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Conserved domains on  [gi|15596012|ref|NP_249506|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

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
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];
2-305 2.63e-38

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.15  E-value: 2.63e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  82 SIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVValldegeavsrRLGI 161
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----------RLGP 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 162 DSEAEFQRLELGHEQLVAVCAPDaagQPLFNLDRLqtealsflgyseechlgwalepllrdsglflqrhhsSSQTEGLRF 241
Cdd:COG0583 150 PPDPGLVARPLGEERLVLVASPD---HPLARRAPL------------------------------------VNSLEALLA 190
                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596012 242 FAQSRLGVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLI-RRRLPLPGEAERLWTFLGELAR 305
Cdd:COG0583 191 AVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVwRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-305 2.63e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.15  E-value: 2.63e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  82 SIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVValldegeavsrRLGI 161
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----------RLGP 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 162 DSEAEFQRLELGHEQLVAVCAPDaagQPLFNLDRLqtealsflgyseechlgwalepllrdsglflqrhhsSSQTEGLRF 241
Cdd:COG0583 150 PPDPGLVARPLGEERLVLVASPD---HPLARRAPL------------------------------------VNSLEALLA 190
                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596012 242 FAQSRLGVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLI-RRRLPLPGEAERLWTFLGELAR 305
Cdd:COG0583 191 AVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVwRRRRHLSPAVRAFLDFLREALA 255
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-303 1.13e-35

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 130.56  E-value: 1.13e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   82 SIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDylpQCLSRLRDGSVDYVVALLDEGEAvsrrlgi 161
Cdd:PRK10082  91 ELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVD---EAVDKLREGQSDCIFSFHDEDLL------- 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  162 dsEAEFQRLELGHEQLVAVCAPDAAGQPLFNLDRLQteaLSFLGYSEECHLGWAL-EPLLRDSGLFLQRHHSSSQTEGLR 240
Cdd:PRK10082 161 --EAPFDHIRLFESQLFPVCASDEHGEALFNLAQPH---FPLLNYSRNSYMGRLInRTLTRHSELSFSTFFVSSMSELLK 235
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012  241 FFAQSRLGVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLIRRRLPLPGEAERLWTFLGEL 303
Cdd:PRK10082 236 QVALDGCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELREL 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
91-305 6.38e-23

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: 93.89  E-value: 6.38e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    91 QRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVVALLDEgeavsrrlgidSEAEFQRL 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-----------DDPGLEAR 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   171 ELGHEQLVAVCAPDaagQPLFNLDRLQTEALS---FLGYSEECHLGWALEPLLRDSGLFLQRHHSSSQTEGLRFFAQSRL 247
Cdd:pfam03466  70 PLGEEPLVLVAPPD---HPLARGEPVSLEDLAdepLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGL 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596012   248 GVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLIRRRL-PLPGEAERLWTFLGELAR 305
Cdd:pfam03466 147 GIALLPRSAVARELADGRLVALPLPEPPLPRELYLVWRKGrPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
93-300 3.19e-11

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: 61.46  E-value: 3.19e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  93 RIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDyvVALLdegeavsrrLGIDSEAEFQRLEL 172
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIV---------ALPVDDPGLESEPL 69
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 173 GHEQLVAVCAPDAagqPLFNLDRLQTEALS---FLGYSEECHLGWALEPLLRDSGLFLQRHHSSSQTEGLRFFAQSRLGV 249
Cdd:cd05466  70 FEEPLVLVVPPDH---PLAKRKSVTLADLAdepLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGI 146
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15596012 250 AWLPHTLVREdLASRRLVRAGGQRFDVPLRYTLI-RRRLPLPGEAERLWTFL 300
Cdd:cd05466 147 ALLPESAVEE-LADGGLVVLPLEDPPLSRTIGLVwRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-305 2.63e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.15  E-value: 2.63e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  82 SIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVValldegeavsrRLGI 161
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----------RLGP 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 162 DSEAEFQRLELGHEQLVAVCAPDaagQPLFNLDRLqtealsflgyseechlgwalepllrdsglflqrhhsSSQTEGLRF 241
Cdd:COG0583 150 PPDPGLVARPLGEERLVLVASPD---HPLARRAPL------------------------------------VNSLEALLA 190
                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596012 242 FAQSRLGVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLI-RRRLPLPGEAERLWTFLGELAR 305
Cdd:COG0583 191 AVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVwRRRRHLSPAVRAFLDFLREALA 255
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-303 1.13e-35

