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Conserved domains on  [gi|1515829270|gb|ROR00497|]
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DNA-binding transcriptional LysR family regulator [Streptomyces sp. 2132.2]

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];
2-296 1.62e-30

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.35  E-value: 1.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVKGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRE-LTLGTVDVVLgqRYHHLPaaaPRGV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDaLLEGELDLAI--RLGPPP---DPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 161 SVSPLLDDPLVVVTAADQggegpvllrdlaaldlavpppatdcgqailqgcRQSGFTPtpryVTADITAQLTLARAGLAT 240
Cdd:COG0583   156 VARPLGEERLVLVASPDH---------------------------------PLARRAP----LVNSLEALLAAVAAGLGI 198

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1515829270 241 ALVPRMAI--DPTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAAQE 296
Cdd:COG0583   199 ALLPRFLAadELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-296 1.62e-30

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.35  E-value: 1.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVKGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRE-LTLGTVDVVLgqRYHHLPaaaPRGV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDaLLEGELDLAI--RLGPPP---DPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 161 SVSPLLDDPLVVVTAADQggegpvllrdlaaldlavpppatdcgqailqgcRQSGFTPtpryVTADITAQLTLARAGLAT 240
Cdd:COG0583   156 VARPLGEERLVLVASPDH---------------------------------PLARRAP----LVNSLEALLAAVAAGLGI 198

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1515829270 241 ALVPRMAI--DPTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAAQE 296
Cdd:COG0583   199 ALLPRFLAadELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 6.58e-25

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: 98.82  E-value: 6.58e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGQRYHHLPAAAPRGVSVSPLLDDPLVVV 173
Cdd:cd08423     3 RVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRaGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLDLV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAAD--QGGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAIDPT 251
Cdd:cd08423    83 LPADhpLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALGAR 162

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1515829270 252 TPGIRTSPIADhPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08423   163 PPGVVVRPLRP-PPTRRIYAAVRAGAARRPAVAAALEAL 200
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-295 1.09e-18

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: 82.34  E-value: 1.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGqryhhLPAAAPRGVSVSPLLDDPLVVV 173
Cdd:pfam03466   5 RIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLeGELDLAIR-----RGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAADQG--GEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAI--D 249
Cdd:pfam03466  80 APPDHPlaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVarE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1515829270 250 PTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAAQ 295
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-73 1.96e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 1.96e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   4 IRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-296 1.62e-30

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.35  E-value: 1.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVKGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRE-LTLGTVDVVLgqRYHHLPaaaPRGV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDaLLEGELDLAI--RLGPPP---DPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 161 SVSPLLDDPLVVVTAADQggegpvllrdlaaldlavpppatdcgqailqgcRQSGFTPtpryVTADITAQLTLARAGLAT 240
Cdd:COG0583   156 VARPLGEERLVLVASPDH---------------------------------PLARRAP----LVNSLEALLAAVAAGLGI 198

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1515829270 241 ALVPRMAI--DPTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAAQE 296
Cdd:COG0583   199 ALLPRFLAadELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 6.58e-25

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: 98.82  E-value: 6.58e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGQRYHHLPAAAPRGVSVSPLLDDPLVVV 173
Cdd:cd08423     3 RVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRaGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLDLV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAAD--QGGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAIDPT 251
Cdd:cd08423    83 LPADhpLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALGAR 162

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1515829270 252 TPGIRTSPIADhPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08423   163 PPGVVVRPLRP-PPTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-290 3.34e-19

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: 83.42  E-value: 3.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGqryhHLPAAAPRGVSVsPLLDDPLVVV 173
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLeGELDLAIV----ALPVDDPGLESE-PLFEEPLVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAAD--QGGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAI-DP 250
Cdd:cd05466    78 VPPDhpLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVeEL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1515829270 251 TTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd05466   158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-295 1.09e-18

