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Conserved domains on  [gi|490236828|ref|WP_004135136|]
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MULTISPECIES: LysR family transcriptional regulator [Gardnerella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-190 1.73e-36

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.14  E-value: 1.73e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  81 RYKSTK--PRPQLcSVATQHYmFAIEAFVDMIRSInSDEY---EFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdvig 155
Cdd:COG0583   81 ELRALRggPRGTL-RIGAPPS-LARYLLPPLLARF-RARHpgvRLELREGNSDRLVDALLEGELDLAIRLGP-------- 149

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490236828 156 klLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLS 190
Cdd:COG0583  150 --PPDPGLVARPLGEERLVLVASPDHPLARRAPLV 182
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 119-294 4.58e-14

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: 69.55  E-value: 4.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDynkdvigkllREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd05466   30 ELSLVEGGSSELLEALLEGELDLAIVALPV----------DDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 199 FIQYEQGEEGSF----FFAEEAVwptRPPKKINVSDRATILNFIIGLNGYTICTGINNGDLNNEKIVTIPLKCDD-TMLV 273
Cdd:cd05466  100 LILFERGSGLRRlldrAFAEAGF---TPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDPPlSRTI 176

                        170       180
                 ....*....|....*....|.
gi 490236828 274 GWITNERTKLSKASLAYLTQL 294
Cdd:cd05466  177 GLVWRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-190 1.73e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.14  E-value: 1.73e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  81 RYKSTK--PRPQLcSVATQHYmFAIEAFVDMIRSInSDEY---EFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdvig 155
Cdd:COG0583   81 ELRALRggPRGTL-RIGAPPS-LARYLLPPLLARF-RARHpgvRLELREGNSDRLVDALLEGELDLAIRLGP-------- 149

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490236828 156 klLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLS 190
Cdd:COG0583  150 --PPDPGLVARPLGEERLVLVASPDHPLARRAPLV 182
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 5-205 1.12e-20

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 89.41  E-value: 1.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828    5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQA----DLLEE 80
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEaeaeFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   81 RYKSTKPRPQLCSVATQHYMFAIEAFVDMIRSInsdeyEFSIRETRTKNIIKQVSDMRADLGLLylsdynkdviGKLLRE 160
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGI-----EVSVRIGNSQEVLQALQSYRVDVAVS----------SEVVDD 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490236828  161 KHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQG 205
Cdd:TIGR03339 146 PRLDRVVLGNDPLVAVVHRQHPLAERESVTLEELAGQPLLMREPG 190
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-208 2.04e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 89.28  E-value: 2.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYARQVIEQADLL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  79 E---ERYkSTKPRPQLcSVATQH----YMF--AIEAFVDMIRSINsdeyeFSIRETRTKNIIKQVSDMRADLGLlylsdy 149
Cdd:PRK12682  81 KrigDDF-SNQDSGTL-TIATTHtqarYVLprVVAAFRKRYPKVN-----LSLHQGSPDEIARMVISGEADIGI------ 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490236828 150 nkdVIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQGEEG 208
Cdd:PRK12682 148 ---ATESLADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTG 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-61 1.41e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.41e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 490236828    5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDG 61
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 119-294 4.58e-14

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: 69.55  E-value: 4.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDynkdvigkllREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd05466   30 ELSLVEGGSSELLEALLEGELDLAIVALPV----------DDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 199 FIQYEQGEEGSF----FFAEEAVwptRPPKKINVSDRATILNFIIGLNGYTICTGINNGDLNNEKIVTIPLKCDD-TMLV 273
Cdd:cd05466  100 LILFERGSGLRRlldrAFAEAGF---TPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDPPlSRTI 176

                        170       180
                 ....*....|....*....|.
gi 490236828 274 GWITNERTKLSKASLAYLTQL 294
Cdd:cd05466  177 GLVWRKGRYLSPAARAFLELL 197
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 119-205 3.43e-11

