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Conserved domains on  [gi|1079341433|ref|WP_070140578|]
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MULTISPECIES: LysR family transcriptional regulator [Bacillus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444082)

LysR family transcriptional regulator with an N-terminal DNA binding motif and a C-terminal inducer binding domain

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|11741199

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-279 2.36e-73

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: 223.25  E-value: 2.36e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVET--VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVTQNK 169
Cdd:cd08442     2 LRLGSMETtaAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 170 ---AFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVHC 246
Cdd:cd08442    82 hppVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSI 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1079341433 247 HAIPEKYGSISTVFIRRKDSYmTNSMRSFLKTI 279
Cdd:cd08442   162 HPLPEPFADVTTWLVWRKDSF-TAALQAFLDLL 193
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.62e-22

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 87.06  E-value: 3.62e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-279 2.36e-73

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: 223.25  E-value: 2.36e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVET--VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVTQNK 169
Cdd:cd08442     2 LRLGSMETtaAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 170 ---AFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVHC 246
Cdd:cd08442    82 hppVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSI 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1079341433 247 HAIPEKYGSISTVFIRRKDSYmTNSMRSFLKTI 279
Cdd:cd08442   162 HPLPEPFADVTTWLVWRKDSF-TAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-282 1.03e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.03e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  81 VFLD-SETPSGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDV 157
Cdd:COG0583    81 ELRAlRGGPRGTLRIGAPPSLARylLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 158 STEKLMLVTqnkafhieeftttpllvfnqGCGYRsklerwlkdeglLPKRIMEFNILETILNSVALGLGITLVPQSAVQH 237
Cdd:COG0583   161 GEERLVLVA--------------------SPDHP------------LARRAPLVNSLEALLAAVAAGLGIALLPRFLAAD 208

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1079341433 238 LSKAGKVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTIEEH 282
Cdd:COG0583   209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-282 1.77e-42

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: 144.74  E-value: 1.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  89 SGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT 166
Cdd:pfam03466   1 SGRLRIGAPPTLASylLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 -------QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLS 239
Cdd:pfam03466  81 ppdhplaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1079341433 240 KAGKVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTIEEH 282
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-280 4.57e-27

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 107.03  E-value: 4.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQVF 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  83 LDSET-PSGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVST 159
Cdd:CHL00180   87 EDLKNlQRGTLIIGASQTTGTylMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILEITP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 160 ---EKLMLV-------TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKR---IMEFNILETILNSVALGLG 226
Cdd:CHL00180  167 yveDELALIipkshpfAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRfkiEMELNSIEAIKNAVQSGLG 246

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079341433 227 ITLVPQSAVQHLSKAGKVHChaipekyGSISTVFIRRKDSYMTNSMRSFLKTIE 280
Cdd:CHL00180  247 AAFVSVSAIEKELELGLLHW-------IKIENITIKRMLSIITNPNRYKSKASE 293
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.62e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 87.06  E-value: 3.62e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-80 3.88e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 62.27  E-value: 3.88e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-279 2.36e-73

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: 223.25  E-value: 2.36e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVET--VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVTQNK 169
Cdd:cd08442     2 LRLGSMETtaAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 170 ---AFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVHC 246
Cdd:cd08442    82 hppVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSI 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1079341433 247 HAIPEKYGSISTVFIRRKDSYmTNSMRSFLKTI 279
Cdd:cd08442   162 HPLPEPFADVTTWLVWRKDSF-TAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-282 1.03e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.03e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  81 VFLD-SETPSGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDV 157
Cdd:COG0583    81 ELRAlRGGPRGTLRIGAPPSLARylLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 158 STEKLMLVTqnkafhieeftttpllvfnqGCGYRsklerwlkdeglLPKRIMEFNILETILNSVALGLGITLVPQSAVQH 237
Cdd:COG0583   161 GEERLVLVA--------------------SPDHP------------LARRAPLVNSLEALLAAVAAGLGIALLPRFLAAD 208

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1079341433 238 LSKAGKVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTIEEH 282
Cdd:COG0583   209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-282 1.77e-42

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: 144.74  E-value: 1.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  89 SGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT 166
Cdd:pfam03466   1 SGRLRIGAPPTLASylLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 -------QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLS 239
Cdd:pfam03466  81 ppdhplaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1079341433 240 KAGKVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTIEEH 282
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-279 3.76e-39

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: 135.81  E-value: 3.76e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT--- 166
Cdd:cd05466     2 LRIGASPSIAAylLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVppd 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 ----QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLsKAG 242
Cdd:cd05466    82 hplaKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL-ADG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1079341433 243 KVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTI 279
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-279 1.03e-28

