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Conserved domains on  [gi|515541492|ref|WP_016974545|]
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LysR family transcriptional regulator [Pseudomonas tolaasii]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

LysR family transcriptional regulator similar to Pseudomonas aeruginosa HTH-type transcriptional regulator PtxR, which regulates the toxA (exotoxin) and regA genes; substrate binding domain-containing protein is a type 2 periplasmic binding protein (PBP2), similar to the regulatory domain of Vibrio vulnificus virulence gene regulator AphB that has been implicated in acid resistance and pathogenesis

Gene Ontology:  GO:0001216|GO:0032993|GO:0006355
PubMed:  19047729|8257110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-297 1.81e-76

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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 further 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 231.95  E-value: 1.81e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGsDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGG-GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515541492 257 GTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08422  160 GRLVRVLPDW----RPPPLPIYAVYPSRRHLPAKVRAFIDF 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.03e-18

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.20  E-value: 1.03e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492    9 FKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-297 1.81e-76

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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 further 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 231.95  E-value: 1.81e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGsDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGG-GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515541492 257 GTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08422  160 GRLVRVLPDW----RPPPLPIYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-303 2.08e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 193.16  E-value: 2.08e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  87 ALQEQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQ--TDTYVDPLQDGT-DLLFRIGVLNDSGMQARIF 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGElDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 164 APQRFRIAASPAY-LARHGTPShpdelvnhqclaykgitgqqrwffrrdgsdwtpysvkgpitgNHADTLTHAAEQGLGL 242
Cdd:COG0583  161 GEERLVLVASPDHpLARRAPLV------------------------------------------NSLEALLAAVAAGLGI 198

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515541492 243 VVFPSWLIGEGLRAGTLQAVlteyEVATTLEPQQIAALWPGSRRLSLKVRTVIDYFAECFG 303
Cdd:COG0583  199 ALLPRFLAADELAAGRLVAL----PLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-300 2.88e-43

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 150.53  E-value: 2.88e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   1 MQGLNELSFkalrlFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQ 80
Cdd:PRK14997   1 KTDLNDFAW-----FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  81 LESASQALQEQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRI--GVLNDSGM 158
Cdd:PRK14997  76 AQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 159 QARIFAPQRFRIAASPAYLARHGTPSHPDELVNHQCLAYKGITGQQRW-FFRRDGSDWTPYSVKGPITGNHAdTLTHAAE 237
Cdd:PRK14997 156 VMRVLADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWeLYGPQGARAEVHFTPRMITTDML-ALREAAM 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515541492 238 QGLGLVVFPSWLIGEGLRAGTLQAVLTEYevattlEPQQ--IAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:PRK14997 235 AGVGLVQLPVLMVKEQLAAGELVAVLEEW------EPRRevIHAVFPSRRGLLPSVRALVDFLTE 293
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-300 9.44e-29

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: 109.30  E-value: 9.44e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   96 SGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTY--VDPLQDGT-DLLFRIGVLNDSGMQARIFAPQRFRIAA 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEGElDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  173 SPAYLARHGTPSHPDELVNHQCLAYKGITGqQRWFFRRDGSDwTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGE 252
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG-LRDLLDRALRA-AGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 515541492  253 GLRAGTLQAV-LTEYEVattlePQQIAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:pfam03466 159 ELADGRLVALpLPEPPL-----PRELYLVWRKGRPLSPAVRAFIEFLRE 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.03e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.20  E-value: 1.03e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492    9 FKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-124 4.64e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 71.25  E-value: 4.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 515541492  87 ALQEQEAEPSGLVRIN-APMVFGQRHLSPWLGELCRRYP 124
Cdd:PRK11233  81 AVHNVGQALSGQVSIGlAPGTAASSLTMPLLQAVRAEFP 119
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
7-94 4.23e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 4.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHG--SFSEVARRESLAPSSISRQIQLMEQAlgqQLLYRHT-------RAVSPTEAGR-LLGHHARL 76
Cdd:COG1846   36 LTPAQFRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRaLLEEARPA 112