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: 61.40  E-value: 3.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLlylsdynkdvIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08434   30 TFELHQGSTDELLDDLKNGELDLAL----------CSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEP 99


                 ....*..
gi 490236828 199 FIQYEQG 205
Cdd:cd08434  100 FVLLSPG 106
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-190 1.73e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.14  E-value: 1.73e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  81 RYKSTK--PRPQLcSVATQHYmFAIEAFVDMIRSInSDEY---EFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdvig 155
Cdd:COG0583   81 ELRALRggPRGTL-RIGAPPS-LARYLLPPLLARF-RARHpgvRLELREGNSDRLVDALLEGELDLAIRLGP-------- 149

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490236828 156 klLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLS 190
Cdd:COG0583  150 --PPDPGLVARPLGEERLVLVASPDHPLARRAPLV 182
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 5-205 1.12e-20

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 89.41  E-value: 1.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828    5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQA----DLLEE 80
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEaeaeFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   81 RYKSTKPRPQLCSVATQHYMFAIEAFVDMIRSInsdeyEFSIRETRTKNIIKQVSDMRADLGLLylsdynkdviGKLLRE 160
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGI-----EVSVRIGNSQEVLQALQSYRVDVAVS----------SEVVDD 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490236828  161 KHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQG 205
Cdd:TIGR03339 146 PRLDRVVLGNDPLVAVVHRQHPLAERESVTLEELAGQPLLMREPG 190
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-208 2.04e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 89.28  E-value: 2.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYARQVIEQADLL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  79 E---ERYkSTKPRPQLcSVATQH----YMF--AIEAFVDMIRSINsdeyeFSIRETRTKNIIKQVSDMRADLGLlylsdy 149
Cdd:PRK12682  81 KrigDDF-SNQDSGTL-TIATTHtqarYVLprVVAAFRKRYPKVN-----LSLHQGSPDEIARMVISGEADIGI------ 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490236828 150 nkdVIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQGEEG 208
Cdd:PRK12682 148 ---ATESLADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTG 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-61 1.41e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.41e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 490236828    5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDG 61
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-205 1.14e-17

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 81.56  E-value: 1.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYARQVIEQADLL 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  79 EERYKSTKPRPQLC-SVATQH----YMF--AIEAFVDmirsiNSDEYEFSIRETRTKNIIKQVSDMRADLGLL--YLSDY 149
Cdd:PRK12684  81 KRVGKEFAAQDQGNlTIATTHtqarYALpaAIKEFKK-----RYPKVRLSILQGSPTQIAEMVLHGQADLAIAteAIADY 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490236828 150 nkdvigkllreKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQG 205
Cdd:PRK12684 156 -----------KELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFA 200
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-77 2.61e-15

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 74.72  E-value: 2.61e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVI---EQADL 77
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILrqcEQAQL 80
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-202 3.62e-15

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 74.55  E-value: 3.62e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDcGSMN--EAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYARQVIEQAdl 77
Cdd:PRK12681   1 MKLQQLRYIVEVVN-HNLNvsATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKV-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  78 leERYKS-----TKPRPQLCSVATQH----YMF--AIEAFVDMIRSINsdeyeFSIRETRTKNIIKQVSDMRADLGL--- 143
Cdd:PRK12681  78 --ESIKSvagehTWPDKGSLYIATTHtqarYALppVIKGFIERYPRVS-----LHMHQGSPTQIAEAAAKGNADFAIate 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 144 -LYLSDynkDVIgkLLrekhlefhPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQY 202
Cdd:PRK12681 151 aLHLYD---DLI--ML--------PCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTY 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 119-294 4.58e-14

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: 69.55  E-value: 4.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDynkdvigkllREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd05466   30 ELSLVEGGSSELLEALLEGELDLAIVALPV----------DDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 199 FIQYEQGEEGSF----FFAEEAVwptRPPKKINVSDRATILNFIIGLNGYTICTGINNGDLNNEKIVTIPLKCDD-TMLV 273
Cdd:cd05466  100 LILFERGSGLRRlldrAFAEAGF---TPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDPPlSRTI 176

