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Conserved domains on  [gi|15597402|ref|NP_250896|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 105-303 6.86e-55

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08435:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 201  Bit Score: 177.47  E-value: 6.86e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08435   1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08435  81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 265 PGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08435 161 LRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
27-75 1.19e-13

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 1.19e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15597402    27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGE 75
Cdd:pfam00126  12 ETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 105-303 6.86e-55

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 177.47  E-value: 6.86e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08435   1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08435  81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 265 PGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08435 161 LRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
27-311 5.71e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.88  E-value: 5.71e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRV 106
Cdd:COG0583  14 EEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTL 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 107 TVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVVGA 186
Cdd:COG0583  94 RIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP--PPDPGLVARPLGEERLVLVASP 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 187 QNPLSQARKLdwgelqeltwvlqqhpspmrgivnqafhnaridlpssiveTTSIMTLLSLLQQTDMIGITPRSVIEDYPG 266
Cdd:COG0583 172 DHPLARRAPL----------------------------------------VNSLEALLAAVAAGLGIALLPRFLAADELA 211

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 15597402 267 KHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMASVHAEQAR 311
Cdd:COG0583 212 AGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-310 2.25e-38

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: 134.72  E-value: 2.25e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   104 GRVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVV 183
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP--PDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   184 VGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIED 263
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLR-PRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 15597402   264 YPGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMASVHAEQA 310
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09791 PRK09791
LysR family transcriptional regulator;
29-311 4.22e-25

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 102.15  E-value: 4.22e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTV 108
Cdd:PRK09791  20 GSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLAGQINI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  109 GAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVVGAQN 188
Cdd:PRK09791 100 GMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVFCRPGH 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  189 PLSQARKLDwgELQELTWVLqqhPSPmRGIVNQAFHNARIDL---PSSIVETTSIMTLLSLLQQTDMIGITPRSVIED-Y 264
Cdd:PRK09791 180 PAIGARSLK--QLLDYSWTM---PTP-HGSYYKQLSELLDDQaqtPQVGVVCETFSACISLVAKSDFLSILPEEMGCDpL 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 15597402  265 PGKHLLAilpIQLEPRLP--PYGLITRRNrvhssAMQTFMASVHAEQAR 311
Cdd:PRK09791 254 HGQGLVM---LPVSEILPkaTYYLIQRRD-----TRQTPLTASLITLFR 294
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
27-75 1.19e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 1.19e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15597402    27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGE 75
Cdd:pfam00126  12 ETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
26-78 8.77e-05

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 41.35  E-value: 8.77e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597402  26 EELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLP-----RGMRATPFGETLI 78
Cdd:COG2005  31 DETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggkggGGARLTPEGRRLL 88
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 28-93 2.83e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 38.77  E-value: 2.83e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597402   28 LGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMRE 93
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
 
Name Accession Description Interval E-value
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 105-303 6.86e-55

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 177.47  E-value: 6.86e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08435   1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08435  81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 265 PGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08435 161 LRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
27-311 5.71e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.88  E-value: 5.71e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRV 106
Cdd:COG0583  14 EEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTL 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 107 TVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVVGA 186
Cdd:COG0583  94 RIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP--PPDPGLVARPLGEERLVLVASP 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 187 QNPLSQARKLdwgelqeltwvlqqhpspmrgivnqafhnaridlpssiveTTSIMTLLSLLQQTDMIGITPRSVIEDYPG 266
Cdd:COG0583 172 DHPLARRAPL----------------------------------------VNSLEALLAAVAAGLGIALLPRFLAADELA 211

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 15597402 267 KHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMASVHAEQAR 311
Cdd:COG0583 212 AGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-310 2.25e-38

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: 134.72  E-value: 2.25e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   104 GRVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVV 183
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP--PDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   184 VGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIED 263
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLR-PRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 15597402   264 YPGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMASVHAEQA 310
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 105-305 2.31e-34

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: 124.25  E-value: 2.31e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVV 184
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP--VDDPGLESEPLFEEPLVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd05466  79 PPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFT-PNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597402 265 PGKHlLAILPIQlEPRLP-PYGLITRRNRVHSSAMQTFMASV 305
Cdd:cd05466 158 ADGG-LVVLPLE-DPPLSrTIGLVWRKGRYLSPAARAFLELL 197
PRK09791 PRK09791
LysR family transcriptional regulator;
29-311 4.22e-25