                         90
                 ....*....|....*...
gi 515541492  77 MLEQLESASQALQEQEAE 94
Cdd:COG1846  113 LEALLAELLAGLSEEELE 130
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-297 1.81e-76

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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 further 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 231.95  E-value: 1.81e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGsDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGG-GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515541492 257 GTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08422  160 GRLVRVLPDW----RPPPLPIYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-303 2.08e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 193.16  E-value: 2.08e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  87 ALQEQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQ--TDTYVDPLQDGT-DLLFRIGVLNDSGMQARIF 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGElDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 164 APQRFRIAASPAY-LARHGTPShpdelvnhqclaykgitgqqrwffrrdgsdwtpysvkgpitgNHADTLTHAAEQGLGL 242
Cdd:COG0583  161 GEERLVLVASPDHpLARRAPLV------------------------------------------NSLEALLAAVAAGLGI 198

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515541492 243 VVFPSWLIGEGLRAGTLQAVlteyEVATTLEPQQIAALWPGSRRLSLKVRTVIDYFAECFG 303
Cdd:COG0583  199 ALLPRFLAADELAAGRLVAL----PLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-297 2.74e-55

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 6. 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: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 178.13  E-value: 2.74e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDS-GMQARIFAPQRFRIAASPA 175
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 176 YLARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLR 255
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515541492 256 AGTLQAVLTEYEVattlEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08475  161 RGELVEVLPELAP----EGLPIHAVWPRTRHLPPKVRAAVDA 198
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-297 1.09e-53

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 8. 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: 176166  Cd Length: 197  Bit Score: 173.96  E-value: 1.09e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08477   81 LARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVK-VPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515541492 257 GTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08477  160 GRLVELLPDY----LPPPRPMHLLYPPDRRPTPKLRSFIDF 196
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-298 9.94e-49

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 5. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 161.48  E-value: 9.94e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  95 PSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQA-RIFAPQRFRIAAS 173
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAvPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 174 PAYLARHGTPSHPDELVNHQCLAYK-GITGQ-QRWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIG 251
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRfPTSGAlYRWEFERGGRELE-VDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 515541492 252 EGLRAGTLQAVLTEYevATTLEPqqIAALWPGSRRLSLKVRTVIDYF 298
Cdd:cd08474  160 EHLASGRLVRVLEDW--SPPFPG--GYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-297 1.30e-47

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: 158.18  E-value: 1.30e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFgqRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08476    1 GRLRVSLPLVG--GLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYK-GITGQ-QRWFFRRDGSDwTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGL 254
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRfPTTGKlEPWPLRGDGGD-PELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 515541492 255 RAGTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08476  158 ADGRLVTVLDDY----VEERGQFRLLWPSSRHLSPKLRVFVDF 196
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-300 1.19e-45

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 2. 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: 176160  Cd Length: 201  Bit Score: 153.45  E-value: 1.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08471   81 LARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERS-VRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 515541492 257 GTLQAVLTEYEvattLEPQQIAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:cd08471  160 GRLQRVLEDFE----PPPLPVHLVHPEGRLAPAKVRAFVDFAVP 199
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-300 2.70e-44

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. 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: 176159  Cd Length: 197  Bit Score: 149.77  E-value: 2.70e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLaykgITGQQRWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08470   81 LERHGTPHSLADLDRHNCL----LGTSDHWRFQENGRERS-VRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 515541492 257 GTLQAVLTEYEvattLEPQQIAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:cd08470  156 GRLVPVLEDYR----PPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-300 6.98e-44

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 3. 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: 176161  Cd Length: 202  Bit Score: 148.81  E-value: 6.98e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQR--WFFRRDGSDwTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGL 254
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFSARTGRVlpWEFQRDGEE-REVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 515541492 255 RAGTLQAVLTEYevatTLEPQQIAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:cd08472  160 ASGRLVEVLPDW----RPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-300 2.88e-43