                        170       180
                 ....*....|....*....|.
gi 490236828 274 GWITNERTKLSKASLAYLTQL 294
Cdd:cd05466  177 GLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-200 1.25e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.99  E-value: 1.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEqaDLLEE 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ--DLEAG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  81 RYK----STKPRPQLCSVAT---QHYMFA--IEAFVDMIRSInsdeyEFSIRETRTKNIIKQVSDMRADLGLLYLSDYNK 151
Cdd:PRK11242  79 RRAihdvADLSRGSLRLAMTptfTAYLIGplIDAFHARYPGI-----TLTIREMSQERIEALLADDELDVGIAFAPVHSP 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 490236828 152 DVigkllrekhlEFHPLFRATLHVFLSRNNPLAAH-KSLSLEDLKPYPFI 200
Cdd:PRK11242 154 EI----------EAQPLFTETLALVVGRHHPLAARrKALTLDELADEPLV 193
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-208 2.26e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 69.30  E-value: 2.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYA-RQVIEQADL 77
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVeRMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  78 --LEERYkSTKPRPQLcSVATQHYM--FAIEAFVDMIRSINSDeYEFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdv 153
Cdd:PRK12683  81 rrLAEQF-ADRDSGHL-TVATTHTQarYALPKVVRQFKEVFPK-VHLALRQGSPQEIAEMLLNGEADIGIATEA------ 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490236828 154 igkLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQGEEG 208
Cdd:PRK12683 152 ---LDREPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTG 203
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-83 3.75e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.51  E-value: 3.75e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   2 TLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEqadLLEER 81
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILA---LCEET 82


                 ..
gi 490236828  82 YK 83
Cdd:CHL00180  83 CR 84
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-205 8.08e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 67.41  E-value: 8.08e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  81 RYKSTKPRPQLCSVAT-QHYMFAieafvDMIRSINSD----EYEFSIRETRtkNIIKQVSDMRADLGLLYLSDYNKDVIG 155
Cdd:PRK10837  83 LFREDNGALRIYASSTiGNYILP-----AMIARYRRDypqlPLELSVGNSQ--DVINAVLDFRVDIGLIEGPCHSPELIS 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 490236828 156 kllrekhlefHPLFRATLHVFLSRNNPLaAHKSLSLEDLKPYPFIQYEQG 205
Cdd:PRK10837 156 ----------EPWLEDELVVFAAPDSPL-ARGPVTLEQLAAAPWILRERG 194
PRK09791 PRK09791
LysR family transcriptional regulator;
3-74 2.52e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 66.32  E-value: 2.52e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490236828   3 LLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQ 74
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEE 78
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 6-200 7.95e-12

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 64.74  E-value: 7.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828    6 LKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYA-------RQVIeqADLL 78
Cdd:TIGR02424   8 LQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAgaslaalRQGV--ASLS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   79 EERYKSTKPRP--QLCSVATQHYMFAIEAFvdmirsinsdeyefsiRETRTKNIIKQVSDMRAdlgllYLSDYNKD---- 152
Cdd:TIGR02424  86 QLGEGEGPTVRigALPTVAARLMPEVVKRF----------------LARAPRLRVRIMTGPNA-----YLLDQLRVgald 144

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 490236828  153 -VIGKLL---REKHLEFHPLFRATLhVFLSRNN-PLAAHKSLSLEDLKPYPFI 200
Cdd:TIGR02424 145 lVVGRLGapeTMQGLSFEHLYNEPV-VFVVRAGhPLLAAPSLPVASLADYPVL 196
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 119-205 3.43e-11

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: 61.40  E-value: 3.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLlylsdynkdvIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08434   30 TFELHQGSTDELLDDLKNGELDLAL----------CSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEP 99