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 130.56  E-value: 1.13e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   82 SIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDylpQCLSRLRDGSVDYVVALLDEGEAvsrrlgi 161
Cdd:PRK10082  91 ELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVD---EAVDKLREGQSDCIFSFHDEDLL------- 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  162 dsEAEFQRLELGHEQLVAVCAPDAAGQPLFNLDRLQteaLSFLGYSEECHLGWAL-EPLLRDSGLFLQRHHSSSQTEGLR 240
Cdd:PRK10082 161 --EAPFDHIRLFESQLFPVCASDEHGEALFNLAQPH---FPLLNYSRNSYMGRLInRTLTRHSELSFSTFFVSSMSELLK 235
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012  241 FFAQSRLGVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLIRRRLPLPGEAERLWTFLGEL 303
Cdd:PRK10082 236 QVALDGCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELREL 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
91-305 6.38e-23

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: 93.89  E-value: 6.38e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    91 QRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVVALLDEgeavsrrlgidSEAEFQRL 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-----------DDPGLEAR 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   171 ELGHEQLVAVCAPDaagQPLFNLDRLQTEALS---FLGYSEECHLGWALEPLLRDSGLFLQRHHSSSQTEGLRFFAQSRL 247
Cdd:pfam03466  70 PLGEEPLVLVAPPD---HPLARGEPVSLEDLAdepLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGL 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596012   248 GVAWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLIRRRL-PLPGEAERLWTFLGELAR 305
Cdd:pfam03466 147 GIALLPRSAVARELADGRLVALPLPEPPLPRELYLVWRKGrPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-63 1.52e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.72  E-value: 1.52e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596012     7 LKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGR 63
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
7-121 5.46e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 71.03  E-value: 5.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    7 LKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLqgvAQDAVRALDNLRQSIRE- 85
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRY---FLDIREIFDQLAEATRKl 87
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15596012   86 RDEDAQRRIRFCAPhilsSVFFPHWI-PRLqADFRSA 121
Cdd:PRK11139  88 RARSAKGALTVSLL----PSFAIQWLvPRL-SSFNEA 119
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-104 2.70e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 68.69  E-value: 2.70e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   26 CHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQSIRERDEDAQRRIR-FCA------ 98
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSlFCSvtaays 80

                 ....*...
gi 15596012   99 --PHILSS 104
Cdd:PRK11716  81 hlPPILDR 88
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
93-300 3.19e-11

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: 61.46  E-value: 3.19e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  93 RIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDyvVALLdegeavsrrLGIDSEAEFQRLEL 172
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIV---------ALPVDDPGLESEPL 69
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 173 GHEQLVAVCAPDAagqPLFNLDRLQTEALS---FLGYSEECHLGWALEPLLRDSGLFLQRHHSSSQTEGLRFFAQSRLGV 249
Cdd:cd05466  70 FEEPLVLVVPPDH---PLAKRKSVTLADLAdepLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGI 146
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15596012 250 AWLPHTLVREdLASRRLVRAGGQRFDVPLRYTLI-RRRLPLPGEAERLWTFL 300
Cdd:cd05466 147 ALLPESAVEE-LADGGLVVLPLEDPPLSRTIGLVwRKGRYLSPAARAFLELL 197
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-86 2.94e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 57.32  E-value: 2.94e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596012   10 FLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQdavRALDNLRQSIRER 86
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALK---SSLDTLNQEILDI 95
PRK10341 PRK10341
transcriptional regulator TdcA;
10-151 3.60e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.79  E-value: 3.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   10 FLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQSIRERDED 89
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012   90 AQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVVA-LLDE 151
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGtLSNE 157
PRK09986 PRK09986
LysR family transcriptional regulator;
2-83 3.67e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.65  E-value: 3.67e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQgvaQDAVRALDNLRQ 81
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILM---EESRRLLDNAEQ 83

