896597 508 DSVVLRTDVQGYVPHPSSTTHLREVYKQ 535
Cdd:PRK15109  512 RLQAYRYDIKGLVLSPFGNASFAGVYRE 539
PBP2_SgrR_like cd08507
The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related ...
62-401 2.80e-17

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: 84.24  E-value: 2.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  62 LYDSLVELDPQNlSTVLPSLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLLHLNmaqattwkSYGFTAD 141
Cdd:cd08507    35 IFDGLVRYDEEN-GEIEPDLAHHWESNDDLTHWTFYLRKGVRFHNGRELTAEDVVFTLLRLRELE--------SYSWLLS 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 142 NVEKmIRAKDAHTVEIELPKPNdpklviYSLATLGSGSVLdrqTIMPHEKNGDWGNG--WLttnaaGSGPFKLDVWQAKD 219
Cdd:cd08507   106 HIEQ-IESPSPYTVDIKLSKPD------PLFPRLLASANA---SILPADILFDPDFArhPI-----GTGPFRVVENTDKR 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 220 vLRISRVEGYWRGDAKMRRV---IFRHMTESQAL-----RLMIEKGDIDVATGMSVPDinalkqnqGVvvdevkkgtiYY 291
Cdd:cd08507   171 -LVLEAFDDYFGERPLLDEVeiwVVPELYENLVYppqstYLQYEESDSDEQQESRLEE--------GC----------YF 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 292 VAMSLKNEHFAKPKVREAVRYLIDydginktvmtgygfyhqrPIQkgMDATLPN-------PGYKLDV----ARAKALLA 360
Cdd:cd08507   232 LLFNQRKPGAQDPAFRRALSELLD------------------PEA--LIQHLGGerqrgwfPAYGLLPewprEKIRRLLK 291
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 2238896597 361 EAGYPngfATTLRV--LSDQPFLNLATSVQSTLAQAGIKARIH 401
Cdd:cd08507   292 ESEYP---GEELTLatYNQHPHREDAKWIQQRLAKHGIRLEIH 331
PRK09755 PRK09755
ABC transporter substrate-binding protein;
1-533 4.06e-12

ABC transporter substrate-binding protein;


Pssm-ID: 182060  Cd Length: 535  Bit Score: 68.63  E-value: 4.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597   1 MKARAILRIL-LLSTLCMAAVPAVLSAKTPDDQLIVGMNMNNMLSLDPAAMTGNEVVGVIVNLYDSLVELDPQnlSTVLP 79
Cdd:PRK09755    1 MYTRNLLWLVsLVSAAPLYAADVPANTPLAPQQVFRYNNHSDPGTLDPQKVEENTAAQIVLDLFEGLVWMDGE--GQVQP 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597  80 SLAKSWSVSDDGKVITFNLVDNARFHSGNAVTAQDFAWSMNRLL---------------HLNMAQATTwksyGFTADNVE 144
Cdd:PRK09755   79 AQAERWEILDGGKRYIFHLRSGLQWSDGQPLTAEDFVLGWQRAVdpktaspfagylaqaHINNAAAIV----AGKADVTS 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 145 KMIRAKDAHTVEIELPKPNDPKLVIYSLATLGSgsvldrqtiMPHEKNGDWGNGWLT-TNAAGSGPFKLDVWQAKDVLRI 223
Cdd:PRK09755  155 LGVKATDDRTLEVTLEQPVPWFTTMLAWPTLFP---------VPHHVIAKHGDSWSKpENMVYNGAFVLDQWVVNEKITA 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 224 SRVEGYwrGDAK---MRRVIFRHMTESQALRLMIEKGDIDVaTGMSVPDINALKQNQGVVVDEVKKGTIYYVAMSLKNEH 300
Cdd:PRK09755  226 RKNPKY--RDAQhtvLQQVEYLALDNSVTGYNRYRAGEVDL-TWVPAQQIPAIEKSLPGELRIIPRLNSEYYNFNLEKPP 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 301 FAKPKVREAVRYLIDYDGINKTV--MTGYGFYHQRPIQKGMDAT----LPNPGYKlDVARAKALLAEAGYPNGFATTLRV 374
Cdd:PRK09755  303 FNDVRVRRALYLTVDRQLIAQKVlgLRTPATTLTPPEVKGFSATtfdeLQKPMSE-RVAMAKALLKQAGYDASHPLRFEL 381
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 375 LSDQPFLNLATSVQ-STLAQAGIKARIHSGTGN-QVYGAMRdRNFDMLVGRGGGGVDPHPHSSLrsvaYNPDNSDAARlt 452
Cdd:PRK09755  382 FYNKYDLHEKTAIAlSSEWKKWLGAQVTLRTMEwKTYLDAR-RAGDFMLSRQSWDATYNDASSF----LNTLKSDSEE-- 454
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 453 NFQGWRTSFYDKQLNElidrALLEKDPARQKQLYAEVQNRYEALYPaIIPVSQMIDSVVLRTDVQGYVPH-PSSTTHLRE 531
Cdd:PRK09755  455 NVGHWKNAQYDALLNQ----ATQITDATKRNALYQQAEVIINQQAP-LIPIYYQPLIKLLKPYVGGFPLHnPQDYVYSKE 529

                  ..
gi 2238896597 532 VY 533
Cdd:PRK09755  530 LY 531
COG3889 COG3889
Extracellular solute-binding protein, contains Ig-fold domain [General function prediction ...
238-328 5.01e-08

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


Pssm-ID: 443097 [Multi-domain]  Cd Length: 878  Bit Score: 55.80  E-value: 5.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2238896597 238 RVIFRH-MTESQALRlMIEKGDIDV-ATGMSVPDINALKQNQGVVVDEVKKGtiyYVAMSL-----KNEH---FAKPKVR 307
Cdd:COG3889    40 KVIFIVySDEEQALE-EVESGDIDLyFFGIPPSLAQKLKSRPGLDVYSAPGG---SYDLLLnpappGNGKfnpFAIKEIR 115
                          90       100
                  ....*....|....*....|.
gi 2238896597 308 EAVRYLIDYDGINKTVMTGYG 328
Cdd:COG3889   116 FAMNYLIDRDYIVNEILGGYG 136
 
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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