                 ....*..
gi 490236828 199 FIQYEQG 205
Cdd:cd08434  100 FVLLSPG 106
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-208 8.08e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 61.75  E-value: 8.08e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIV-LTSDGAEFLTYARQVIEQ---- 74
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEasnv 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  75 ---ADLLeeryksTKPRPQLCSVATQHYM--FAIEAFVDMIRSINSdEYEFSIRETRTKNIIKQVSDMRADLGLlyLSDy 149
Cdd:PRK12679  81 rrlADLF------TNDTSGVLTIATTHTQarYSLPEVIKAFRELFP-EVRLELIQGTPQEIATLLQNGEADIGI--ASE- 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490236828 150 nkdvigKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQGEEG 208
Cdd:PRK12679 151 ------RLSNDPQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITG 203
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 119-205 1.61e-10

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: 59.61  E-value: 1.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  119 EFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdvigklLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:pfam03466  32 ELELTEGNSEELLDLLLEGELDLAIRRGP----------PDDPGLEARPLGEEPLVLVAPPDHPLARGEPVSLEDLADEP 101


                  ....*..
gi 490236828  199 FIQYEQG 205
Cdd:pfam03466 102 LILLPPG 108
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 119-286 1.68e-10

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 59.48  E-value: 1.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDYnkdvigkllrEKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08412   30 EVRVVEGNQEELEEGLRSGELDLALTYDLDL----------PEDIAFEPLARLPPYVWLPADHPLAGKDEVSLADLAAEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 199 FIQYEQGEEGSFF---FAEEAVWPtrppkkiNVSDRATILNFIIGL----NGYTIctginngdLNN----------EKIV 261
Cdd:cd08412  100 LILLDLPHSREYFlslFAAAGLTP-------RIAYRTSSFEAVRSLvangLGYSL--------LNDrpyrpwsydgKRLV 164

                        170       180
                 ....*....|....*....|....*.
gi 490236828 262 TIPLKCD-DTMLVGWITNERTKLSKA 286
Cdd:cd08412  165 RRPLADPvPPLRLGLAWRRGARLTRA 190
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-202 3.40e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.03  E-value: 3.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQ-ADLLEERYK 83
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQiSQALQACNE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  84 STKPRPQL---CSVATQHYMFAIEAFvdmirSINSDEYEFSIRETRTKNiiKQVSDMRADLGLLYLSDynkdvigkLLRE 160
Cdd:PRK15421  86 PQQTRLRIaieCHSCIQWLTPALENF-----HKNWPQVEMDFKSGVTFD--PQPALQQGELDLVMTSD--------ILPR 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490236828 161 KHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQY 202
Cdd:PRK15421 151 SGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIY 192
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-76 3.40e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 56.70  E-value: 3.40e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQAD 76
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAE 76
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-200 5.78e-09

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: 54.84  E-value: 5.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDYNKDvigkllrekhLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08440   30 RVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPD----------LEFEPLLRDPFVLVCPKDHPLARRRSVTWAELAGYP 99


                 ..
gi 490236828 199 FI 200
Cdd:cd08440  100 LI 101
PRK12680 PRK12680
LysR family transcriptional regulator;
1-203 1.89e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.63  E-value: 1.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCG-SMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGI-VLTSDGAEFLTYARQVIEQADLL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  79 EErYKSTKPRP---QLcSVATQHYM--FAIEAFVDMIRSiNSDEYEFSIRETRTKNIIKQVSDMRADLGLLYLSDyNKDV 153
Cdd:PRK12680  81 RT-YAANQRREsqgQL-TLTTTHTQarFVLPPAVAQIKQ-AYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAG-GEPS 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490236828 154 IGKLLrekhlefhPLFRATLHVFLSRNNPL-AAHKSLSLEDLKPYPFIQYE 203
Cdd:PRK12680 157 AGIAV--------PLYRWRRLVVVPRGHALdTPRRAPDMAALAEHPLISYE 199
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-92 8.05e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.67  E-value: 8.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   5 QLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQgIVLTSDGAEFLTYARQV-IEQADLLEERYK 83
Cdd:PRK13348   6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVaLLEADLLSTLPA 84