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: 108.73  E-value: 1.03e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT--- 166
Cdd:cd08420     2 LRIGASTTIGEylLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVppd 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 ----QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRI---MEFNILETILNSVALGLGITLVPQSAVQHLS 239
Cdd:cd08420    82 hplaGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1079341433 240 KAGKVhcHAIPEKYGSISTVF--IRRKDSYMTNSMRSFLKTI 279
Cdd:cd08420   162 ELGRL--VALPVEGLRLTRPFslIYHKDKYLSPAAEAFLEFL 201
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-280 4.57e-27

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 107.03  E-value: 4.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQVF 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  83 LDSET-PSGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVST 159
Cdd:CHL00180   87 EDLKNlQRGTLIIGASQTTGTylMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILEITP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 160 ---EKLMLV-------TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKR---IMEFNILETILNSVALGLG 226
Cdd:CHL00180  167 yveDELALIipkshpfAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRfkiEMELNSIEAIKNAVQSGLG 246

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079341433 227 ITLVPQSAVQHLSKAGKVHChaipekyGSISTVFIRRKDSYMTNSMRSFLKTIE 280
Cdd:CHL00180  247 AAFVSVSAIEKELELGLLHW-------IKIENITIKRMLSIITNPNRYKSKASE 293
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-282 1.62e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 102.73  E-value: 1.62e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  81 VFLDSETPS-GILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAgLTEELIRE-VIDHQLDGAFISGPIKHPLIEQYD 156
Cdd:PRK11242   81 AIHDVADLSrGSLRLAMTPTFTAylIGPLIDAFHARYPGITLTIRE-MSQERIEAlLADDELDVGIAFAPVHSPEIEAQP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 157 VSTEKLMLVT--------QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGIT 228
Cdd:PRK11242  160 LFTETLALVVgrhhplaaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLAT 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433 229 LVPQS-AVQHlskAGKVHCHAIPEKYGSiSTVFIRRKDSYMTNSMRSFLKTIEEH 282
Cdd:PRK11242  240 LLPAAiAREH---DGLCAIPLDPPLPQR-TAALLRRKGAYRSAAARAFIELALER 290
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-234 2.14e-23

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 96.97  E-value: 2.14e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRH-KRGMTLTAEGRKMLVYVHKILQDVEEL 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQV---FLDSETpsGILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAF----ISG---- 145
Cdd:PRK12684   81 KRVgkeFAAQDQ--GNLTIATTHTQAryALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateaIADykel 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 146 --------------PIKHPLIEQYDVSTEKLM---LVTQNKAFhieeftttpllvfnqgCGyRSKLERWLKDEGLLPKRI 208
Cdd:PRK12684  159 vslpcyqwnhcvvvPPDHPLLERKPLTLEDLAqypLITYDFAF----------------AG-RSKINKAFALRGLKPDIV 221

                         250       260
                  ....*....|....*....|....*.
gi 1079341433 209 MEFNILETILNSVALGLGITLVPQSA 234
Cdd:PRK12684  222 LEAIDADVIKTYVELGLGVGIVADMA 247
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-279 9.47e-23

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: 92.57  E-value: 9.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETV--STLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV---- 165
Cdd:cd08414     2 LRIGFVGSAlyGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAlpad 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 ---TQNKAFHIEEFTTTPLLVF--NQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSaVQHLSK 240
Cdd:cd08414    82 hplAARESVSLADLADEPFVLFprEPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPAS-VARLQR 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1079341433 241 AGkVHCHAIPEKYGSISTVFIRRKDSyMTNSMRSFLKTI 279
Cdd:cd08414   161 PG-VVYRPLADPPPRSELALAWRRDN-ASPALRAFLELA 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-282 1.56e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 94.67  E-value: 1.56e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRH-KRGMTLTAEGRKMLVYVHKILQDVEEL 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQVFLD-SETPSGILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD--------------GA 141
Cdd:PRK12682   81 KRIGDDfSNQDSGTLTIATTHTQAryVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADigiatesladdpdlAT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 142 F--------ISGPIKHPLIEQYDVSTEKLmlvtqnkafhieefTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNI 213
Cdd:PRK12682  161 LpcydwqhaVIVPPDHPLAQEERITLEDL--------------AEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAID 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079341433 214 LETILNSVALGLGITLVPQSAVQHLSKAGKVhchAIPEKY---GSISTVFIRRkDSYMTNSMRSFLKTIEEH 282
Cdd:PRK12682  227 SDVIKTYVRLGLGVGIVAEMAYRPDRDGDLV---ALPAGHlfgPNTAWVALKR-GAYLRNYVYKFIELCAPH 294
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.62e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 87.06  E-value: 3.62e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-283 3.80e-20