                 ..
gi 15596012   82 SI 83
Cdd:PRK09986  84 SL 85
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-94 4.83e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.35  E-value: 4.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    1 MIDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLR 80
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80
                         90
                 ....*....|....
gi 15596012   81 QSIRERDEDAQRRI 94
Cdd:PRK10094  81 SELQQVNDGVERQV 94
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
20-81 5.64e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 56.52  E-value: 5.64e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012   20 SRAAQECHVSVSGLSRRIQTLEQWLGAPVFERH-KHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKR 82
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
1-81 7.54e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 55.72  E-value: 7.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    1 MIDLVmlkdflvlCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLR 80
Cdd:PRK11074   9 VVDAV--------ARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETR 80

                 .
gi 15596012   81 Q 81
Cdd:PRK11074  81 R 81
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
2-201 7.72e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 52.85  E-value: 7.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLqgvAQDAVRALDNLRQ 81
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVF---LQDARAILEQAEK 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   82 SI----RERDEDAQRRIRFCAphILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDyvVALLdegeavsr 157
Cdd:PRK09906  78 AKlrarKIVQEDRQLTIGFVP--SAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELD--VGFM-------- 145
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 15596012  158 RLGIDSEaEFQRLELGHEQLVAVCAPDaagQPLFNLDRLQTEAL 201
Cdd:PRK09906 146 RHPVYSD-EIDYLELLDEPLVVVLPVD---HPLAHEKEITAAQL 185
rbcR CHL00180
LysR transcriptional regulator; Provisional
17-80 1.51e-07

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 51.94  E-value: 1.51e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596012   17 KSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGR-------QLQGVAQDAVRALDNLR 80
Cdd:CHL00180  20 GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllrygnRILALCEETCRALEDLK 90
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
2-65 3.45e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 3.45e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQL 65
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-92 7.16e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.97  E-value: 7.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    1 MIDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKhALELTEAGRQLQGVAQdAVRALDN-L 79
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLR-QVALLEAdL 78
                         90
                 ....*....|...
gi 15596012   80 RQSIRERDEDAQR 92
Cdd:PRK13348  79 LSTLPAERGSPPT 91
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
10-83 8.75e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 49.57  E-value: 8.75e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15596012   10 FLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQSI 83
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
109-286 1.26e-06