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 102.15  E-value: 4.22e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTV 108
Cdd:PRK09791  20 GSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLAGQINI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  109 GAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVVGAQN 188
Cdd:PRK09791 100 GMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVFCRPGH 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  189 PLSQARKLDwgELQELTWVLqqhPSPmRGIVNQAFHNARIDL---PSSIVETTSIMTLLSLLQQTDMIGITPRSVIED-Y 264
Cdd:PRK09791 180 PAIGARSLK--QLLDYSWTM---PTP-HGSYYKQLSELLDDQaqtPQVGVVCETFSACISLVAKSDFLSILPEEMGCDpL 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 15597402  265 PGKHLLAilpIQLEPRLP--PYGLITRRNrvhssAMQTFMASVHAEQAR 311
Cdd:PRK09791 254 HGQGLVM---LPVSEILPkaTYYLIQRRD-----TRQTPLTASLITLFR 294
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 27-312 1.88e-23

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 97.72  E-value: 1.88e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREEL--VA-LESGNL 103
Cdd:PRK11242  14 EHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIhdVAdLSRGSL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  104 grvTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRipSGARTDDLVFDSLGEEELCVV 183
Cdd:PRK11242  94 ---RLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF--APVHSPEIEAQPLFTETLALV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  184 VGAQNPLSQARK-LDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:PRK11242 169 VGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVT-PRVAIEANSISAVLEIVRRGRLATLLPAAIAR 247

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 15597402  263 DYPGKHllailPIQLEPRLPPYG--LITRRNRVHSSAMQTFMASVHAEQARH 312
Cdd:PRK11242 248 EHDGLC-----AIPLDPPLPQRTaaLLRRKGAYRSAAARAFIELALERRAEI 294
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-305 1.84e-22

TThe 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: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 92.59  E-value: 1.84e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGriPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08440   1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIG--SEPEADPDLEFEPLLRDPFVLVC 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE-- 262
Cdd:cd08440  79 PKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLT-LRPAYEVSHMSTALGMVAAGLGVAVLPALALPla 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597402 263 DYPGkhlLAILPIQlEPRLP-PYGLITRRNRVHSSAMQTFMASV 305
Cdd:cd08440 158 DHPG---LVARPLT-EPVVTrTVGLIRRRGRSLSPAAQAFLDLL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
29-302 4.96e-22

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 94.16  E-value: 4.96e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTV 108
Cdd:PRK10341  22 GSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSF 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  109 GAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVVGAQN 188
Cdd:PRK10341 102 GFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHVEPLFESEFVLVASKSR 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  189 PLSQARKLDwgELQELTWVLQQHPSPMRGIVNQAFHNARIDLpSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDYpGKH 268
Cdd:PRK10341 182 TCTGTTTLE--SLKNEQWVLPQTNMGYYSELLTTLQRNGISI-ENIVKTDSVVTIYNLVLNADFLTVIPCDMTSPF-GSN 257

                        250       260       270
                 ....*....|....*....|....*....|....
gi 15597402  269 LLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFM 302
Cdd:PRK10341 258 QFITIPIEETLPVAQYAAVWSKNYRIKKAASVLV 291
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 105-311 2.11e-20

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 87.02  E-value: 2.11e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08418   1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDwgELQELTWVLqqhPSPMRGIVNQAFHNARID--LPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:cd08418  81 RKDHPLQGARSLE--ELLDASWVL---PGTRMGYYNNLLEALRRLgyNPRVAVRTDSIVSIINLVEKADFLTILSRDMGR 155

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 15597402 263 DYpgKHLLAILPIQLEPRLPP--YGLITRRNRvhssaMQTFMASVHAEQAR 311
Cdd:cd08418 156 GP--LDSFRLITIPVEEPLPSadYYLIYRKKS-----RLTPLAEQLVELFR 199
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-305 1.85e-19

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: 84.48  E-value: 1.85e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVV 184
Cdd:cd08414   1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPP--PDPPGLASRPLLREPLVVAL 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVL-QQHPSP-MRGIVNQAFHNARIdLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:cd08414  79 PADHPLAARESVSLADLADEPFVLfPREPGPgLYDQILALCRRAGF-TPRIVQEASDLQTLLALVAAGLGVALVPASVAR 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597402 263 DY-PGkhlLAILPIQLEPRLPPYGLITRRNRvHSSAMQTFMASV 305
Cdd:cd08414 158 LQrPG---VVYRPLADPPPRSELALAWRRDN-ASPALRAFLELA 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 105-303 1.40e-18

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. 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: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 82.15  E-value: 1.40e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDV--VLGRIPSgartDDLVFDSLGEEELCV 182
Cdd:cd08420   1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLglVEGPVDH----PDLIVEPFAEDELVL 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 183 VVGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDL--PSSIVETTSIMTLLSLLQQTDMIGITPRSV 260
Cdd:cd08420  77 VVPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGldLNIVMELGSTEAIKEAVEAGLGISILSRLA 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597402 261 IEDYPGKHLLAILPIQlEPRLP-PYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08420 157 VRKELELGRLVALPVE-GLRLTrPFSLIYHKDKYLSPAAEAFLE 199
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 105-303 7.90e-18