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 87.82  E-value: 3.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQVF 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  83 LDSEtpsGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHP-LIEQYDVST 159
Cdd:PRK10837   85 REDN---GALRIYASSTIGNyiLPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPeLISEPWLED 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 160 EKLMLVTQN-----KAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEglLP--KRIMEFNILETILNSVALGLGITLVPQ 232
Cdd:PRK10837  162 ELVVFAAPDsplarGPVTLEQLAAAPWILRERGSGTREIVDYLLLSH--LPrfELAMELGNSEAIKHAVRHGLGISCLSR 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1079341433 233 SAVQHLSKAGKVHCHAIPEKYGSISTVFIRRKDSYMTNSMRSFLKTIEEHH 283
Cdd:PRK10837  240 RVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQEAN 290
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-284 1.17e-19

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 86.75  E-value: 1.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  81 VFLDSETPSGILKIGTVET--VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVS 158
Cdd:PRK09906   81 RARKIVQEDRQLTIGFVPSaeVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 159 TEKLMLV--TQNKAFHIEEFTTTPLLVFN-------QGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITL 229
Cdd:PRK09906  161 DEPLVVVlpVDHPLAHEKEITAAQLDGVNfistdpaYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCTI 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433 230 VPQSAVQHLSKAgkVHCHAIPEKYGSISTVFIRRKDSyMTNSMRSFLKTIEEHHH 284
Cdd:PRK09906  241 IPGYMNNFNTGQ--VVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERLA 292
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-250 1.53e-19

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: 84.19  E-value: 1.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPL-IEQYDVSTEKLMLVT-- 166
Cdd:cd08436     2 LAIGTITSLAAvdLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPgLASRELAREPLVAVVap 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 -----QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSka 241
Cdd:cd08436    82 dhplaGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLP-- 159


                  ....*....
gi 1079341433 242 gkvHCHAIP 250
Cdd:cd08436   160 ---GLAALP 165
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-236 1.32e-17

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 81.01  E-value: 1.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRH-KRGMTLTAEGRKMLVYVHKILQD---V 75
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRgKRLLGMTEPGKALLVIAERILNEasnV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  76 EELKQVFLDSEtpSGILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELI--------------REVIDHQLD 139
Cdd:PRK12679   81 RRLADLFTNDT--SGVLTIATTHTQArySLPEVIKAFRELFPEVRLELIQGTPQEIAtllqngeadigiasERLSNDPQL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 140 GAF--------ISGPIKHPLIEQYDVSteklmlvtqnkafhIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEF 211
Cdd:PRK12679  159 VAFpwfrwhhsLLVPHDHPLTQITPLT--------------LESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSA 224

                         250       260
                  ....*....|....*....|....*
gi 1079341433 212 NILETILNSVALGLGITLVPQSAVQ 236
Cdd:PRK12679  225 QDSDVIKTYVALGLGIGLVAEQSSG 249
PRK09986 PRK09986
LysR family transcriptional regulator;
3-236 1.37e-17

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 80.92  E-value: 1.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEE-LKQV 81
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQsLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  82 FLDSETPSGILKIGTVETV--STLPTILSSYYKSYPNVDLSLQ--------AGLTEELI-----REVIDHQLDGaFISG- 145
Cdd:PRK09986   89 EQIGRGEAGRIEIGIVGTAlwGRLRPAMRHFLKENPNVEWLLRelspsmqmAALERRELdagiwRMADLEPNPG-FTSRr 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 146 ----------PIKHPLieqydVSTEKLMLvtqnKAFHIEEFTTTPllvFNQGcGYRSKLERWLKDEGLLPKRIMEFNILE 215
Cdd:PRK09986  168 lhesafavavPEEHPL-----ASRSSVPL----KALRNEYFITLP---FVHS-DWGKFLQRVCQQAGFSPQIIRQVNEPQ 234

                         250       260
                  ....*....|....*....|.
gi 1079341433 216 TILNSVALGLGITLVPQSAVQ 236
Cdd:PRK09986  235 TVLAMVSMGIGITLLPDSYAQ 255
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-230 1.98e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 80.47  E-value: 1.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRH-KRGMTLTAEGRKMLVYVHKILQDVEEL 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQV---FLDSEtpSGILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD-------------- 139
Cdd:PRK12683   81 RRLaeqFADRD--SGHLTVATTHTQAryALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADigiatealdrepdl 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 140 GAF--------ISGPIKHPLieqydvsteklmlvTQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEF 211
Cdd:PRK12683  159 VSFpyyswhhvVVVPKGHPL--------------TGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTA 224

                         250
                  ....*....|....*....
gi 1079341433 212 NILETILNSVALGLGITLV 230
Cdd:PRK12683  225 LDADVIKTYVELGMGVGIV 243
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 100-279 8.90e-17

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: 76.42  E-value: 8.90e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 100 VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT-------QNKAFH 172
Cdd:cd08434    12 TSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVpkdhplaGRDSVD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 173 IEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVH-CHAIPE 251
Cdd:cd08434    92 LAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPGVKKIPiKDPDAE 171