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: 82.34  E-value: 1.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGqryhhLPAAAPRGVSVSPLLDDPLVVV 173
Cdd:pfam03466   5 RIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLeGELDLAIR-----RGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAADQG--GEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAI--D 249
Cdd:pfam03466  80 APPDHPlaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVarE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1515829270 250 PTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAAQ 295
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 4.15e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 62.79  E-value: 4.15e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   4 IRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGR 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-73 1.96e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 1.96e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   4 IRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 2-177 5.64e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 62.09  E-value: 5.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVkGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAV--TCLITDQaQLRELTLGTVDVVLGQRYHHLPaaaprG 159
Cdd:PRK09906   81 RARKI-VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIelVSLITTQ-QEEKLRRGELDVGFMRHPVYSD-----E 153

                         170
                  ....*....|....*...
gi 1515829270 160 VSVSPLLDDPLVVVTAAD 177
Cdd:PRK09906  154 IDYLELLDEPLVVVLPVD 171
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 2-181 8.03e-11

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 61.62  E-value: 8.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVKGTVGAATTLAALPSTVARMVA-PALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDV-VLgqrYHHLPAAapr 158
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMnGQLDMaVI---YEHSPVA--- 154

                         170       180
                  ....*....|....*....|...
gi 1515829270 159 GVSVSPLLDDPLVVVTAADQGGE 181
Cdd:PRK11233  155 GLSSQPLLKEDLFLVGTQDCPGQ 177
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 95-290 9.96e-11

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: 59.83  E-value: 9.96e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCL-ITDQAQLRELTLGTVDVVLGqryhHLPAAAPrGVSVSPLLDDPLVVV 173
Cdd:cd08414     3 RIGFVGSALYGLLPRLLRRFRARYPDVELELReMTTAEQLEALRAGRLDVGFV----RPPPDPP-GLASRPLLREPLVVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAAD--QGGEGPVLLRDLAALDLAVPPPATDCG--QAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAID 249
Cdd:cd08414    78 LPADhpLAARESVSLADLADEPFVLFPREPGPGlyDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVAR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1515829270 250 PTTPGIRTSPIADHPIqRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08414   158 LQRPGVVYRPLADPPP-RSELALAWRRDNASPALRAFLELA 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 3.21e-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: 55.61  E-value: 3.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLGQRyhhlpAAAPRGVSVSPLLDDPLVVV 173
Cdd:cd08440     3 RVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRsGEVDFGIGSE-----PEADPDLEFEPLLRDPFVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAADQ--GGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAIDPT 251
Cdd:cd08440    78 CPKDHplARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1515829270 252 -TPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08440   158 dHPGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-72 7.65e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 55.75  E-value: 7.65e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCpDGRTVALTEAGRVLLDHAERI 72
Cdd:PRK13348    1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLV-RGRPCRPTPAGQRLLRHLRQV 71
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 14-173 2.16e-08

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 54.46  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  14 AARG-SITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILaAVAEAENAVEAVKGTVGa 92
Cdd:PRK11139   17 AARHlSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF-DQLAEATRKLRARSAKG- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  93 ATTLAALPSTVARMVAPALTTLASRHPQLAVTCLITDqaQLRELTLGTVDVVLGQRYHHLPaaaprGVSVSPLLDDPLVV 172
Cdd:PRK11139   95 ALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVD--RLEDFLRDDVDVAIRYGRGNWP-----GLRVEKLLDEYLLP 167


                  .
gi 1515829270 173 V 173
Cdd:PRK11139  168 V 168
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 3.26e-08

