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Conserved domains on  [gi|84375176|gb|EAP92093|]
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putative transcriptional regulator, LysR family [Vibrio splendidus 12B01]

Protein Classification

LysR family transcription regulator( domain architecture ID 1003099)

LysR family transcription regulator similar to LrhA which is involved in control of the transcription of flagellar, motility, and chemotaxis genes

Gene Ontology:  GO:0003700|GO:0006355
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15092 super family cl36469
DNA-binding transcriptional repressor LrhA; Provisional
 5-259 7.26e-44

DNA-binding transcriptional repressor LrhA; Provisional


The actual alignment was detected with superfamily member PRK15092:

Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 151.33  E-value: 7.26e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    5 FNMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTA 84
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   85 LKQVkRYEDKQ-PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLT 163
Cdd:PRK15092  89 CSSL-MYSNLQgVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  164 HDIGVWISNPDYVFDDSKPVPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDL 243
Cdd:PRK15092 168 TSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDL 247

                        250
                 ....*....|....*....
gi 84375176  244 RIL---DDMPPLPAVDIVL 259
Cdd:PRK15092 248 RVLgesEGLPPLPDTEYLL 266
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-259 7.26e-44

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 151.33  E-value: 7.26e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    5 FNMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTA 84
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   85 LKQVkRYEDKQ-PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLT 163
Cdd:PRK15092  89 CSSL-MYSNLQgVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  164 HDIGVWISNPDYVFDDSKPVPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDL 243
Cdd:PRK15092 168 TSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDL 247

                        250
                 ....*....|....*....
gi 84375176  244 RIL---DDMPPLPAVDIVL 259
Cdd:PRK15092 248 RVLgesEGLPPLPDTEYLL 266
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-267 1.55e-40

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.16  E-value: 1.55e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  87 QVKRYEDKQ--PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYW--L 162
Cdd:COG0583  81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVArpL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176 163 THDIGVWISNPDYVFDDSKPVplalfqtdckyhaaavngltkqgtpyqllacSNTASAQRAIVKAGLAIGAMGKLSVTSD 242
Cdd:COG0583 161 GEERLVLVASPDHPLARRAPL-------------------------------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                       250       260       270
                ....*....|....*....|....*....|
gi 84375176 243 -----LRILDDMPPLPAVDIVLILASKHHP 267
Cdd:COG0583 210 laagrLVALPLPDPPPPRPLYLVWRRRRHL 239
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 97-269 1.22e-34

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain 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: 176130  Cd Length: 185  Bit Score: 123.60  E-value: 1.22e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  97 LRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLTHDIGVWISNPDYV 176
Cdd:cd08439   2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGYI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176 177 FDDSKPVPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDLRIL---DDMPPLP 253
Cdd:cd08439  82 LAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILgesEGLPPLP 161

                       170
                ....*....|....*.
gi 84375176 254 AVDIVLILASKHHPVL 269
Cdd:cd08439 162 DTGYTLCLDPNRPSEL 177
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-67 9.92e-20

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 9.92e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 84375176     9 IDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAG 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-259 7.26e-44

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 151.33  E-value: 7.26e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    5 FNMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTA 84
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   85 LKQVkRYEDKQ-PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLT 163
Cdd:PRK15092  89 CSSL-MYSNLQgVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  164 HDIGVWISNPDYVFDDSKPVPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDL 243
Cdd:PRK15092 168 TSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDL 247

                        250
                 ....*....|....*....
gi 84375176  244 RIL---DDMPPLPAVDIVL 259
Cdd:PRK15092 248 RVLgesEGLPPLPDTEYLL 266
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-267 1.55e-40

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.16  E-value: 1.55e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  87 QVKRYEDKQ--PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYW--L 162
Cdd:COG0583  81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVArpL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176 163 THDIGVWISNPDYVFDDSKPVplalfqtdckyhaaavngltkqgtpyqllacSNTASAQRAIVKAGLAIGAMGKLSVTSD 242
Cdd:COG0583 161 GEERLVLVASPDHPLARRAPL-------------------------------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                       250       260       270
                ....*....|....*....|....*....|
gi 84375176 243 -----LRILDDMPPLPAVDIVLILASKHHP 267
Cdd:COG0583 210 laagrLVALPLPDPPPPRPLYLVWRRRRHL 239
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 97-269 1.22e-34