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 47.96  E-value: 1.26e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 109 HW-IPRLqADFRSAKFSVDCDYLPQC-LSRLRDGSVDYVValldegeavsrRLGIDSEAEFQRLELGHEQLVAVCAPD-A 185
Cdd:cd08432  13 RWlIPRL-ARFQARHPDIDLRLSTSDrLVDFAREGIDLAI-----------RYGDGDWPGLEAERLMDEELVPVCSPAlL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 186 AGQPLFNLDRLqtealsflgyseechlgwALEPLLRDSG-----LFLQRHHSSSQTEGLRF--FAQSRL---------GV 249
Cdd:cd08432  81 AGLPLLSPADL------------------ARHTLLHDATrpeawQWWLWAAGVADVDARRGprFDDSSLalqaavaglGV 142
                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15596012 250 AWLPHTLVREDLASRRLVRAGGQRFDVPLRYTLIRRR 286
Cdd:cd08432 143 ALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLVYPP 179
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
20-202 2.85e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.12  E-value: 2.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   20 SRAAQECHVSVSGLSRRIQTLEQWLGAPVFERH-KHALELTEAGRQLQGVAQDAVRALDNLRQSIRERDEDAQRRIRFCA 98
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVAT 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   99 PHILSSvffpHWIPRLQADFRSAkfsvdcdyLPQCLSRLRDGSVDYVVALLDEGEAvsrRLGIDSEAEFQrlelgHEQLV 178
Cdd:PRK12683 100 THTQAR----YALPKVVRQFKEV--------FPKVHLALRQGSPQEIAEMLLNGEA---DIGIATEALDR-----EPDLV 159
                        170       180       190
                 ....*....|....*....|....*....|...
gi 15596012  179 ---------AVCAPDaaGQPLFNLDRLQTEALS 202
Cdd:PRK12683 160 sfpyyswhhVVVVPK--GHPLTGRENLTLEAIA 190
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
20-81 3.09e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 48.06  E-value: 3.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012   20 SRAAQECHVSVSGLSRRIQTLEQWLGAPVFERH-KHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNIKR 82
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-278 3.99e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.46  E-value: 3.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    1 MIDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKhALELTEAGRQLQGVAQDaVRAL-DNL 79
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRHARQ-VRLLeAEL 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   80 RQSIRERDEDAQR-RI----------------RFCAPHilssvffpHWIPRLQADfrsakfsvDCDYlpqCLSRLRDGSV 142
Cdd:PRK03635  79 LGELPALDGTPLTlSIavnadslatwflpalaPVLARS--------GVLLDLVVE--------DQDH---TAELLRRGEV 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  143 dyVVALLDEGEAVSrrlGIDSEAefqrleLGHEQLVAVCAPDAAGQPL---FNLDRL-QTEALSFlGYSEECHLGWaLEP 218
Cdd:PRK03635 140 --VGAVTTEPQPVQ---GCRVDP------LGAMRYLAVASPAFAARYFpdgVTAEALaKAPAVVF-NRKDDLQDRF-LRQ 206
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596012  219 LLRDSGLFLQRHHSSSqTEGlrFFAQSRLGVAW--LPHTLVREDLASRRLVR-AGGQRFDVPL 278
Cdd:PRK03635 207 AFGLPPGSVPCHYVPS-SEA--FVRAALAGLGWgmIPELQIEPELASGELVDlTPGRPLDVPL 266
PRK09791 PRK09791
LysR family transcriptional regulator;
2-146 4.57e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.45  E-value: 4.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGrqlQGVAQDAVRALDNLR- 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAG---ESFYQHASLILEELRa 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596012   81 --QSIRERDEDAQRRIRFCAPHILSSVFFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDYVV 146
Cdd:PRK09791  82 aqEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
2-94 7.06e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.95  E-value: 7.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    2 IDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQ 81
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90
                         90
                 ....*....|...
gi 15596012   82 SIRERDEDAQRRI 94
Cdd:PRK15092  91 SLMYSNLQGVLTI 103
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
4-154 8.09e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 46.56  E-value: 8.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    4 LVMLKDFlvlcriKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLQGVAQDAVRALDNLRQSI 83
Cdd:PRK11151   9 LVALAEH------RHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   84 RERDEDAQRR-----IRFCAPHILssvffPHWIPRLQADFRSAKFsvdcdYL-----PQCLSRLRDGSVD-YVVALLDEG 152
Cdd:PRK11151  83 SQQGETMSGPlhiglIPTVGPYLL-----PHIIPMLHQTFPKLEM-----YLheaqtHQLLAQLDSGKLDcAILALVKES 152