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: 79.91  E-value: 7.90e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVV 184
Cdd:cd08415   1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP--LDHPGLESEPLASGRAVCVL 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08415  79 PPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVE-PRIVIETQLSHTACALVAAGLGVAIVDPLTAAGY 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15597402 265 PGkHLLAILPiqLEPRLP-PYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08415 158 AG-AGLVVRP--FRPAIPfEFALVRPAGRPLSRLAQAFID 194
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-280 9.92e-15

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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 71.48  E-value: 9.92e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08436   1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP-ERRPPGLASRELAREPLVAVV 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFhnARIDLPSSIV-ETTSIMTLLSLLQQTDMIGITPRSVIED 263
Cdd:cd08436  80 APDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAF--AAAGVRRRVAfEVSDVDLLLDLVARGLGVALLPASVAAR 157

                       170
                ....*....|....*..
gi 15597402 264 YPGkhlLAILPIQLEPR 280
Cdd:cd08436 158 LPG---LAALPLEPAPR 171
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 104-301 2.55e-14

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: 70.25  E-value: 2.55e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 104 GRVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLgrIPSGARTDDLVFDSLGEEELCVV 183
Cdd:cd08411   1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAAL--LALPVDEPGLEEEPLFDEPFLLA 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 184 VGAQNPLSQARKLDWGELQELT-WVLQQ-HpsPMRGIVNQAFHNARIDLPSSIvETTSIMTllsLLQQTDM-IGIT--PR 258
Cdd:cd08411  79 VPKDHPLAKRKSVTPEDLAGERlLLLEEgH--CLRDQALELCRLAGAREQTDF-EATSLET---LRQMVAAgLGITllPE 152

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15597402 259 SVIEDYPG-KHLLAILPIQlEPRlpPY---GLITRRNRVHSSAMQTF 301
Cdd:cd08411 153 LAVPSEELrGDRLVVRPFA-EPA--PSrtiGLVWRRSSPRAAAFEAL 196
rbcR CHL00180
LysR transcriptional regulator; Provisional
 29-230 3.28e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.59  E-value: 3.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFA---ELSGMREELVALESGNLgr 105
Cdd:CHL00180  20 GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceETCRALEDLKNLQRGTL-- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  106 vTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLD--VVLGRIPSGARtDDLVFDSLGEEELCVV 183
Cdd:CHL00180  98 -IIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDiaIVGGEVPTELK-KILEITPYVEDELALI 175

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 15597402  184 VGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDL 230
Cdd:CHL00180 176 IPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDS 222
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 106-305 9.06e-14

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 68.72  E-value: 9.06e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 106 VTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL-GRIPsgaRTDDLVFDSLGEEELCVVV 184
Cdd:cd08434   2 VRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALcSPVP---DEPDIEWIPLFTEELVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08434  79 PKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFT-PKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNP 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597402 265 PGkhlLAILPIQlEPRLP-PYGLITRRNRVHSSAMQTFMASV 305
Cdd:cd08434 158 PG---VKKIPIK-DPDAErTIGLAWLKDRYLSPAARRFKDFV 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 105-303 1.14e-13

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 68.35  E-value: 1.14e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgarTDDLVFDS--LGEEELCV 182
Cdd:cd08438   1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP----VDEEEFDSqpLCNEPLVA 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 183 VVGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIdLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:cd08438  77 VLPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGF-TPNIAARSSQWDFIAELVAAGLGVALLPRSIAQ 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597402 263 DYPGKhLLAILPIQlEPRLP-PYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08438 156 RLDNA-GVKVIPLT-DPDLRwQLALIWRKGRYLSHAARAWLA 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
27-75 1.19e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 1.19e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15597402    27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGE 75
Cdd:pfam00126  12 ETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 104-305 2.98e-12

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 64.27  E-value: 2.98e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 104 GRVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRipSGARTDDLVFDSLGEEELCVV 183
Cdd:cd08425   1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAF--APVRSPDIDAQPLFDERLALV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 184 VGAQNPLSQARK-LDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:cd08425  79 VGATHPLAQRRTaLTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIK-PRIAIEANSISAVLEVVRRGRLATILPDAIAR 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 15597402 263 DYPGKHLLAilpiqLEPRLPPYG--LITRRNRVHSSAMQTFMASV 305
Cdd:cd08425 158 EQPGLCAVA-----LEPPLPGRTaaLLRRKGAYRSAAARAFAALA 197
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 105-275 7.75e-12

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has 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: 176124  Cd Length: 198  Bit Score: 63.38  E-value: 7.75e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLgrIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08433   1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLAL--LYGPPPIPGLSTEPLLEEDLFLVG 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLpSSIVETTSIMTLLSLLQQTdmIGIT--PRSVIE 262
Cdd:cd08433  79 PADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTL-NVVVEIDSVATLKALVAAG--LGYTilPASAVA 155

                       170
                ....*....|...
gi 15597402 263 DYPGKHLLAILPI 275
Cdd:cd08433 156 AEVAAGRLVAAPI 168
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 105-302 1.04e-11