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain 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: 176130  Cd Length: 185  Bit Score: 123.60  E-value: 1.22e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  97 LRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLTHDIGVWISNPDYV 176
Cdd:cd08439   2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGYI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176 177 FDDSKPVPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDLRIL---DDMPPLP 253
Cdd:cd08439  82 LAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILgesEGLPPLP 161

                       170
                ....*....|....*.
gi 84375176 254 AVDIVLILASKHHPVL 269
Cdd:cd08439 162 DTGYTLCLDPNRPSEL 177
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-67 9.92e-20

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 9.92e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 84375176     9 IDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAG 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 7-157 5.02e-16

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 76.61  E-value: 5.02e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLalrshaeQLVALHNTALK 86
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGL-------LLVDQARTVLR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   87 QVKRYED---KQ------PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSE 157
Cdd:PRK11151  74 EVKVLKEmasQQgetmsgPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESE 153
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-244 2.68e-14

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 70.01  E-value: 2.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    97 LRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYW--LTHDIGVWISNPD 174
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEArpLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84375176   175 YVFDDSKPV--------PLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSVTSDLR 244
Cdd:pfam03466  84 HPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-158 1.40e-13

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 69.41  E-value: 1.40e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 84375176   87 QVKRY-EDKQPLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEE 158
Cdd:PRK09906  81 RARKIvQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE 153
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-157 7.70e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 67.29  E-value: 7.70e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   12 LRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQlvALHN-----TALK 86
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARR--ALQDleagrRAIH 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 84375176   87 QVKRYEDKQpLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIV---TRAPDSE 157
Cdd:PRK11242  84 DVADLSRGS-LRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAfapVHSPEIE 156
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-277 2.24e-12

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain 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 substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 64.54  E-value: 2.24e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  97 LRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYW--LTHDIGVWISNPD 174
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESepLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176 175 YVFDDSKPVPLA--------LFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIVKAGLAIGAMGKLSV----TSD 242
Cdd:cd05466  82 HPLAKRKSVTLAdladepliLFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVeelaDGG 161

                       170       180       190
                ....*....|....*....|....*....|....*.
gi 84375176 243 LRILDDMPPLPAVDIVLI-LASKHHPVLDKEVLNQL 277
Cdd:cd05466 162 LVVLPLEDPPLSRTIGLVwRKGRYLSPAARAFLELL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-70 1.11e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 63.71  E-value: 1.11e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   11 ALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLAL 70
Cdd:PRK11139  10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRY 69
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-79 7.85e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 61.36  E-value: 7.85e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVA 79
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PRK09986 PRK09986
LysR family transcriptional regulator;
7-89 8.62e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 61.28  E-value: 8.62e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86


                 ...
gi 84375176   87 QVK 89
Cdd:PRK09986  87 RVE 89
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-90 1.99e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.98  E-value: 1.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    6 NMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKeGRNLILTEAGLALRSHAEQLVALHNTAL 85
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLL 79


                 ....*
gi 84375176   86 KQVKR 90
Cdd:PRK13348  80 STLPA 84
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-150 3.61e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 59.65  E-value: 3.61e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    4 DFNMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVAL--- 80
Cdd:CHL00180   2 DLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALcee 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 84375176   81 HNTALKQVKRYEdKQPLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQ--IFSLPSITlreW-LDDGRLDAAIV 150
Cdd:CHL00180  82 TCRALEDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQlqVHSTRRIA---WnVANGQIDIAIV 150
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
7-158 4.65e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 58.88  E-value: 4.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 84375176   87 QVKRYEDKQPLRLGCPEDYNDTIL-PKVIRLLQKAEPtcsIQIFSLpsITLRE----WLDDGRLDAAIVTRAPDSEE 158
Cdd:PRK03601  81 EVAHTSQHNELSIGASASLWECMLtPWLGRLYQNQEA---LQFEAR--IAQRQslvkQLHERQLDLLITTEAPKMDE 152
PRK12680 PRK12680
LysR family transcriptional regulator;
7-279 5.18e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 56.17  E-value: 5.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETS-SFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNL-ILTEAGLALRSHAEQLVALHNT- 83
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNi 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   84 ---ALKQvkRYEDKQPLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRApDSEEGY 160
Cdd:PRK12680  81 rtyAANQ--RRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTA-GGEPSA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  161 WLT---------------HDIGVWISNPDYVFDDSKpvPLALFQTDCKYHAAAVNGLTKQGTPYQLLACSNTASAQRAIV 225
Cdd:PRK12680 158 GIAvplyrwrrlvvvprgHALDTPRRAPDMAALAEH--PLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYV 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 84375176  226 KAGLAIGAMGKLSVTS---DLRILDDMPPLP-----------------AVDIVLILAskhhPVLDKEVLNQLVE 279
Cdd:PRK12680 236 RAGLGVGLLAEMAVNAndeDLRAWPAPAPIAeciawavlprdrvlrdyALELVHVLA----PQIDKRDLRRVLD 305
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-99 2.09e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.01  E-value: 2.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKeGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90
                 ....*....|...
gi 84375176   87 QVKRyEDKQPLRL 99
Cdd:PRK03635  81 ELPA-LDGTPLTL 92
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
15-101 4.95e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 53.23  E-value: 4.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   15 FLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGL------------ALRSHaEQLVALHN 82
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRiyyqgcrrmlheVQDVH-EQLYAFNN 88