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 150.53  E-value: 2.88e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   1 MQGLNELSFkalrlFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQ 80
Cdd:PRK14997   1 KTDLNDFAW-----FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  81 LESASQALQEQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRI--GVLNDSGM 158
Cdd:PRK14997  76 AQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 159 QARIFAPQRFRIAASPAYLARHGTPSHPDELVNHQCLAYKGITGQQRW-FFRRDGSDWTPYSVKGPITGNHAdTLTHAAE 237
Cdd:PRK14997 156 VMRVLADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWeLYGPQGARAEVHFTPRMITTDML-ALREAAM 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515541492 238 QGLGLVVFPSWLIGEGLRAGTLQAVLTEYevattlEPQQ--IAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:PRK14997 235 AGVGLVQLPVLMVKEQLAAGELVAVLEEW------EPRRevIHAVFPSRRGLLPSVRALVDFLTE 293
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-298 2.92e-43

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 9. 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: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 146.97  E-value: 2.92e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYK------GItgqqrWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLI 250
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRendedfGL-----WRLRNGDGEAT-VRVRGALSSNDGEVVLQWALDGHGIILRSEWDV 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 515541492 251 GEGLRAGTLQAVLTEYEvattLEPQQIAALWPGSRRLSLKVRTVIDYF 298
Cdd:cd08479  155 APYLRSGRLVRVLPDWQ----LPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 95-297 2.23e-39

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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 further 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 137.08  E-value: 2.23e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  95 PSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASP 174
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 175 AYLARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRdgSDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGL 254
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKD--ADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 515541492 255 RAGTLQAVLTEyevaTTLEPQQ-IAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08478  159 AEGRLIPLFAE----QTSDVRQpINAVYYRNTALSLRIRCFIDF 198
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-297 6.72e-39

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 10. 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: 176169  Cd Length: 198  Bit Score: 135.93  E-value: 6.72e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  97 GLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAY 176
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 177 LARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRA 256
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVA-LPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515541492 257 GTLQAVLTEYEVAttlEPQQIAALWPGSRRLSLKVRTVIDY 297
Cdd:cd08480  160 GRLVPVLEEYNPG---DREPIHAVYVGGGRLPARVRAFLDF 197
PRK09801 PRK09801
LysR family transcriptional regulator;
10-299 8.57e-37

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 133.62  E-value: 8.57e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  10 KALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQALQ 89
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  90 EQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFR 169
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 170 IAASPAYLARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWL 249
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 515541492 250 IGEGLRAGTLQAVLTEYevattlepQQIAALWPGSRRL---SLKVRTVIDYFA 299
Cdd:PRK09801 249 VLPFLESGKLVQVLPEY--------AQSANIWAVYREPlyrSMKLRVCVEFLA 293
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
10-302 6.65e-35

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 128.72  E-value: 6.65e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  10 KALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQALQ 89
Cdd:PRK10632   5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  90 EQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFR 169
Cdd:PRK10632  85 AFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMV 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 170 IAASPAYLARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDwTPYSVKGPITGNHADTLTHAAEQGLGLVVFP-SW 248
Cdd:PRK10632 165 VCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGIS-TRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPlMW 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 515541492 249 LIGEgLRAGTLQAVLTEYEVattlEPQQIAALWPGSRRLSLKVRTVIDYFAECF 302
Cdd:PRK10632 244 VIDE-INRGELEILFPRYQS----DPRPVYALYTEKDKLPLKVQVCINYLTDYF 292
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-298 9.93e-30

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 4. 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: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 111.88  E-value: 9.93e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  95 PSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRI--GVLNDSGMQARIFAPQRFRIAA 172
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVrfPPLEDSSLVMRVLGQSRQRLVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 173 SPAYLARHGTPSHPDELVNHQCLAYKGITGQQRW-FFRRDGSDWT-PYSVKgpITGNHADTLTHAAEQGLGLVVFPSWLI 250
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWrLEGPDGESITvRHRPR--LVTDDLLTLRQAALAGVGIALLPDHLC 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 515541492 251 GEGLRAGTLQAVLTEYevatTLEPQQIAALWPgSRR-LSLKVRTVIDYF 298
Cdd:cd08473  159 REALRAGRLVRVLPDW----TPPRGIVHAVFP-SRRgLLPAVRALIDFL 202
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-300 9.44e-29