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 62.89  E-value: 1.04e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFdsLGEEELCVVV 184
Cdd:cd08457   1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIE--TRSLPAVVAV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08457  79 PMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVK-RRPIIEVNLSHTALSLVREGLGIAIIDPATAIGL 157

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 265 PGKHlLAILPiqLEPRLP-PYGLITRRNRVHSSAMQTFM 302
Cdd:cd08457 158 PLDG-IVIRP--FDTFIDaGFLVVRAANGPPSTMVDRFI 193
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 105-303 4.19e-11

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 61.28  E-value: 4.19e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDvvLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08456   1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCD--LGLVSTLHEPPGIERERLLRIDGVCVL 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08456  79 PPGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVK-RRIVVETSYAATICALVAAGVGVSVVNPLTALDY 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15597402 265 PGKHLLAilpIQLEPRLP-PYGLITRRNRVHSSAMQTFMA 303
Cdd:cd08456 158 AAAGLVV---RRFSPAVPfEVSLIRPKHRPSSALVAAFSA 194
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 105-297 7.56e-11

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: 60.31  E-value: 7.56e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVV 184
Cdd:cd08417   1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFP--ELPPGLRSQPLFEDRFVCVA 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARkLDWGELQELTWVLQQHPSPMRGIVNQAFhnARIDLPSSI-VETTSIMTLLSLLQQTDMIGITPRSVIED 263
Cdd:cd08417  79 RKDHPLAGGP-LTLEDYLAAPHVLVSPRGRGHGLVDDAL--AELGLSRRVaLTVPHFLAAPALVAGTDLIATVPRRLAEA 155

                       170       180       190
                ....*....|....*....|....*....|....
gi 15597402 264 YPGKHLLAILPIQLEPRLPPYGLITRRNRVHSSA 297
Cdd:cd08417 156 LAERLGLRVLPLPFELPPFTVSLYWHPRRDRDPA 189
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 118-299 1.08e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 59.96  E-value: 1.08e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 118 LLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgarTDDLVFDS--LGEEELCVVVGAQNPLSQaRK 195
Cdd:cd08466  14 LLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVP----FRDPSFKSelLFEDELVCVARKDHPRIQ-GS 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 196 LDWGELQE---LTWVLQQHPSPMRGIVNQAFHNARidlpSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDYPGKHLLAI 272
Cdd:cd08466  89 LSLEQYLAekhVVLSLRRGNLSALDLLTEEVLPQR----NIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQLNLQI 164

                       170       180
                ....*....|....*....|....*..
gi 15597402 273 LPIQLEPRLPPYGLITRRNRVHSSAMQ 299
Cdd:cd08466 165 LPLPFKTKPIPLYMVWHKSRERDPAHQ 191
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 31-228 1.93e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 60.78  E-value: 1.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   31 LRRAADEIGMTQPAATKMLHEAEDLLGVELFERlpRGMR---ATPFGETLIYYSRMIFAELSGMR---EELVALESGNLg 104
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIR--HGKRlkgLTEPGKAVLDVIERILREVGNIKrigDDFSNQDSGTL- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  105 rvTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGrIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:PRK12682  96 --TIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA-TESLADDPDLATLPCYDWQHAVIV 172

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 15597402  185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARI 228
Cdd:PRK12682 173 PPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGL 216
PRK09986 PRK09986
LysR family transcriptional regulator;
33-207 8.46e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.58  E-value: 8.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   33 RAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTVGAI- 111
Cdd:PRK09986  26 RAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEIGIVg 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  112 PALASSLLTRTIATLKQsHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVVGAQNPLS 191
Cdd:PRK09986 106 TALWGRLRPAMRHFLKE-NPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLHESAFAVAVPEEHPLA 184

                        170
                 ....*....|....*.
gi 15597402  192 QARKLDWGELQELTWV 207
Cdd:PRK09986 185 SRSSVPLKALRNEYFI 200
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 27-243 2.09e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 2.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRV 106
Cdd:PRK11233  14 DIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQV 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  107 TVGAIPALASSLLTRTI-ATLKQSHPRLSMSIQVDTSDVLVQALQQDQLD--VVLGRIPsgarTDDLVFDSLGEEELCVV 183
Cdd:PRK11233  94 SIGLAPGTAASSLTMPLlQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDmaVIYEHSP----VAGLSSQPLLKEDLFLV 169

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  184 VGAQNPlsqARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTL 243
Cdd:PRK11233 170 GTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLT-AKVIGEIESIATL 225
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 32-202 2.58e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 57.35  E-value: 2.58e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   32 RRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMReELVALESGNL-GRVTVGA 110
Cdd:PRK11151  19 RRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLK-EMASQQGETMsGPLHIGL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  111 IPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLD-VVLGRIP-SGARTDDLVFDslgeEELCVVVGAQN 188
Cdd:PRK11151  98 IPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDcAILALVKeSEAFIEVPLFD----EPMLLAVYEDH 173