                         90
                 ....*....|....*....
gi 84375176   83 TALKQvkryedkqpLRLGC 101
Cdd:PRK10632  89 TPIGT---------LRIGC 98
PRK09801 PRK09801
LysR family transcriptional regulator;
12-192 5.32e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 53.12  E-value: 5.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   12 LRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALKQVKRY 91
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   92 EDKQP--LRLGCPEDYNDTILPKVIRLLQKAEPTCSIQiFSLPSITLREWLDDGRLDAAIVTRAPDSEEGYWLTHDIGVW 169
Cdd:PRK09801  91 KTRPEgmIRIGCSFGFGRSHIAPAITELMRNYPELQVH-FELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180
                 ....*....|....*....|....
gi 84375176  170 ISNPDYVFDDSKPVPLA-LFQTDC 192
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQeLSRHDC 193
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 21-67 1.29e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 51.87  E-value: 1.29e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 84375176   21 TSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAG 67
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG 62
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-159 1.77e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.58  E-value: 1.77e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   25 TRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLI-LTEAGLALRSHAEQ-LVALHNtaLKQVKR-YEDKQPLRLgc 101
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERmLLDAEN--LRRLAEqFADRDSGHL-- 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84375176  102 pedyndTI----------LPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEG 159
Cdd:PRK12683  96 ------TVatthtqaryaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPD 157
PRK10341 PRK10341
transcriptional regulator TdcA;
15-151 3.85e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.63  E-value: 3.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   15 FLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALKQVKR--YE 92
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGmsSE 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 84375176   93 DKQPLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVT 151
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGT 153
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-76 6.47e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 6.47e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 84375176   36 SAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQ 76
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQ 46
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
15-67 1.35e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 48.84  E-value: 1.35e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 84375176   15 FLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAG 67
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-151 1.45e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 48.83  E-value: 1.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   25 TRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLI-LTEAGLALRSHAEQLVALHNTaLKQVKRY---EDKQPLRLG 100
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGN-IKRIGDDfsnQDSGTLTIA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 84375176  101 CPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVT 151
Cdd:PRK12682  99 TTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 15-86 1.82e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.15  E-value: 1.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   15 FLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAG-------LALRSHA---EQLVALHNTA 84
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGrllypraLALLEQAveiEQLFREDNGA 90


                 ..
gi 84375176   85 LK 86
Cdd:PRK10837  91 LR 92
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
25-159 2.03e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 48.05  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   25 TRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLI-LTEAGLALRSHAEQLvaLHNT-ALKQV-KRYEDKqplrlgc 101
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERI--LQEVeNLKRVgKEFAAQ------- 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84375176  102 pEDYNDTI----------LPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEEG 159
Cdd:PRK12684  91 -DQGNLTIatthtqaryaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKE 157
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-102 2.05e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 48.06  E-value: 2.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTALK 86
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90
                 ....*....|....*...
gi 84375176   87 QVK--RYEDKQPLRLGCP 102
Cdd:PRK14997  82 AIAalQVEPRGIVKLTCP 99
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 98-247 4.38e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain 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: 176158  Cd Length: 221  Bit Score: 46.63  E-value: 4.38e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176  98 RLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVT--RAPDSEEGYWLTHDIGVWISNPDy 175
Cdd:cd08469   3 VIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIfeQIPPRFRRRTLFDEDEVWVMRKD- 81