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: 109.30  E-value: 9.44e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   96 SGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTY--VDPLQDGT-DLLFRIGVLNDSGMQARIFAPQRFRIAA 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEGElDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  173 SPAYLARHGTPSHPDELVNHQCLAYKGITGqQRWFFRRDGSDwTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGE 252
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG-LRDLLDRALRA-AGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 515541492  253 GLRAGTLQAV-LTEYEVattlePQQIAALWPGSRRLSLKVRTVIDYFAE 300
Cdd:pfam03466 159 ELADGRLVALpLPEPPL-----PRELYLVWRKGRPLSPAVRAFIEFLRE 202
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-265 2.98e-27

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 107.62  E-value: 2.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   8 SFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQA 87
Cdd:PRK11139   7 PLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  88 LQEQEAEPSglVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQR 167
Cdd:PRK11139  87 LRARSAKGA--LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 168 FRIAASPAYLARHGTPSHPDELVNHQCLAYKGITGQQRWFFRRDGSDWTPYsvKGPITgNHADTLTHAAEQGLGLVVFPS 247
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQ--QGPIF-SHSSMALQAAIHGQGVALGNR 241

                        250
                 ....*....|....*...
gi 515541492 248 WLIGEGLRAGTLQAVLTE 265
Cdd:PRK11139 242 VLAQPEIEAGRLVCPFDT 259
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.03e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.20  E-value: 1.03e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492    9 FKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-191 1.12e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 81.59  E-value: 1.12e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   4 LNELSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHharLMLEQLES 83
Cdd:PRK10086  11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFW---ALKSSLDT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  84 ASQALQEQE-AEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARI 162
Cdd:PRK10086  88 LNQEILDIKnQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHF 167

                        170       180
                 ....*....|....*....|....*....
gi 515541492 163 FAPQRFRIAASPAYLARHGTPSHPDELVN 191
Cdd:PRK10086 168 LMDEEILPVCSPEYAERHALTGNPDNLRH 196
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-279 1.54e-17

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 81.17  E-value: 1.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRhTRAVSPTEAG-RLLGHHARLMLEQLESAS 85
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGqRLLRHLRQVALLEADLLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  86 QALQEQEAEPSGLVRINAPmvfgqrHLSPWLG----ELCRRyPKLQLDIQQTDtyvdplQDGT-DLLFR---IGVLNDSG 157
Cdd:PRK13348  81 TLPAERGSPPTLAIAVNAD------SLATWFLpalaAVLAG-ERILLELIVDD------QDHTfALLERgevVGCVSTQP 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 158 --MQARIFAP---QRFRIAASPAYLARHgtpsHPDELVNHQCLA-----YKGITGQQRWFFRRDGsdwtPYSVKGPIT-- 225
Cdd:PRK13348 148 kpMRGCLAEPlgtMRYRCVASPAFAARY----FAQGLTRHSALKapavaFNRKDTLQDSFLEQLF----GLPVGAYPRhy 219

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515541492 226 --GNHAdtLTHAAEQGLGLVVFPSWLIGEGLRAGTLQAVLTEYEVATTL-----EPQQIAA 279
Cdd:PRK13348 220 vpSTHA--HLAAIRHGLGYGMVPELLIGPLLAAGRLVDLAPGHPVDVALywhhwEVESPTM 278
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-132 1.10e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 73.07  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  12 LRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQALQEQ 91
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 515541492  92 EAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQ 132
Cdd:PRK11242  86 ADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRE 126
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-124 4.64e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 71.25  E-value: 4.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 515541492  87 ALQEQEAEPSGLVRIN-APMVFGQRHLSPWLGELCRRYP 124
Cdd:PRK11233  81 AVHNVGQALSGQVSIGlAPGTAASSLTMPLLQAVRAEFP 119
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-298 1.26e-13