                        170
                 ....*....|....
gi 15597402  189 PLSQARKLDWGELQ 202
Cdd:PRK11151 174 PWANRDRVPMSDLA 187
PRK12680 PRK12680
LysR family transcriptional regulator;
34-195 3.28e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 57.32  E-value: 3.28e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   34 AADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRA-TPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTVGAIP 112
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  113 ALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELcVVVGAQNPLSQ 192
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLYRWRRL-VVVPRGHALDT 180


                 ...
gi 15597402  193 ARK 195
Cdd:PRK12680 181 PRR 183
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
33-279 3.92e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 56.56  E-value: 3.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   33 RAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLgrVTVGAIP 112
Cdd:PRK03601  20 RAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQHNE--LSIGASA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  113 ALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVVGAQNPLSQ 192
Cdd:PRK03601  98 SLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTEA--PKMDEFSSQLLGHFTLALYTSAPSKKKS 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  193 AR---KLDWGElqeltwVLQQHPSPMrgIVNQafhnariDLPssIVETTSIMTLLSLLQQTDMIGITPRSVIEDYPGKHL 269
Cdd:PRK03601 176 ELnyiRLEWGA------DFQQHEAGL--IGAD-------EVP--ILTTSSAELARQLLATLNGCAFLPVHWAKEKGGLHT 238

                        250
                 ....*....|
gi 15597402  270 LAILPIQLEP 279
Cdd:PRK03601 239 VPDSTTLSRP 248
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 27-220 9.89e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.46  E-value: 9.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGEtLIYYSRMIFAELSGMREELVALESGNLgrv 106
Cdd:PRK10837  16 KSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGR-LLYPRALALLEQAVEIEQLFREDNGAL--- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  107 TVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDvvLGRIPSGARTDDLVFDSLGEEELCVVVGA 186
Cdd:PRK10837  92 RIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVD--IGLIEGPCHSPELISEPWLEDELVVFAAP 169

                        170       180       190
                 ....*....|....*....|....*....|....
gi 15597402  187 QNPLSQaRKLDWGELQELTWVLQQHPSPMRGIVN 220
Cdd:PRK10837 170 DSPLAR-GPVTLEQLAAAPWILRERGSGTREIVD 202
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
30-137 2.08e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 54.62  E-value: 2.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   30 SLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSgmrEELVALESGNL-GRVTV 108
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN---QEILDIKNQELsGTLTV 106

                         90       100
                 ....*....|....*....|....*....
gi 15597402  109 GAIPALASSLLTRTIATLKQSHPRLSMSI 137
Cdd:PRK10086 107 YSRPSIAQCWLVPRLADFTRRYPSISLTI 135
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 30-156 4.20e-08

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 53.69  E-value: 4.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   30 SLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETliYYS--RMIFAELSGMREELvaLESGNLGRVT 107
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQR--YFLdiREIFDQLAEATRKL--RARSAKGALT 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15597402  108 VGAIPALASSLLTRTIATLKQSHPRLSMSIQvdTSDVLVQALQQDqLDV 156
Cdd:PRK11139  98 VSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK--AVDRLEDFLRDD-VDV 143
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 105-305 5.00e-08

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 52.12  E-value: 5.00e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPAlASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLD-VVLGRIPSGArtdDLVFDSLGEEELCVV 183
Cdd:cd08419   1 RLRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDlAIMGRPPEDL---DLVAEPFLDNPLVVI 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 184 VGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLPSSivettsiMTLLSL--LQQTDM----IGITP 257
Cdd:cd08419  77 APPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVR-------MELGSNeaIKQAVMaglgLSVLS 149

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15597402 258 RSVIEDYPGKHLLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFMASV 305
Cdd:cd08419 150 LHTLALELATGRLAVLDVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-301 6.40e-08

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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 51.93  E-value: 6.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRipSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08426   1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAF--SPPPEPGIRVHSRQPAPIGAVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGI-TPRSVIED 263
Cdd:cd08426  79 PPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQ-LEPVLISNSIETLKQLVAAGGGISLlTELAVRRE 157

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 264 YPGKHLLAiLPI-QLEPRLPPYGLITRRNRVHSSAMQTF 301
Cdd:cd08426 158 IRRGQLVA-VPLaDPHMNHRQLELQTRAGRQLPAAASAF 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 26-202 6.46e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 52.85  E-value: 6.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   26 EELgSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIF--AELSGMREELVALESGNL 103
Cdd:PRK09906  14 EEL-NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILeqAEKAKLRARKIVQEDRQL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  104 grvTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSgaRTDDLVFDSLGEEELCVV 183
Cdd:PRK09906  93 ---TIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPV--YSDEIDYLELLDEPLVVV 167