                         170       180
                  ....*....|....*....|....*....
gi 1079341433 252 KygsisTVFI-RRKDSYMTNSMRSFLKTI 279
Cdd:cd08434   172 R-----TIGLaWLKDRYLSPAARRFKDFV 195
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-235 4.38e-16

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: 74.53  E-value: 4.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIK--------HPLIEqydvstEK 161
Cdd:cd08427     2 LRLGAIATVLTglLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFplpkdlvwTPLVR------EP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 162 LMLVTQNKAFHIEEFT---TTPLLVFNqgcgyRSK-----LERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQS 233
Cdd:cd08427    76 LVLIAPAELAGDDPREllaTQPFIRYD-----RSAwggrlVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDI 150


                  ..
gi 1079341433 234 AV 235
Cdd:cd08427   151 AV 152
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 91-242 4.85e-15

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: 71.82  E-value: 4.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  91 ILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV--- 165
Cdd:cd08415     1 TLRIAALPALALslLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVlpp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 ----TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKA 241
Cdd:cd08415    81 ghplARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAGA 160


                  .
gi 1079341433 242 G 242
Cdd:cd08415   161 G 161
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-237 3.23e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 71.00  E-value: 3.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  36 IKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQVfLDSETP--SGILKI-GTVETV-STLPTILSSYY 111
Cdd:PRK11716   12 IQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHT-LDQQGPslSGELSLfCSVTAAySHLPPILDRFR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 112 KSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPL-IEQYDVSTEKLMLVTQNKAFHIEEFTT--------TPLL 182
Cdd:PRK11716   91 AEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPAsVAFSPIDEIPLVLIAPALPCPVRQQLSqekpdwsrIPFI 170

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1079341433 183 VFNQGCGyRSKLERWLKDEGLLPkrimefNIL------ETILNSVALGLGITLVPQSAVQH 237
Cdd:PRK11716  171 LPEHGPA-RRRIDLWFRRHKIKP------NIYatvsghEAIVSMVALGCGVGLLPEVVLEN 224
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-242 4.59e-14

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: 69.07  E-value: 4.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVS-TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPikhPliEQYDVSTEKLM---LV-- 165
Cdd:cd08419     2 LRLAVVSTAKyFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP---P--EDLDLVAEPFLdnpLVvi 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 -------TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHL 238
Cdd:cd08419    77 appdhplAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALE 156


                  ....
gi 1079341433 239 SKAG 242
Cdd:cd08419   157 LATG 160
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-246 9.32e-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: 68.32  E-value: 9.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  90 GILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVT- 166
Cdd:cd08411     1 GPLRLGVIPTIAPylLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 ------QNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAV-QHLS 239
Cdd:cd08411    81 kdhplaKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVpSEEL 160


                  ....*..
gi 1079341433 240 KAGKVHC 246
Cdd:cd08411   161 RGDRLVV 167
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-242 2.59e-13

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: 67.17  E-value: 2.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  94 IGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV------ 165
Cdd:cd08440     4 VAALPSLAAtlLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVcpkdhp 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079341433 166 -TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAG 242
Cdd:cd08440    84 lARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG 161
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-282 1.90e-12

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 66.21  E-value: 1.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKR-------GMTLTAEGRKMLVYVhKILQ 73
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRkvlftqaGLLLVDQARTVLREV-KVLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  74 DVEELKqvfldSETPSGILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD----------GA 141
Cdd:PRK11151   80 EMASQQ-----GETMSGPLHIGLIPTVGPylLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDcailalvkesEA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 142 FISGPIkhplieqYDvstEKLMLV-------TQNKAFHIEEFTTTPLLVFNQG-CgyrsklerwLKDEGL------LPKR 207
Cdd:PRK11151  155 FIEVPL-------FD---EPMLLAvyedhpwANRDRVPMSDLAGEKLLMLEDGhC---------LRDQAMgfcfeaGADE 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 208 IMEF--NILETILNSVALGLGITLVPQSAVQHLSKAGKVH---CHAiPEKYGSISTVFirRKDSYMTNSMRSFLKTIEEH 282
Cdd:PRK11151  216 DTHFraTSLETLRNMVAAGSGITLLPALAVPNERKRDGVCylpCIK-PEPRRTIGLVY--RPGSPLRSRYEQLAEAIRAR 292
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-125 3.96e-12