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: 68.40  E-value: 1.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  99 VRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTY--VDPLQDGT-DLLFRIGVLNDSGMQARIFAPQRFRIAASPA 175
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSelLEALLEGElDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 176 YLARHGTPSHPDELVNHQCLAYKGITGQQRW---FFRRDGSdwTPYSVkgpITGNHADTLTHAAEQGLGLVVFPSWLIGE 252
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLRRLldrAFAEAGF--TPNIA---LEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 515541492 253 GLRAGtlqavLTEYEVATTLEPQQIAALWPGSRRLSLKVRTVIDYF 298
Cdd:cd05466  157 LADGG-----LVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-130 1.84e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 69.45  E-value: 1.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  10 KALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQALQ 89
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515541492  90 EQEA--EPSGLVRINApMVFGQRHLSPWLGELCRRYPKLQLDI 130
Cdd:PRK10094  85 QVNDgvERQVNIVINN-LLYNPQAVAQLLAWLNERYPFTQFHI 126
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 99-261 2.00e-13

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: 67.61  E-value: 2.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  99 VRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAYLA 178
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 179 RHGTPShPDELVNHQCLAYKGITGQQRWFFRRDGSDwTPYSVKGPiTGNHADTLTHAAEQGLGLVVFPSWLIGEGLRAGT 258
Cdd:cd08432   82 GLPLLS-PADLARHTLLHDATRPEAWQWWLWAAGVA-DVDARRGP-RFDDSSLALQAAVAGLGVALAPRALVADDLAAGR 158


                 ...
gi 515541492 259 LQA 261
Cdd:cd08432  159 LVR 161
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-128 1.08e-12

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 66.77  E-value: 1.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  35 PSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQALQEQEAEPSGLVRINAPMVFGQRHLSP 114
Cdd:PRK11716   5 PSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPP 84

                         90
                 ....*....|....
gi 515541492 115 WLGELCRRYPKLQL 128
Cdd:PRK11716  85 ILDRFRAEHPLVEI 98
PRK09791 PRK09791
LysR family transcriptional regulator;
9-130 8.03e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.78  E-value: 8.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   9 FKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQAL 88
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 515541492  89 QEQEAEPSGLVRINA---------PMVFGQRHlspwlgelcRRYPKLQLDI 130
Cdd:PRK09791  87 RQRQGQLAGQINIGMgasiarslmPAVISRFH---------QQHPQVKVRI 128
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-103 1.52e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 63.64  E-value: 1.52e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   6 ELSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRhTRAVSPTEAGRLLGHHARlMLEQLES-A 84
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHAR-QVRLLEAeL 78

                         90       100
                 ....*....|....*....|
gi 515541492  85 SQALQEQEAEPSGL-VRINA 103
Cdd:PRK03635  79 LGELPALDGTPLTLsIAVNA 98
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-107 1.65e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 63.64  E-value: 1.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  12 LRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLES----ASQA 87
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKaklrARKI 85

                         90       100
                 ....*....|....*....|
gi 515541492  88 LQEQEAEPSGLVRINAPMVF 107
Cdd:PRK09906  86 VQEDRQLTIGFVPSAEVNLL 105
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-131 3.33e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 62.73  E-value: 3.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   5 NELSF--KALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLE 82
Cdd:CHL00180   1 TDLPFtlDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 515541492  83 SASQALQEQEAEPSGLVRINAPMVFGQrHLSPWLGEL-CRRYPKLQLDIQ 131
Cdd:CHL00180  81 ETCRALEDLKNLQRGTLIIGASQTTGT-YLMPRLIGLfRQRYPQINVQLQ 129
PRK09986 PRK09986
LysR family transcriptional regulator;
1-88 5.03e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.27  E-value: 5.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   1 MQGLNELSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMleq 80
Cdd:PRK09986   1 MERLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRL--- 77