                        170
                 ....*....|....*....
gi 15597402  184 VGAQNPLSQARKLDWGELQ 202
Cdd:PRK09906 168 LPVDHPLAHEKEITAAQLD 186
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-226 6.86e-08

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 51.83  E-value: 6.86e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQ-VDTSDVLVqALQQDQLDV-VLGRIPSGARTDDLVFDS--LGEEEL 180
Cdd:cd08423   1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLReAEPPESLD-ALRAGELDLaVVFDYPVTPPPDDPGLTRvpLLDDPL 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 15597402 181 CVVVGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNA 226
Cdd:cd08423  80 DLVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAA 125
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 113-208 1.79e-07

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 50.64  E-value: 1.79e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 113 ALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSgARTDDLVFDSLGEEELCVVVGAQNPLSQ 192
Cdd:cd08451  10 AAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPV-ARSDGLVLELLLEEPMLVALPAGHPLAR 88

                        90
                ....*....|....*.
gi 15597402 193 ARKLDWGELQELTWVL 208
Cdd:cd08451  89 ERSIPLAALADEPFIL 104
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 31-229 7.34e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 50.04  E-value: 7.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   31 LRRAADEIGMTQPAATKMLHEAEDLLGVELFERlpRGMRAT----PFGETLIYYSRMIFaELSGMREELVALESGNLGRV 106
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIR--RGKRLTgltePGKELLQIVERMLL-DAENLRRLAEQFADRDSGHL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  107 TVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGrIPSGARTDDLVFDSLGEEELCVVVGA 186
Cdd:PRK12683  96 TVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA-TEALDREPDLVSFPYYSWHHVVVVPK 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15597402  187 QNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARID 229
Cdd:PRK12683 175 GHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLV 217
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-301 1.99e-06

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: 47.57  E-value: 1.99e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08427   1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLVWTPLVREPLVLIA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLdwgeLQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRS--VIE 262
Cdd:cd08427  81 PAELAGDDPREL----LATQPFIRYDRSAWGGRLVDRFLRRQGIR-VREVMELDSLEAIAAMVAQGLGVAIVPDIavPLP 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597402 263 DYPGkhlLAILPIqlePRLPPY---GLITRRNRVHSSAMQTF 301
Cdd:cd08427 156 AGPR---VRVLPL---GDPAFSrrvGLLWRRSSPRSRLIQAL 191
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
27-192 2.27e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 48.26  E-value: 2.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRV 106
Cdd:PRK10094  15 ETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQV 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  107 TVgaipaLASSLL------TRTIATLKQSHP----RLSMSIQVDTSDVLVqalqQDQLDVVLGRIPSGARTDDLVFDSLG 176
Cdd:PRK10094  95 NI-----VINNLLynpqavAQLLAWLNERYPftqfHISRQIYMGVWDSLL----YEGFSLAIGVTGTEALANTFSLDPLG 165

                        170
                 ....*....|....*.
gi 15597402  177 EEELCVVVGAQNPLSQ 192
Cdd:PRK10094 166 SVQWRFVMAADHPLAN 181
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
29-158 5.76e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 47.32  E-value: 5.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSgmreelVALESGNLGRVTV 108
Cdd:PRK15421  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS------QALQACNEPQQTR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15597402  109 GAIPALASSL---LTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL 158
Cdd:PRK15421  91 LRIAIECHSCiqwLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM 143
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 27-158 5.98e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.95  E-value: 5.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIF-----AELSGMREELValesg 101
Cdd:PRK15092  24 DLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfndeACSSLMYSNLQ----- 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15597402  102 nlGRVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL 158
Cdd:PRK15092  99 --GVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 29-239 7.00e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.91  E-value: 7.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLI------YYS-RMIFAELSGMREelvaLESG 101
Cdd:PRK11013  19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFeevqrsYYGlDRIVSAAESLRE----FRQG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  102 NLgrvTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL---GRIPSGARTDDLvfdsLGEE 178
Cdd:PRK11013  95 QL---SIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLtetLHTPAGTERTEL----LTLD 167

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597402  179 ELCvVVGAQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDlPSSIVETTS 239
Cdd:PRK11013 168 EVC-VLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVK-RRMVVETHS 226
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
27-192 1.24e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 46.29  E-value: 1.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   27 ELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGEtlIYYS--RMIFAELSGMREELVALESGNLG 104
Cdd:PRK10632  15 EFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGR--IYYQgcRRMLHEVQDVHEQLYAFNNTPIG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIqvdTSDVLVQALQQDQLDVVlgrIPSGARTDDLVFDS-LGEEELcVV 183
Cdd:PRK10632  93 TLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL---VTGIPAPDLIADGLDVV---IRVGALQDSSLFSRrLGAMPM-VV 165