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 65.17  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 ME-LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRkmlVYVH---KILQDVE 76
Cdd:PRK10632    1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGR---IYYQgcrRMLHEVQ 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1079341433  77 EL-KQVFLDSETPSGILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGL 125
Cdd:PRK10632   78 DVhEQLYAFNNTPIGTLRIGCSSTMAqnVLAGLTAKMLKEYPGLSVNLVTGI 129
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-245 7.11e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 64.70  E-value: 7.11e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRkmLVYVHK--ILQDVEEl 78
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGK--ILYTHAraILRQCEQ- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQVFLDS--ETPSGILKI----GTVETVSTLPtILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFI------SGP 146
Cdd:PRK11233   78 AQLAVHNvgQALSGQVSIglapGTAASSLTMP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIyehspvAGL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 147 IKHPLIEqydvstEKLMLVTQN----KAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVA 222
Cdd:PRK11233  157 SSQPLLK------EDLFLVGTQdcpgQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIA 230

                         250       260
                  ....*....|....*....|...
gi 1079341433 223 LGLGITLVPQSAVQHLSKAGKVH 245
Cdd:PRK11233  231 SGMGVTVLPESAARSLCGAVNGW 253
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-135 1.24e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 63.71  E-value: 1.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQVFLDS 85
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1079341433  86 ETPsGILkigtveTVSTLPTI--------LSSYYKSYPNVDLSLQAGLTEE-LIREVID 135
Cdd:PRK11139   91 SAK-GAL------TVSLLPSFaiqwlvprLSSFNEAHPDIDVRLKAVDRLEdFLRDDVD 142
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-124 1.46e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.87  E-value: 1.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLvyvHKILQDVEELKQVF 82
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTLNQEI 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1079341433  83 LD--SETPSGILkigtveTVSTLPTI--------LSSYYKSYPNVDLSLQAG 124
Cdd:PRK10086   93 LDikNQELSGTL------TVYSRPSIaqcwlvprLADFTRRYPSISLTILTG 138
PRK09791 PRK09791
LysR family transcriptional regulator;
1-163 2.25e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 63.24  E-value: 2.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDV----E 76
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraaqE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  77 ELKQVFLDSetpSGILKIGTVETV--STLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD---GAFISGPIKHPL 151
Cdd:PRK09791   85 DIRQRQGQL---AGQINIGMGASIarSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDftiNTYYQGPYDHEF 161

                         170
                  ....*....|..
gi 1079341433 152 ieqydvSTEKLM 163
Cdd:PRK09791  162 ------TFEKLL 167
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-279 2.79e-11

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: 61.42  E-value: 2.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIG--TVETVSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV---- 165
Cdd:cd08438     2 LRLGlpPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVlprg 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 ---TQNKAFHIEEFTTTPLLVFNQGcgyrSKLERWLKD----EGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHL 238
Cdd:cd08438    82 hplAGRKTVSLADLADEPFILFNED----FALHDRIIDacqqAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1079341433 239 SKAGkVHChaIPEKYGSIS--TVFIRRKDSYMTNSMRSFLKTI 279
Cdd:cd08438   158 DNAG-VKV--IPLTDPDLRwqLALIWRKGRYLSHAARAWLALL 197
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-80 3.88e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 62.27  E-value: 3.88e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 92-265 1.08e-10

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 59.82  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVE--TVSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLML----- 164
Cdd:cd08452     2 LVIGFVGaaIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLalpkq 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 165 --VTQNKAFHIEEFTTTPLLVFNQGCGYRSKLE--RWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAvQHLSK 240
Cdd:cd08452    82 hpLASKEEITIEDLRDEPIITVAREAWPTLYDEiiQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSA-KKLFN 160

                         170       180
                  ....*....|....*....|....*
gi 1079341433 241 AGKVHcHAIPEKYGSISTVFIRRKD 265
Cdd:cd08452   161 LEVAY-RKIDQINLNAEWSIAYRKD 184
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-139 5.33e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 58.89  E-value: 5.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQdveelkq 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR------- 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079341433  81 vFLDSETPS-------GILKIGTV-ETVST-LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD 139
Cdd:PRK15092   84 -FNDEACSSlmysnlqGVLTIGASdDTADTiLPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVD 150
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-250 6.35e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 58.66  E-value: 6.35e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVE----ELKQV 81
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLEsmpsELQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  82 FLDSETPSGILKIGTVETVSTLPTILSSYYKSYP-------------------NVDLSLQAGLT-EELIREVID----HQ 137
Cdd:PRK10094   87 NDGVERQVNIVINNLLYNPQAVAQLLAWLNERYPftqfhisrqiymgvwdsllYEGFSLAIGVTgTEALANTFSldplGS 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 138 LDGAFISGPiKHPLIEQYDVSTEKLMlvTQNKAFHIEEFTTTpllvfnqgcgyRSKLERWL---KDEGLLPKrimefniL 214
Cdd:PRK10094  167 VQWRFVMAA-DHPLANVEEPLTEAQL--RRFPAVNIEDSART-----------LTKRVAWRlpgQKEIIVPD-------M 225