                 ....*...
gi 515541492  81 LESASQAL 88
Cdd:PRK09986  78 LDNAEQSL 85
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 12-130 3.27e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 53.88  E-value: 3.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  12 LRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAG-RLLGhHARLMLEQLESASQALQE 90
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGiQLLG-YARKILRFNDEACSSLMY 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 515541492  91 QEAEpsGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDI 130
Cdd:PRK15092  95 SNLQ--GVLTIGASDDTADTILPFLLNRVSSVYPKLALDV 132
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-259 2.39e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.21  E-value: 2.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   3 GLNELSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLE 82
Cdd:PRK10082   7 GLHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  83 SASQALQEQEAEPSGLVRINApmvfgQRHLS-PWLGELCRRYPKL---QLDIQQTDTYVDPLQDG-TDLLFRigvLNDSG 157
Cdd:PRK10082  87 SNLAELRGGSDYAQRKIKIAA-----AHSLSlGLLPSIISQMPPLftwAIEAIDVDEAVDKLREGqSDCIFS---FHDED 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 158 MQA------RIFAPQRFRIAASPAY---LARHGTPSHPdeLVNHQCLAYKGitgqqrWFFRRDGSDWTPYSVKGPITGNH 228
Cdd:PRK10082 159 LLEapfdhiRLFESQLFPVCASDEHgeaLFNLAQPHFP--LLNYSRNSYMG------RLINRTLTRHSELSFSTFFVSSM 230

                        250       260       270
                 ....*....|....*....|....*....|.
gi 515541492 229 ADTLTHAAEQGLGLVVFPSWLIGEGLRAGTL 259
Cdd:PRK10082 231 SELLKQVALDGCGIAWLPEYAIQQEIRSGQL 261
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
26-132 2.56e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 51.13  E-value: 2.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  26 EVARR--------ESLAPSS--ISRQIQLMEQALGQQLLYRH-TRAVSPTEAGRLLGHHARLMLEQLESASQALQEQEAE 94
Cdd:PRK12684  11 EAVRQnfnlteaaKALYTSQpgVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQ 90

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 515541492  95 PSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQ 132
Cdd:PRK12684  91 DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQ 128
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-257 5.01e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 50.40  E-value: 5.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  87 ALQEQEAEPsglVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYvDP----LQDGTDLLFRIGVLNDSGMQARI 162
Cdd:PRK15421  82 ACNEPQQTR---LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTF-DPqpalQQGELDLVMTSDILPRSGLHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 163 FAPQRFRIAASPAYLARHGTPSHPDELVNHQCLAY---KGITGQQRWFFRRDGSDWTPYSVKGPItgnhadTLTHAAEQG 239
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYpvqRSRLDVWRHFLQPAGVSPSLKSVDNTL------LLIQMVAAR 231

                        250
                 ....*....|....*...
gi 515541492 240 LGLVVFPSWLIGEGLRAG 257
Cdd:PRK15421 232 MGIAALPHWVVESFERQG 249
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 7-82 7.09e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.94  E-value: 7.09e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLE 82
Cdd:PRK11074   2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQ 77
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-130 7.72e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.69  E-value: 7.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQLESASQ 86
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQ 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 515541492  87 ALQEQEaepsGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDI 130
Cdd:PRK10837  83 LFREDN----GALRIYASSTIGNYILPAMIARYRRDYPQLPLEL 122
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 107-297 3.55e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 43.82  E-value: 3.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 107 FGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAYLARHGtPSHP 186
Cdd:cd08481   10 FGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 187 DELVN----HQClaykgiTGQQRW--FFRRDGSDwtpysVKGPITGNHAD---TLTHAAEQGLGLVVFPSWLIGEGLRAG 257
Cdd:cd08481   89 ADLAHlpllQQT------TRPEAWrdWFEEVGLE-----VPTAYRGMRFEqfsMLAQAAVAGLGVALLPRFLIEEELARG 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 515541492 258 TLQ-----AVLTEYevATTLepqqiaaLWPGSRRLSLKVRTVIDY 297
Cdd:cd08481  158 RLVvpfnlPLTSDK--AYYL-------VYPEDKAESPPVQAFRDW 193
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 12-143 3.94e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 44.64  E-value: 3.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  12 LRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLMLEQL----ESASQa 87
Cdd:PRK11151   6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkEMASQ- 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515541492  88 lqeQEAEPSGLVRINAPMVFGQrHLSPW-LGELCRRYPKLQLDIQ--QTDTYVDPLQDG 143
Cdd:PRK11151  85 ---QGETMSGPLHIGLIPTVGP-YLLPHiIPMLHQTFPKLEMYLHeaQTHQLLAQLDSG 139
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-77 1.80e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 42.30  E-value: 1.80e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515541492   1 MQGLNelsFKALRLFVAVLDHGSFSEVARRESLAPSSISRQIQLMEQALGQQLLYRHTRAVSPTEAGRLLGHHARLM 77
Cdd:PRK11062   1 MSHIN---YNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 99-267 1.83e-04