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 52.60  E-value: 3.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTcLITDQAQ--LRELTLGTVDV-VLGqryhhLPAAAPRGVSVSPLLDDPLV 171
Cdd:cd08436     3 AIGTITSLAAVDLPELLARFHRRHPGVDIR-LRQAGSDdlLAAVREGRLDLaFVG-----LPERRPPGLASRELAREPLV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 172 VVTAADQ--GGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAiD 249
Cdd:cd08436    77 AVVAPDHplAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASV-A 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1515829270 250 PTTPGIRTSPIADHPIqRLLFAATRhSDSPNPTTTAVIAAL 290
Cdd:cd08436   156 ARLPGLAALPLEPAPR-RRLYLAWS-APPPSPAARAFLELL 194
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-73 1.43e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.07  E-value: 1.43e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK10632    1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRML 73
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-73 3.76e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 50.58  E-value: 3.76e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK10094    1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PRK09801 PRK09801
LysR family transcriptional regulator;
5-123 3.77e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.80  E-value: 3.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   5 RRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILaavaeaenavE 84
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEIL----------T 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1515829270  85 AVKGTVGAATTLAALPSTVARM----------VAPALTTLASRHPQLAV 123
Cdd:PRK09801   79 QYQRLVDDVTQIKTRPEGMIRIgcsfgfgrshIAPAITELMRNYPELQV 127
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-73 4.22e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 50.34  E-value: 4.22e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1515829270   1 MLdIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK11242    1 ML-LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL 72
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-124 6.30e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 49.99  E-value: 6.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   7 LHMLKTV--AARG--SITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDG-RTVALTEAGRVLLDHAERILAAVAE--- 78
Cdd:PRK12682    3 LQQLRFVreAVRRnlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNikr 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1515829270  79 -AENAVEAVKGTVGAATTlaalpSTVARMVAP-ALTTLASRHPQLAVT 124
Cdd:PRK12682   83 iGDDFSNQDSGTLTIATT-----HTQARYVLPrVVAAFRKRYPKVNLS 125
PRK10341 PRK10341
transcriptional regulator TdcA;
5-72 3.25e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.93  E-value: 3.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1515829270   5 RRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERI 72
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI 77
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-294 3.49e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 47.70  E-value: 3.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAE 80
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  81 NAVEAVKGTvgaATTLAALPSTVARMVAPALTTLASRHPQLAV--TCLITDQAQlRELTLGTVDVVLGQRYhhLPAAapr 158
Cdd:PRK15421   81 QACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNWPQVEMdfKSGVTFDPQ-PALQQGELDLVMTSDI--LPRS--- 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 159 GVSVSPLLDDPLVVVTAADQ--GGEGPVLLRDLAALDLAVPP---PATDCGQAILQgcrQSGFTPTPRYVTAD-ITAQLT 232
Cdd:PRK15421  152 GLHYSPMFDYEVRLVLAPDHplAAKTRITPEDLASETLLIYPvqrSRLDVWRHFLQ---PAGVSPSLKSVDNTlLLIQMV 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1515829270 233 LARAGLATalVPRMAIDP-TTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAALRTAA 294
Cdd:PRK15421  229 AARMGIAA--LPHWVVESfERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHA 289
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-71 1.12e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 45.92  E-value: 1.12e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCpDGRTVALTEAGRVLLDHAER 71
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLV-RTQPCRPTEAGQRLLRHARQ 70
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 130-290 2.68e-05

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: 44.09  E-value: 2.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 130 QAQLRELTLGTVDVVLGqryhHLPAAAPRGVSVSPLLDDPLVVVTAAD--QGGEGPVLLRDLAALDLAVPPPATDCG--Q 205
Cdd:cd08451    40 AELLEALREGRLDAAFV----RPPVARSDGLVLELLLEEPMLVALPAGhpLARERSIPLAALADEPFILFPRPVGPGlyD 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 206 AILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAIDPTTPGIRTSPIADHPIQRLLFAATRHSDsPNPTTTA 285
Cdd:cd08451   116 AIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQLQAPGVVYRPLAGAPLTAPLALAYRRGE-RSPAVRN 194