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1079341433 215 ETILNSVALGLGITLVPQSAVQHLSKAGKVHCHAIP 250
Cdd:PRK10094  226 ETKIAAHLAGVGIGFLPKSLCQSMIDNQQLVSRVIP 261
PRK09801 PRK09801
LysR family transcriptional regulator;
4-139 1.61e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.74  E-value: 1.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   4 RDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQD----VEELK 79
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQyqrlVDDVT 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079341433  80 QVfldSETPSGILKIGTVETV--STLPTILSSYYKSYPNVDLSLqaglteelirEVIDHQLD 139
Cdd:PRK09801   89 QI---KTRPEGMIRIGCSFGFgrSHIAPAITELMRNYPELQVHF----------ELFDRQID 137
PRK10341 PRK10341
transcriptional regulator TdcA;
6-231 2.26e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 57.18  E-value: 2.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKIlqdVEELKQVF--L 83
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI---TREMKNMVneI 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  84 DSETPSGILKIG----TVETVSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAF--ISGPIK------HPL 151
Cdd:PRK10341   89 NGMSSEAVVDVSfgfpSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKlqdlhvEPL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 152 IE-QYDVSTEKLMlvTQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLV 230
Cdd:PRK10341  169 FEsEFVLVASKSR--TCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVI 246


                  .
gi 1079341433 231 P 231
Cdd:PRK10341  247 P 247
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-244 7.65e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 55.79  E-value: 7.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQDVEELKQ 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  81 VFLDSETPSGILKIGTVETVSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFI------SGPIKHPLIEq 154
Cdd:PRK15421   82 ACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTsdilprSGLHYSPMFD- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 155 YDVsteKLML-----VTQNKAFHIEEFTTTPLLVFNQgcgYRSKLERW---LKDEGLLPKRIMEFNILeTILNSVALGLG 226
Cdd:PRK15421  161 YEV---RLVLapdhpLAAKTRITPEDLASETLLIYPV---QRSRLDVWrhfLQPAGVSPSLKSVDNTL-LLIQMVAARMG 233

                         250
                  ....*....|....*...
gi 1079341433 227 ITLVPQSAVQHLSKAGKV 244
Cdd:PRK15421  234 IAALPHWVVESFERQGLV 251
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-235 1.78e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 54.52  E-value: 1.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMT-LTAEGRKMLVYVHKILQDVEEL 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQVFLDSETPS-GILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAF------------- 142
Cdd:PRK12681   81 KSVAGEHTWPDkGSLYIATTHTQAryALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIatealhlyddlim 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 143 ---------ISGPIKHPLIEQYDVSteklmlvtqnkafhIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNI 213
Cdd:PRK12681  161 lpcyhwnrsVVVPPDHPLAKKKKLT--------------IEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATD 226

                         250       260
                  ....*....|....*....|..
gi 1079341433 214 LETILNSVALGLGITLVPQSAV 235
Cdd:PRK12681  227 ADVIKTYVRLGLGVGVIASMAV 248
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 101-245 5.40e-08

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 51.81  E-value: 5.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 101 STLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPL-IEQYDVSTEKLML--------VTQNKAF 171
Cdd:cd08430    13 SFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPArLAFLPLATSPLVFiapniacaVTQQLSQ 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 172 HIEEFTTTPLLVFNQGCGyRSKLERWLKDEGLLPkrimefNIL------ETILNSVALGLGITLVPQSAVQHLSKAGKVH 245
Cdd:cd08430    93 GEIDWSRLPFILPERGLA-RERLDQWFRRRGIKP------NIYaqvaghEAIVSMVALGCGVGIVPELVLDNSPLKDKVR 165
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 90-277 6.33e-08

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: 51.95  E-value: 6.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  90 GILKIGTVETVST--LPTILSSYYKSYPNVDLSLQAgLTEELIRE-VIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV- 165
Cdd:cd08425     1 GSLRLAMTPTFTAylIGPLIDRFHARYPGIALSLRE-MPQERIEAaLADDRLDLGIAFAPVRSPDIDAQPLFDERLALVv 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 -------TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPqSAVQHl 238
Cdd:cd08425    80 gathplaQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILP-DAIAR- 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1079341433 239 SKAGKVHCHAIPEKYGSiSTVFIRRKDSYMTNSMRSFLK 277
Cdd:cd08425   158 EQPGLCAVALEPPLPGR-TAALLRRKGAYRSAAARAFAA 195
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
21-139 6.46e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 52.71  E-value: 6.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  21 AAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKI----LQDVEELKQVFLDSEtpsgiLKIGT 96
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLmntwQAAKKEVAHTSQHNE-----LSIGA 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1079341433  97 VETV--STLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLD 139
Cdd:PRK03601   96 SASLweCMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLD 140
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 114-245 7.02e-08