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 41.56  E-value: 1.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  99 VRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLNDSGMQARIFAPQRFRIAASPAYLa 178
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 179 RHGTPSHPDELVNHQCLAYKGITGQQRWfFRRDGSDwtpYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRAGT 258
Cdd:cd08483   81 GDRKVDSLADLAGLPWLQERGTNEQRVW-LASMGVV---PDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGR 156


                 ....*....
gi 515541492 259 LqAVLTEYE 267
Cdd:cd08483  157 L-TVLFEEE 164
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 110-261 1.88e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI 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: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 41.62  E-value: 1.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492 110 RHLSPWLGELCRRYPKLQLDIQQTDTYVDPLQDGTDLLFRIGVLN-DSGMQARIFAPQRFRIAASPAYLARHGTPSHPDE 188
Cdd:cd08482   13 RWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSLAPTVPLRQAPAA 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515541492 189 LvNHQCLAYKGITGQQRWFFRRDGSDWTPYSVKGPITGNHADTLTHAAEQGLGLVVFPSWLIGEGLRAGTLQA 261
Cdd:cd08482   93 A-LLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLVA 164
cysB PRK12681
HTH-type transcriptional regulator CysB;
12-132 7.36e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.65  E-value: 7.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  12 LRLFVAVLDHG-SFSEVArrESLAPSS--ISRQIQLMEQALGQQLLYR---HTRAVSPteAGRLLGHHARLMLEQLESAS 85
Cdd:PRK12681   6 LRYIVEVVNHNlNVSATA--EGLYTSQpgISKQVRMLEDELGIQIFARsgkHLTQVTP--AGEEIIRIAREILSKVESIK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 515541492  86 QALQEQEAEPSGLVRINAPMVFGQRHLSPWLGELCRRYPKLQLDIQQ 132
Cdd:PRK12681  82 SVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQ 128
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
7-94 4.23e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 4.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492   7 LSFKALRLFVAVLDHG--SFSEVARRESLAPSSISRQIQLMEQAlgqQLLYRHT-------RAVSPTEAGR-LLGHHARL 76
Cdd:COG1846   36 LTPAQFRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRaLLEEARPA 112

                         90
                 ....*....|....*...
gi 515541492  77 MLEQLESASQALQEQEAE 94
Cdd:COG1846  113 LEALLAELLAGLSEEELE 130
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-132 7.40e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 37.66  E-value: 7.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515541492  25 SEVARRESLAPSSISRQIQLMEQALGQQLLYRH-TRAVSPTEAGRLLGHHARLMLEQLESASQALQEQEAEPSGLVRINA 103
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                         90       100
                 ....*....|....*....|....*....
gi 515541492 104 PMVFGQRHLSPWLGELCRRYPKLQLDIQQ 132
Cdd:PRK12682 100 THTQARYVLPRVVAAFRKRYPKVNLSLHQ 128
 
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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