                 ....*....
gi 15597402  184 VGAQNPLSQ 192
Cdd:PRK10632 166 CAAKSYLAQ 174
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
30-228 2.02e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 45.35  E-value: 2.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   30 SLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRA-TPFGETLIYYSRMIFAELSGMR---EELVALESGNLgr 105
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQEVENLKrvgKEFAAQDQGNL-- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  106 vTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGrIPSGARTDDLVFDSLGEEELCVVVG 185
Cdd:PRK12684  96 -TIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIA-TEAIADYKELVSLPCYQWNHCVVVP 173

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15597402  186 AQNPLSQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARI 228
Cdd:PRK12684 174 PDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGL 216
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 105-301 4.02e-05

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has 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: 176128  Cd Length: 198  Bit Score: 43.86  E-value: 4.02e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIqVDTSDV-LVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVV 183
Cdd:cd08437   1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDT-YEGGSAeLLEQLLQGDLDIALLGSLTPLENSALHSKIIKTQHFMII 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 184 VGAQNPLSQARKLDWGEL-QELTWVLQQHpspmrGIVNQAF----HNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPR 258
Cdd:cd08437  80 VSKDHPLAKAKKVNFADLkKENFILLNEH-----FVHPKAFdslcQQANFQ-PNIVYRTNDIHILKSMVRENVGIGFLTD 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597402 259 SVIEDYPgkHLLAIlPIQLEPRLPPY-GLITRRNRVHSSAMQTF 301
Cdd:cd08437 154 IAVKPDD--HLVAI-PLLDNEQPTFYiSLAHRKDQLLTPAQKKL 194
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 115-299 5.95e-05

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. 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. 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: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 43.20  E-value: 5.95e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 115 ASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSL-GEEELCVVVGAQNPLSQA 193
Cdd:cd08468  11 ALAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEERDwWEDTYVVIASRDHPRLSR 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 194 RKLDWGELQELTWVlqqHP-SPMRGIVNQAFhnARIDLPSSIVETT-SIMTLLSLLQQTDMIGITPRSViedypGKHLLA 271
Cdd:cd08468  91 LTLDAFLAERHLVV---TPwNEDRGVVDQVL--EKQGLEREIALQLpNVLNAPFIVASSDLLMTLPRQA-----ARALAE 160

                       170       180       190
                ....*....|....*....|....*....|...
gi 15597402 272 ILPIQLEP---RLPPYGL--ITRRNRVHSSAMQ 299
Cdd:cd08468 161 ALPLELFDlpfDMPPYRLklYSHRQHENSAANQ 193
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
26-78 8.77e-05

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 41.35  E-value: 8.77e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597402  26 EELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLP-----RGMRATPFGETLI 78
Cdd:COG2005  31 DETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggkggGGARLTPEGRRLL 88
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 107-225 2.51e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 41.21  E-value: 2.51e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 107 TVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPsgARTDDLVFDSLGEEELCVVVGA 186
Cdd:cd08450   3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPE--IQSDGIDYQLLLKEPLIVVLPA 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597402 187 QNPLSQARKLDWGELQELTWVLqqhPSPMRGIVNQAFHN 225
Cdd:cd08450  81 DHRLAGREKIPPQDLAGENFIS---PAPTAPVLQQVIEN 116
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-275 3.54e-04

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: 176113  Cd Length: 198  Bit Score: 40.97  E-value: 3.54e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDvvLGRIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08421   1 HVRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRAD--LGIVAGNVDAAGLETRPYRTDRLVVVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKLDWGELQELTWV-LQQHPSPMRGIVNQAfhnARIDLPSSI-VETTSIMTLLSLLQQTDMIGITPRSVIE 262
Cdd:cd08421  79 PRDHPLAGRASVAFADTLDHDFVgLPAGSALHTFLREAA---ARLGRRLRLrVQVSSFDAVCRMVAAGLGIGIVPESAAR 155

                       170
                ....*....|...
gi 15597402 263 DYPGKHLLAILPI 275
Cdd:cd08421 156 RYARALGLRVVPL 168
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 105-287 1.34e-03

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 39.34  E-value: 1.34e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIpsGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08467   1 GFTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRF--AVPPDGLVVRRLYDDGFACLV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLsQARKLDWGELQELTWVLQQHPSPMRGIVNQAFHNARIDLPSSIVeTTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08467  79 RHGHPA-LAQEWTLDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNVAIA-VSSFLTAAATVAATDLIATVPRRVATQV 156