                 ..
gi 15596012  153 EA 154
Cdd:PRK11151 153 EA 154
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-306 2.29e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.39  E-value: 2.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012    1 MIDLVMLKDFLVLCRIKSFSRAAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALELTEAGRQLqgvAQDAVRALDNLR 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEIL---LQLANQVLPQIS 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   81 QSIRERDEDAQRRIRF------CAPHILSSV--FFPHWiPRLQADFRSAkfsvdCDYLPQclSRLRDGSVDYVVAlldeg 152
Cdd:PRK15421  78 QALQACNEPQQTRLRIaiechsCIQWLTPALenFHKNW-PQVEMDFKSG-----VTFDPQ--PALQQGELDLVMT----- 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  153 EAVSRRLGIDSEAEFQRlelgheQLVAVCAPDaagQPLFNLDRLQTEALsflgySEECHLgwaLEPLLRdSGLFLQRH-- 230
Cdd:PRK15421 145 SDILPRSGLHYSPMFDY------EVRLVLAPD---HPLAAKTRITPEDL-----ASETLL---IYPVQR-SRLDVWRHfl 206
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  231 ---------HSSSQTEGLRFFAQSRLGVAWLPHTLVR--------------EDLASR--RLVRAGGQRfdVPLRYTLIRR 285
Cdd:PRK15421 207 qpagvspslKSVDNTLLLIQMVAARMGIAALPHWVVEsferqglvvtktlgEGLWSRlyAAVRDGEQR--QPVTEAFIRS 284
                        330       340
                 ....*....|....*....|....*...
gi 15596012  286 -------RLPLPGEAERLwTFLGELARP 306
Cdd:PRK15421 285 arnhacdHLPFVKSAERP-TYDAPTVRP 311
cysB PRK12681
HTH-type transcriptional regulator CysB;
20-85 1.61e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.58  E-value: 1.61e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596012   20 SRAAQECHVSVSGLSRRIQTLEQWLGAPVFERH-KHALELTEAGRQLQGVAQDAVRALDNLRQSIRE 85
Cdd:PRK12681  20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSgKHLTQVTPAGEEIIRIAREILSKVESIKSVAGE 86
cbl PRK12679
HTH-type transcriptional regulator Cbl;
23-202 2.80e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.02  E-value: 2.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   23 AQECHVSVSGLSRRIQTLEQWLGAPVF-ERHKHALELTEAGRQLQGVAQDAVRALDNLRQSIRERDEDAQRRIRFCAPHI 101
Cdd:PRK12679  23 ANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHT 102
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012  102 LSSVFFPHWIPRLQADFrsakfsvdcdylPQCLSRLRDGSVDYVVALLDEGEA----VSRRLGIDSE-AEFQRLELGHEQ 176
Cdd:PRK12679 103 QARYSLPEVIKAFRELF------------PEVRLELIQGTPQEIATLLQNGEAdigiASERLSNDPQlVAFPWFRWHHSL 170
                        170       180
                 ....*....|....*....|....*.
gi 15596012  177 LVavcapdAAGQPLFNLDRLQTEALS 202
Cdd:PRK12679 171 LV------PHDHPLTQITPLTLESIA 190
PRK12680 PRK12680
LysR family transcriptional regulator;
22-154 2.85e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 38.84  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012   22 AAQECHVSVSGLSRRIQTLEQWLGAPVFERHKHALE-LTEAGRQLQGVAQDAVRALDNLRQSIRERDEDAQRRIRFCAPH 100
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15596012  101 ILSSVFFPHWIPRLQADFrsakfsvdcdylPQCLSRLRDGSVDYVVALLDEGEA 154
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAY------------PQVSVHLQQAAESAALDLLGQGDA 143
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
143-268 6.31e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176165  Cd Length: 197  Bit Score: 37.22  E-value: 6.31e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 143 DYVVALLDEGEAVSRRLG--IDSeaefqRL---ELGHEQLVAVCAPD---AAGQPLFNLDRLQTEALSFLGYSEECHLGW 214
Cdd:cd08476  36 DRLVDVIDEGFDAVIRTGelPDS-----RLmsrRLGSFRMVLVASPDylaRHGTPETPADLAEHACLRYRFPTTGKLEPW 110
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596012 215 alePLLRDSG---LFLQRHHSSSQTEGLRFFAQSRLGVAWLPHTLVREDLASRRLVR 268
Cdd:cd08476 111 ---PLRGDGGdpeLRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVT 164
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
106-279 9.06e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 36.73  E-value: 9.06e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 106 FFPHWIPRLQADFRSAKFSVDCDYLPQCLSRLRDGSVDY-VVALLDEgeavsrrlgidsEAEFQRLELGHEQLVAVCAPD 184
Cdd:cd08411  15 LLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAaLLALPVD------------EPGLEEEPLFDEPFLLAVPKD 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596012 185 aagQPLFNLDRLQTEAL---SFLGYSEECHL-GWALEpLLRDSGLFLQRHHSSSQTEGLRFFAQSRLGVAWLPHTLVRED 260
Cdd:cd08411  83 ---HPLAKRKSVTPEDLageRLLLLEEGHCLrDQALE-LCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPSE 158
                       170
                ....*....|....*....
gi 15596012 261 LASRRLVRAGGQRFDVPLR 279
Cdd:cd08411 159 ELRGDRLVVRPFAEPAPSR 177
 
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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