                 ....*....
gi 490236828  84 STKPRPQLC 92
Cdd:PRK13348  85 ERGSPPTLA 93
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 152-205 1.07e-07

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: 51.40  E-value: 1.07e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490236828 152 DVIGKLLREKHLEFH--PLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFIQYEQG 205
Cdd:cd08438   51 DVGITVLPVDEEEFDsqPLCNEPLVAVLPRGHPLAGRKTVSLADLADEPFILFNED 106
PRK10341 PRK10341
transcriptional regulator TdcA;
11-195 1.86e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.79  E-value: 1.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  11 KIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIeqadllEERYKSTKPRPQ 90
Cdd:PRK10341  17 EVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESIT------REMKNMVNEING 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  91 LCSVATQHYMFAIEAFV------DMI---RSINSDEyEFSIRETRTKNIIKQVSDMRADLGLLYLSDynkdviGKLLREK 161
Cdd:PRK10341  91 MSSEAVVDVSFGFPSLIgftfmsDMInkfKEVFPKA-QVSMYEAQLSSFLPAIRDGRLDFAIGTLSN------EMKLQDL 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 490236828 162 HLEfhPLFRATLHVFLSRNNPLAAhkSLSLEDLK 195
Cdd:PRK10341 164 HVE--PLFESEFVLVASKSRTCTG--TTTLESLK 193
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-74 3.02e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 50.91  E-value: 3.02e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490236828  11 KIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGA-------EFLTYARQVIEQ 74
Cdd:PRK10632  12 KVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRiyyqgcrRMLHEVQDVHEQ 82
PRK09986 PRK09986
LysR family transcriptional regulator;
6-75 4.99e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 50.11  E-value: 4.99e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   6 LKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQA 75
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNA 81
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 119-211 5.13e-07

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: 49.43  E-value: 5.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSdynkdvigklLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08414   30 ELELREMTTAEQLEALRAGRLDVGFVRPP----------PDPPGLASRPLLREPLVVALPADHPLAARESVSLADLADEP 99

                         90
                 ....*....|...
gi 490236828 199 FIQYEQGEEGSFF 211
Cdd:cd08414  100 FVLFPREPGPGLY 112
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
15-116 2.12e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.51  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  15 CGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQ--ADLLEER----YKSTKPR 88
Cdd:PRK10082  25 CRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQleSNLAELRggsdYAQRKIK 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 490236828  89 ------------PQLCSVATQHYMFAIEAF-----VDMIRSINSD 116
Cdd:PRK10082 105 iaaahslslgllPSIISQMPPLFTWAIEAIdvdeaVDKLREGQSD 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-80 2.20e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.49  E-value: 2.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-80 3.30e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 47.88  E-value: 3.30e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490236828   6 LKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
12-96 1.19e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 45.92  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828  12 IVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRsTQGIVLTSDGAEFLTYARQV--IEqADLLEERYKSTKPRP 89
Cdd:PRK03635  13 VVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVrlLE-AELLGELPALDGTPL 90


                 ....*..
gi 490236828  90 QLcSVAT 96
Cdd:PRK03635  91 TL-SIAV 96
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 117-205 1.19e-05

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: 45.18  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 117 EYEFSIRETRTKNIIKQVSDMRADLGLlylsdynkdvIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKP 196
Cdd:cd08420   28 EVRVSLTIGNTEEIAERVLDGEIDLGL----------VEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAA 97


                 ....*....
gi 490236828 197 YPFIQYEQG 205
Cdd:cd08420   98 EPWILREPG 106
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
21-68 1.57e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.78  E-value: 1.57e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 490236828  21 AARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYA 68
Cdd:PRK03601  21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-94 2.21e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 45.19  E-value: 2.21e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490236828  26 YISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEERYKStkPRPQL-------CSV 94
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQ--QGPSLsgelslfCSV 75
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 119-200 2.42e-05