                       170       180
                ....*....|....*....|...
gi 15597402 265 PGKHLLAILPIQLEPRLPPYGLI 287
Cdd:cd08467 157 AAMLPLRVVPPPVDLGTFPVMLI 179
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 105-302 2.03e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 38.68  E-value: 2.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLG---RIPSgartdDLVFDSLGEEELC 181
Cdd:cd08412   1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydlDLPE-----DIAFEPLARLPPY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 182 VVVGAQNPLSQARKLDWGELQELTWVLQQHPsPMRGIVNQAFHNARIDlPSSIVETTSIMTLLSLLQQTDMIGITPRSVI 261
Cdd:cd08412  76 VWLPADHPLAGKDEVSLADLAAEPLILLDLP-HSREYFLSLFAAAGLT-PRIAYRTSSFEAVRSLVANGLGYSLLNDRPY 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15597402 262 ED--YPGKHlLAILPIQLEPRLPPYGLITRRNRVHSSAMQTFM 302
Cdd:cd08412 154 RPwsYDGKR-LVRRPLADPVPPLRLGLAWRRGARLTRAARAFV 195
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-287 2.16e-03

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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 38.42  E-value: 2.16e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 106 VTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL---GRIPSGARTDDLVfdslgeEELCV 182
Cdd:cd08461   2 LVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALttpEYAPDGLRSRPLF------EERYV 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 183 VVGAQNPLSQARKLDWGELQELTWVLQqhpSP----MRGIVNQAFhnARIDLPSSIV-ETTSIMTLLSLLQQTDMIGITP 257
Cdd:cd08461  76 CVTRRGHPLLQGPLSLDQFCALDHIVV---SPsgggFAGSTDEAL--AALGLTRNVVlSVPSFLVVPEILAATDMVAFVP 150

                       170       180       190
                ....*....|....*....|....*....|
gi 15597402 258 RSVIEDYPGkhlLAILPIQLEPrlPPYGLI 287
Cdd:cd08461 151 SRLVPNLEG---LQEVELPLEP--PGFDVV 175
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 28-93 2.83e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 38.77  E-value: 2.83e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597402   28 LGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMRE 93
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
PRK09801 PRK09801
LysR family transcriptional regulator;
29-156 3.11e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 3.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   29 GSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGRVTV 108
Cdd:PRK09801  21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEGMIRI 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15597402  109 GAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVlvqALQQDQLDV 156
Cdd:PRK09801 101 GCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQI---DLVQDNIDL 145
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 98-260 6.32e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 37.26  E-value: 6.32e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402  98 LESGNLGRVTVGAIPALasslltrtIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSgaRTDDLVFDSLGE 177
Cdd:cd08446   3 LDVGYFGSAILDTVPRL--------LRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYP--VEPDIAVENVAQ 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 178 EELCVVVGAQNPLSQARKLDWGELQELTWVLqqHPS-PMRGIVN---QAFHNARIdLPSSIVETTSIMTLLSLLQQTDMI 253
Cdd:cd08446  73 ERLYLAVPKSHPLAARPAVSLADLRNEPLIL--FPRgGRPSFADevlGLFRRAGV-EPRVAQEVEDVVAALALVAAGFGV 149


                ....*..
gi 15597402 254 GITPRSV 260
Cdd:cd08446 150 CIVPESV 156
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 105-303 7.09e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 36.82  E-value: 7.09e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 105 RVTVGAIPALASSLLTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLgrIPSGARTDDLVFDSLGEEELCVVV 184
Cdd:cd08442   1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAF--VAGPVEHPRLEQEPVFQEELVLVS 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 185 GAQNPLSQARKldwgELQELTWVLQQHPSPMRGIVNQAFHNARIdLPSSIVETTSIMTLLSLLQQTDMIGITPRSVIEDY 264
Cdd:cd08442  79 PKGHPPVSRAE----DLAGSTLLAFRAGCSYRRRLEDWLAEEGV-SPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSL 153

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15597402 265 PGKHLLAILPIQLEPRLPPYGLITRRNRVhSSAMQTFMA 303
Cdd:cd08442 154 QGRGSVSIHPLPEPFADVTTWLVWRKDSF-TAALQAFLD 191
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 119-208 7.52e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 36.87  E-value: 7.52e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402 119 LTRTIATLKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVLGRIPSGARTDDLVFDSLGEEELCVVVGAQNPLSQARKLDW 198
Cdd:cd08449  15 LGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASELLWREPMVVALPEEHPLAGRKSLTL 94

                        90
                ....*....|
gi 15597402 199 GELQELTWVL 208
Cdd:cd08449  95 ADLRDEPFVF 104
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
26-158 8.67e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 37.34  E-value: 8.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597402   26 EELGSLRRAADEIGMTQPAATKMLHEAEDLLGVELFERLPRGMRATPFGETLIYYSRMIFAELSGMREELVALESGNLGR 105
Cdd:PRK10082  23 EKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRK 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15597402  106 VTVGAIPALASSLLTRTIatlKQSHPRLSMSIQVDTSDVLVQALQQDQLDVVL 158
Cdd:PRK10082 103 IKIAAAHSLSLGLLPSII---SQMPPLFTWAIEAIDVDEAVDKLREGQSDCIF 152
 
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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