                  ....*
gi 1515829270 286 VIAAL 290
Cdd:cd08451   195 FIALV 199
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 1-73 3.28e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 44.55  E-value: 3.28e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK11074    1 MWSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-126 3.43e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.61  E-value: 3.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   6 RLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAG-RVL------LDH-AERILAAVA 77
Cdd:PRK10086   18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkRVFwalkssLDTlNQEILDIKN 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1515829270  78 EAENaveavkGTVgaatTLAALPSTVARMVAPALTTLASRHPQLAVTCL 126
Cdd:PRK10086   98 QELS------GTL----TVYSRPSIAQCWLVPRLADFTRRYPSISLTIL 136
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-73 6.04e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 43.81  E-value: 6.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1515829270   7 LHMLKTVAARG-SITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDG-RTVALTEAGRVLLDHAERIL 73
Cdd:PRK12684    6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERIL 74
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-73 7.71e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 43.48  E-value: 7.71e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   7 LHMLKT---VAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK15092   13 LDLLRTfvaVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PRK09791 PRK09791
LysR family transcriptional regulator;
6-123 9.96e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 43.21  E-value: 9.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   6 RLHMLKT---VAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAENA 82
Cdd:PRK09791    6 KIHQIRAfveVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1515829270  83 VEAVKGTVGAATTLaALPSTVARMVAPALTTLASR-HPQLAV 123
Cdd:PRK09791   86 IRQRQGQLAGQINI-GMGASIARSLMPAVISRFHQqHPQVKV 126
PRK09986 PRK09986
LysR family transcriptional regulator;
2-290 1.05e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 43.17  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   2 LDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAEN 81
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  82 AVEAVKGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVtclitdqaQLRELTLGTVDVVLGQRyhHLPAAAPRGVS 161
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW--------LLRELSPSMQMAALERR--ELDAGIWRMAD 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 162 VSPLL------------------DDPLV---VVTAADQGGEGPVllrdlaaldlAVPPPATDCGQAILQGCRQSGFTPTP 220
Cdd:PRK09986  157 LEPNPgftsrrlhesafavavpeEHPLAsrsSVPLKALRNEYFI----------TLPFVHSDWGKFLQRVCQQAGFSPQI 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 221 RYVTADITAQLTLARAGLATALVPRMAIDPTTPGIRTSPIaDHPIQRLLFaATRHSDSPNPTTTAVIAAL 290
Cdd:PRK09986  227 IRQVNEPQTVLAMVSMGIGITLLPDSYAQIPWPGVVFRPL-KERIPADLY-AVYHPDQVTPALNKLLAAL 294
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 1.76e-04

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 41.79  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  95 TLAALPSTVARMVAPALTTLASRHPQLAVTCLITDQAQL-RELTLGTVDVVLGQRYHHlpaAAPRGVSVSPLLDDPLVVV 173
Cdd:cd08427     3 RLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELlARVDAGELDAAIVVEPPF---PLPKDLVWTPLVREPLVLI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 TAADQGGEGPvllrdlAALDLAVPPPATD----CGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMA-I 248
Cdd:cd08427    80 APAELAGDDP------RELLATQPFIRYDrsawGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAvP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1515829270 249 DPTTPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08427   154 LPAGPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 98-290 2.20e-04

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: 41.43  E-value: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  98 ALPSTVARMVAPAL-TTLASRHPQLAVTCLITDQAQLRELTL-GTVDVVLgqRYHHlpaAAPRGVSVSPLLDDPLVVVTA 175
Cdd:cd08433     5 GLPPSAASVLAVPLlRAVRRRYPGIRLRIVEGLSGHLLEWLLnGRLDLAL--LYGP---PPIPGLSTEPLLEEDLFLVGP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 176 ADQG--GEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAI--DPT 251
Cdd:cd08433    80 ADAPlpRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVaaEVA 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1515829270 252 TPGIRTSPIADHPIQRLLFAATRHSDSPNPTTTAVIAAL 290
Cdd:cd08433   160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK12680 PRK12680
LysR family transcriptional regulator;
8-259 3.39e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 41.53  E-value: 3.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   8 HMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTV-ALTEAGRVLLDHAERILAAVAEAENAVEAV 86
Cdd:PRK12680    8 YLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  87 KGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVTCL-ITDQAQLRELTLGTVDVVLGQRYHHLPAAaprGVSVSPL 165
Cdd:PRK12680   88 RRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQqAAESAALDLLGQGDADIAIVSTAGGEPSA---GIAVPLY 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 166 LDDPLVVVT---AADQGGEGPVLLRDLAALDLAVPPpATDCGQAILQGCRQSGFTPTPRYVTADITAQLTLARAGLATAL 242
Cdd:PRK12680  165 RWRRLVVVPrghALDTPRRAPDMAALAEHPLISYES-STRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGL 243