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: 51.44  E-value: 7.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 114 YPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVTQNKAFH-------IEEFTTTPLLVFNQ 186
Cdd:cd08433    26 YPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLprgapvpLAELARLPLILPSR 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1079341433 187 GCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVH 245
Cdd:cd08433   106 GHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGRLV 164
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 103-245 9.43e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 51.46  E-value: 9.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 103 LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFisGPIKH--PLIEQYDVSTEKLMLV-------TQNKA-FH 172
Cdd:cd08445    16 LPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGF--GRLRIedPAIRRIVLREEPLVVAlpaghplAQEKApLT 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433 173 IEEFTTTPLLVF--NQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSaVQHLSKAGKVH 245
Cdd:cd08445    94 LAQLADEPLILYpaSPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPAS-VQRLRRDDVVY 167
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 101-249 1.90e-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: 50.25  E-value: 1.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 101 STLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHP--LIEQyDVSTEKLMLV-------TQNKAF 171
Cdd:cd08451    14 PLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdgLVLE-LLLEEPMLVAlpaghplARERSI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 172 HIEEFTTTPLLVFnqgcgyRSKLERWLKDE--------GLLPKRIMEFNILETILNSVALGLGITLVPQSaVQHLSKAGk 243
Cdd:cd08451    93 PLAALADEPFILF------PRPVGPGLYDAiiaacrraGFTPRIGQEAPQMASAINLVAAGLGVSIVPAS-MRQLQAPG- 164


                  ....*.
gi 1079341433 244 VHCHAI 249
Cdd:cd08451   165 VVYRPL 170
PRK12680 PRK12680
LysR family transcriptional regulator;
1-235 1.92e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.55  E-value: 1.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   1 MELRDLQIFQSVADRG-SVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGM-TLTAEGRKMLVYVHKILQDVEEL 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  79 KQVFLDSETPS-GILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFIS-------GPIK 148
Cdd:PRK12680   81 RTYAANQRRESqGQLTLTTTHTQArfVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVStaggepsAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 149 HPLIEQydvstEKLMLV-------TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSV 221
Cdd:PRK12680  161 VPLYRW-----RRLVVVprghaldTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYV 235

                         250
                  ....*....|....
gi 1079341433 222 ALGLGITLVPQSAV 235
Cdd:PRK12680  236 RAGLGVGLLAEMAV 249
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-250 2.59e-07

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: 50.00  E-value: 2.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  95 GTVETVstLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV-------TQ 167
Cdd:cd08426     9 GLAAEL--LPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVvppghplAR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 168 NKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKVhcH 247
Cdd:cd08426    87 QPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQL--V 164


                  ...
gi 1079341433 248 AIP 250
Cdd:cd08426   165 AVP 167
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 100-244 6.94e-07

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: 48.64  E-value: 6.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 100 VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV-------TQNKAFH 172
Cdd:cd08457    12 NGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAvpmghplAQLDVVS 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079341433 173 IEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAGKV 244
Cdd:cd08457    92 PQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDGIV 163
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-238 9.94e-07

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: 48.36  E-value: 9.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVST--LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFI-----SGPIKHPLIEQYDVSTEKLML 164
Cdd:cd08423     2 LRVGAFPTAAAalLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypvTPPPDDPGLTRVPLLDDPLDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 165 VTqnKAFH---------IEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAV 235
Cdd:cd08423    82 VL--PADHplagreevaLADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLAL 159


                  ...
gi 1079341433 236 QHL 238
Cdd:cd08423   160 GAR 162
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 92-231 2.03e-06

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: 47.37  E-value: 2.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIG--TVETVSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV--TQ 167
Cdd:cd08450     2 LTIGflPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVlpAD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079341433 168 NKAFHIEEFT--------------TTPLLvfnqgcgyRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVP 231
Cdd:cd08450    82 HRLAGREKIPpqdlagenfispapTAPVL--------QQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLP 151
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-68 2.99e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 47.66  E-value: 2.99e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRhKRGMTLTAEGRKMLVYV 68
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHL 68
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-235 5.16e-06

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: 46.12  E-value: 5.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  90 GILKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLML-VT 166
Cdd:cd08446     1 GELDVGYFGSAIldTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLaVP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1079341433 167 QN------KAFHIEEFTTTPLLVFNQGC--GYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAV 235
Cdd:cd08446    81 KShplaarPAVSLADLRNEPLILFPRGGrpSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVA 157
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 100-245 7.26e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 45.82  E-value: 7.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 100 VST-----LPTILSSYYKSYPNVDLSLQAGLT----EELIREVIDHqldGAFISGPI-KHPLIEQY-DVSTEKLMLVT-- 166
Cdd:cd08453     7 VSTadysvLPELVRRFREAYPDVELQLREATSdvqlEALLAGEIDA---GIVIPPPGaSAPPALAYrPLLSEPLVLAVpa 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 167 -----QNKAFHIEEFTTTPLLVFNQ-----------GCgYRsklerwlkDEGLLPkRIMEFNI-LETILNSVALGLGITL 229
Cdd:cd08453    84 awaaeGGAPLALAAVAAEPLVIFPRriapafhdavtGY-YR--------AAGQTP-RIAQEAIqMQTIISLVSAGMGVAL 153