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 84375176 176 vfddskpvplalfqtdckyHAAAVNGLTKQG-TPYQLLACSNTASAQRA----IVKAGLAigamgKLSVTSDLRILD 247
Cdd:cd08469  82 -------------------HPAARGALTIETlARYPHIVVSLGGEEEGAvsgfISERGLA-----RQTEMFDRRALE 134
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-74 7.48e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.60  E-value: 7.48e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHA 74
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHA 68
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
6-115 8.12e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 46.59  E-value: 8.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    6 NMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHAEQLVALHNTAL 85
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89

                         90       100       110
                 ....*....|....*....|....*....|..
gi 84375176   86 KQVKRYED--KQPLRLGCPEDYNDTILPKVIR 115
Cdd:PRK10082  90 AELRGGSDyaQRKIKIAAAHSLSLGLLPSIIS 121
PRK09791 PRK09791
LysR family transcriptional regulator;
5-156 2.37e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 45.14  E-value: 2.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    5 FNMDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLALRSHA----EQLVAL 80
Cdd:PRK09791   3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAslilEELRAA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 84375176   81 HNTALKQVKryEDKQPLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDS 156
Cdd:PRK09791  83 QEDIRQRQG--QLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGP 156
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 98-158 3.15e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 43.74  E-value: 3.15e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 84375176  98 RLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEE 158
Cdd:cd08417   3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPG 63
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 15-146 6.44e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 43.83  E-value: 6.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176   15 FLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGLAL-----RSHA--EQLVAlhntALKQ 87
Cdd:PRK11013  12 FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLfeevqRSYYglDRIVS----AAES 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 84375176   88 VKRYEDKQpLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLD 146
Cdd:PRK11013  88 LREFRQGQ-LSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHD 145
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-90 8.13e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 43.47  E-value: 8.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84375176    7 MDIDALRGFLAFVETSSFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGlalrshaEQLVALHNTALK 86
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQG-------EILLQLANQVLP 74


                 ....
gi 84375176   87 QVKR 90
Cdd:PRK15421  75 QISQ 78
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-149 4.63e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to 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: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 40.37  E-value: 4.63e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 84375176  98 RLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSIT-LREWLDDGRLDAAI 149
Cdd:cd08463   3 RIAAPDYLNALFLPELVARFRREAPGARLEIHPLGPDFdYERALASGELDLVI 55
cbl PRK12679
HTH-type transcriptional regulator Cbl;
25-78 9.76e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.18  E-value: 9.76e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 84375176   25 TRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLI-LTEAGLALRSHAEQLV 78
Cdd:PRK12679  20 TEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERIL 74
nhaR PRK11062
transcriptional activator NhaR; Provisional
 23-94 1.48e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.61  E-value: 1.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 84375176   23 SFTRAAKQINRTQSAFSAQMRKLEEELNVTLFQKEGRNLILTEAGlalrshaeQLVAlhntalkqvkRYEDK 94
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG--------ELVF----------RYADK 73
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-158 3.30e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain 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 substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 37.87  E-value: 3.30e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 84375176 109 ILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAPDSEE 158
Cdd:cd08414  14 LLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPG 63
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 96-159 3.48e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 37.89  E-value: 3.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 84375176  96 PLRLGC-PedyndTI----LPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTrAPDSEEG 159
Cdd:cd08411   2 PLRLGViP-----TIapylLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLA-LPVDEPG 64
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-154 3.63e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to 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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 37.55  E-value: 3.63e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 84375176 108 TILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVTRAP 154
Cdd:cd08427  13 GLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPP 59
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 96-151 6.14e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 37.16  E-value: 6.14e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 84375176  96 PLRLGCPEDYNDTILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAIVT 151
Cdd:cd08415   1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLAS 56
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 108-149 7.02e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 36.79  E-value: 7.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 84375176 108 TILPKVIRLLQKAEPTCSIQIFSLPSITLREWLDDGRLDAAI 149
Cdd:cd08459  13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAI 54
 
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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