                         250
                  ....*....|....*..
gi 1515829270 243 VPRMAIDPTTPGIRTSP 259
Cdd:PRK12680  244 LAEMAVNANDEDLRAWP 260
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 130-274 5.12e-04

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: 40.21  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 130 QAQLRELTLGTVDVVLGQryhhlPAAAPRGVSVSPLLDDPLVVVTAADQ--GGEGPVLLRDLAALDLAVPPPATDCGQAI 207
Cdd:cd08434    39 DELLDDLKNGELDLALCS-----PVPDEPDIEWIPLFTEELVLVVPKDHplAGRDSVDLAELADEPFVLLSPGFGLRPIV 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1515829270 208 LQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRMAIdPTTPGIRTSPIADHPIQRLLFAATR 274
Cdd:cd08434   114 DELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTL-LNPPGVKKIPIKDPDAERTIGLAWL 179
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-73 6.91e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 40.44  E-value: 6.91e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   4 IRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL 74
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-179 5.96e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 37.66  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270   1 MLDIRRLHMLKTVAARGSITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERILAAVAEAE 80
Cdd:PRK14997    1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  81 NAVEAVKGTVGAATTLAALPSTVARMVAPALTTLASRHPQLAVtclitdqaQLrELTLGTVDVVlGQRYHHLPAAAPRgv 160
Cdd:PRK14997   81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSL--------QL-EATNRRVDVV-GEGVDVAIRVRPR-- 148

                         170
                  ....*....|....*....
gi 1515829270 161 svsPLLDDPLVVVTAADQG 179
Cdd:PRK14997  149 ---PFEDSDLVMRVLADRG 164
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 19-73 6.50e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 37.72  E-value: 6.50e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1515829270  19 ITAAARSLELTAGAVSQQLAALRNDVGVDLLCPDG-RTVALTEAGRVLLDHAERIL 73
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERML 74
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 98-262 6.81e-03

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: 36.96  E-value: 6.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  98 ALPSTVARMVAPALT-TLASRHPQLAVTCL-ITDQAQLRELTLGTVDVvlGQRYHHLPAAAPRGVSVSPLLDDPLVVV-- 173
Cdd:cd08453     5 AFVSTADYSVLPELVrRFREAYPDVELQLReATSDVQLEALLAGEIDA--GIVIPPPGASAPPALAYRPLLSEPLVLAvp 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270 174 -TAADQGGEGPVLLRDLAALDLAVPPPATDCGQAILQGCRQSGfTPTPRYVTADITAQ--LTLARAGLATALVPRMAIDP 250
Cdd:cd08453    83 aAWAAEGGAPLALAAVAAEPLVIFPRRIAPAFHDAVTGYYRAA-GQTPRIAQEAIQMQtiISLVSAGMGVALVPASLRNL 161

                         170
                  ....*....|..
gi 1515829270 251 TTPGIRTSPIAD 262
Cdd:cd08453   162 ARPGVVYRELAD 173
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
32-73 7.05e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 37.49  E-value: 7.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1515829270  32 AVSQQLAALRNDVGVDLLCPDGRTVALTEAGRVLLDHAERIL 73
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTL 48
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 207-266 7.47e-03

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: 36.77  E-value: 7.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1515829270 207 ILQGCRQSGFTPTPRYVTADITAQLTLARAGLATALVPRM-AIDPTTPGIRTSPIADHPIQ 266
Cdd:cd08438   113 IIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSiAQRLDNAGVKVIPLTDPDLR 173
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 98-177 9.97e-03

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 36.48  E-value: 9.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515829270  98 ALPSTVARMVAPALTTLASRHPQLAVTCLI-TDQAQLRELTLGTVDVVLGQRYhhlPAAAPRGVSVSPLLDDPLVVVTAA 176
Cdd:cd08435     6 AVPAAAPVLLPPAIARLLARHPRLTVRVVEgTSDELLEGLRAGELDLAIGRLA---DDEQPPDLASEELADEPLVVVARP 82


                  .
gi 1515829270 177 D 177
Cdd:cd08435    83 G 83
 
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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