                         170
                  ....*....|....*.
gi 1079341433 230 VPQSaVQHLSKAGKVH 245
Cdd:cd08453   154 VPAS-LRNLARPGVVY 168
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-244 8.48e-06

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: 45.49  E-value: 8.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVET--VSTLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLV---- 165
Cdd:cd08456     2 LRIAVLPAlsQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVlppg 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 166 ---TQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPKRIMEFNILETILNSVALGLGITLVPQSAVQHLSKAG 242
Cdd:cd08456    82 hrlAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAG 161


                  ..
gi 1079341433 243 KV 244
Cdd:cd08456   162 LV 163
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-236 1.07e-05

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 45.31  E-value: 1.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  92 LKIGTVETVS--TLPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISG----------------------PI 147
Cdd:cd08413     2 LTIATTHTQAryVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEalddhpdlvtlpcyrwnhcvivPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 148 KHPLieqydvsteklmlvTQNKAFHIEEFTTTPLLVFNQGCGYRSKLERWLKDEGLLPkrimefNILETILNS------V 221
Cdd:cd08413    82 GHPL--------------ADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEP------NIVLTALDAdviktyV 141

                         170
                  ....*....|....*
gi 1079341433 222 ALGLGITLVPQSAVQ 236
Cdd:cd08413   142 RLGLGVGIIAEMAYD 156
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-246 1.46e-05

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: 44.82  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 103 LPTILSSYYKSYPNVDLSLQAGLTEELIREVIDHQLDGAFISGPIKHPLIEQYDVSTEKLMLVTQNKafHieEFTTTPLL 182
Cdd:cd08421    15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRD--H--PLAGRASV 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079341433 183 VFNQGCGYR-----------SKLERWLKDEGLLPK---RIMEFnilETILNSVALGLGITLVPQSAVQHLSKAGKVHC 246
Cdd:cd08421    91 AFADTLDHDfvglpagsalhTFLREAAARLGRRLRlrvQVSSF---DAVCRMVAAGLGIGIVPESAARRYARALGLRV 165
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-70 9.23e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.22  E-value: 9.23e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHkRGMTLTAEGRKMLVYVHK 70
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQ 70
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-84 1.75e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.22  E-value: 1.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1079341433   6 LQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYRHKRGMTLTAEGRKMLVYVHKILQdveeLKQVFLD 84
Cdd:PRK11062    9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFT----LSQEMLD 83
PRK03902 PRK03902
transcriptional regulator MntR;
7-74 3.63e-03

transcriptional regulator MntR;


Pssm-ID: 179669 [Multi-domain]  Cd Length: 142  Bit Score: 36.90  E-value: 3.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1079341433   7 QIFQSVADRG--SVSGAAKELNYVQSNVTVRIKQL-ENELktpLFYRHKRGMTLTAEGRKM---LVYVHKILQD 74
Cdd:PRK03902   12 QIYLLIEEKGyaRVSDIAEALSVHPSSVTKMVQKLdKDEY---LIYEKYRGLVLTPKGKKIgkrLVYRHELLEQ 82
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-235 8.70e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 37.28  E-value: 8.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433   3 LRDLQIFQSVADRGSVSGAAKELNYVQSNVTVRIKQLENELKTPLFYR-HKR------GMTLTAEGRKMLVYVHKILQDV 75
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvRGRlhptvqGLRLFEEVQRSYYGLDRIVSAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433  76 EELKQvFLDSEtpsgiLKIGT--VETVSTLPTILSSYYKSYPNVDLS------------LQA-----GLTEELI------ 130
Cdd:PRK11013   86 ESLRE-FRQGQ-----LSIAClpVFSQSLLPGLCQPFLARYPDVSLNivpqesplleewLSAqrhdlGLTETLHtpagte 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079341433 131 REVIdHQLDGAFISgPIKHPLIeqydvstEKLMLVTQNkaFHIEEFTTTPLLVfnqgcGYRSKLERWLKDEGLLPKRIME 210
Cdd:PRK11013  160 RTEL-LTLDEVCVL-PAGHPLA-------AKKVLTPDD--FAGENFISLSRTD-----SYRQLLDQLFAEHGVKRRMVVE 223

                         250       260
                  ....*....|....*....|....*.
gi 1079341433 211 FNILETILNSVALGLGITLV-PQSAV 235
Cdd:PRK11013  224 THSAASVCAMVRAGVGVSIVnPLTAL 249
 
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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