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: 44.44  E-value: 2.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLsdynkdvigkLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08411   31 RLYLREDQTERLLEKLRSGELDAALLAL----------PVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAGER 100


                 ..
gi 490236828 199 FI 200
Cdd:cd08411  101 LL 102
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 7-74 6.83e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.78  E-value: 6.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490236828   7 KYIVKIVDC----GSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQ 74
Cdd:PRK11074   4 EYSLEVVDAvartGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKK 75
PRK09801 PRK09801
LysR family transcriptional regulator;
6-90 8.22e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 43.49  E-value: 8.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   6 LKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEERYKST 85
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90


                 ....*
gi 490236828  86 KPRPQ 90
Cdd:PRK09801  91 KTRPE 95
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 119-205 1.42e-04

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: 42.22  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLlylsdynkdVIGKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08413   30 KLSLHQGTPSQIAEMVLKGEADIAI---------ATEALDDHPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLEDLAQYP 100


                 ....*..
gi 490236828 199 FIQYEQG 205
Cdd:cd08413  101 LITYDFG 107
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-98 2.05e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 42.28  E-value: 2.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828   1 MTLLQLKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVIEQADLLEE 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100
                 ....*....|....*....|...
gi 490236828  81 RYKSTKPRPQ-----LCSVATQH 98
Cdd:PRK14997  82 AIAALQVEPRgivklTCPVTLLH 104
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 121-205 4.13e-04

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: 40.62  E-value: 4.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 121 SIRETRTKNIIKQVSDMRADLGLLYLsdynkdvigkLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPFI 200
Cdd:cd08415   32 SLHTLSSSTVVEAVLSGQADLGLASL----------PLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPADLAGEPLI 101


                 ....*
gi 490236828 201 QYEQG 205
Cdd:cd08415  102 SLGRG 106
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
21-61 4.56e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 41.14  E-value: 4.56e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 490236828  21 AARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDG 61
Cdd:PRK10086  34 AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-202 8.47e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 39.94  E-value: 8.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 119 EFSIRETRTKNIIKQVSDMRADLGLLYLSDYNKDvigkllrekhLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYP 198
Cdd:cd08447   30 DLVLREMVTTDQIEALESGRIDLGLLRPPFARPG----------LETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQP 99


                 ....
gi 490236828 199 FIQY 202
Cdd:cd08447  100 FIMY 103
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-72 1.04e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 40.01  E-value: 1.04e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490236828   6 LKYIVKIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGIVLTSDGAEFLTYARQVI 72
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-200 1.23e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 39.21  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 120 FSIRETRTKNIIKQVSDMRADLGLLYlsdynkdvigKLLREKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKPYPF 199
Cdd:cd08426   31 FTVDVASTADVLEAVLSGEADIGLAF----------SPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLAGYPL 100


                 .
gi 490236828 200 I 200
Cdd:cd08426  101 A 101
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
11-82 1.95e-03

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 37.49  E-value: 1.95e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490236828  11 KIVDCGSMNEAARALYISQPALSSSVKELERELNIEIFTRSTQGivlTSDGAEFLT-YARQVIEQADLLEERY 82
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTGG---KGGGGARLTpEGRRLLALYRRLEAEA 98
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 117-200 2.81e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 38.02  E-value: 2.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490236828 117 EYEFSIRETRTKNIIKQVSDMRADLGLLYLSDYNKDvigkllreKHLEFHPLFRATLHVFLSRNNPLAAHKSLSLEDLKP 196
Cdd:cd08449   28 NVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLND--------PPLASELLWREPMVVALPEEHPLAGRKSLTLADLRD 99


                 ....
gi 490236828 197 YPFI 200
Cdd:cd08449  100 EPFV 103
 
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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