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Conserved domains on  [gi|2324969454|gb|UZA73820|]
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LysR family transcriptional regulator [Pseudomonas putida]

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 ...
 92-292 9.08e-63

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: 196.89  E-value: 9.08e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGEL-PDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2324969454 252 GRLQRIFPDWQASPGAanssINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08422   160 GRLVRVLPDWRPPPLP----IYAVYPSRRHLPAKVRAFIDF 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.49e-16

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.65  E-value: 2.49e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2324969454   4 LLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-292 9.08e-63

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: 196.89  E-value: 9.08e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGEL-PDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2324969454 252 GRLQRIFPDWQASPGAanssINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08422   160 GRLVRVLPDWRPPPLP----IYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-297 2.53e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.27  E-value: 2.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   6 AMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIAD 85
Cdd:COG0583     5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  86 RGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGF 162
Cdd:COG0583    85 LRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRlelREGNSDRLVDALLEGELDLAIRLGPP-PDPGLVARPLGEE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 163 QRWLVASPAY-LAGREPLqhpqelldhaclrfrygqkarpwrltcgqdsleldvsgplrSANADMLRETALAGSGIALLA 241
Cdd:COG0583   164 RLVLVASPDHpLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2324969454 242 DWLVREDVLAGRLQRI-FPDWqaspgAANSSINALYMPNHRGSRRVNAFIDFCENLL 297
Cdd:COG0583   203 RFLAADELAAGRLVALpLPDP-----PPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK09801 PRK09801
LysR family transcriptional regulator;
7-276 2.01e-36

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 132.47  E-value: 2.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   7 MKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADR 86
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  87 GEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPnDELVCRRLGGFQRWL 166
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIP-DYYIAHLLTKNKRIL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 167 VASPAYLAGREPLQHPQELLDHACLRFRYGQKARP-WRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLV 245
Cdd:PRK09801  170 CAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGiWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDV 249

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2324969454 246 REDVLAGRLQRIFPDWqaspgAANSSINALY 276
Cdd:PRK09801  250 LPFLESGKLVQVLPEY-----AQSANIWAVY 275
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 1.01e-22

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 93.12  E-value: 1.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSIRLGDPSPnDELVCRRLGGFQRWLVA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVElelTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 169 SPAY-LAGREPLqHPQELLDHACLRFRYGQKAR-PWRLTCGQDSLELDVSgpLRSANADMLRETALAGSGIALLADWLVR 246
Cdd:pfam03466  81 PPDHpLARGEPV-SLEDLADEPLILLPPGSGLRdLLDRALRAAGLRPRVV--LEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2324969454 247 EDVLAGRLQRI-FPDWQASpgaanSSINALYMPNHRGSRRVNAFIDFC 293
Cdd:pfam03466 158 RELADGRLVALpLPEPPLP-----RELYLVWRKGRPLSPAVRAFIEFL 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.49e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.65  E-value: 2.49e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2324969454   4 LLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK09791 PRK09791
LysR family transcriptional regulator;
3-119 3.02e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 59.78  E-value: 3.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   3 KLLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADAS 82
Cdd:PRK09791    6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2324969454  83 IADRGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHP 119
Cdd:PRK09791   86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHP 122
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
23-79 7.45e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 7.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2324969454  23 ARRLGLATSSVTRLVDALEAslgATLLNRST-------RQVSLTEAGARYYQRARGIFEALDEA 79
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLEE---KGLVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAE 119
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
23-85 7.49e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.34  E-value: 7.49e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2324969454   23 ARRLGLATSSVTRLVDALEaslGATLLNRST-----RQV--SLTEAGARYYQRAR-GIFEALDEADASIAD 85
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLE---KKGLVRREPspedrRSVlvSLTEEGRELIEQLLeARSETLAELLAGLTA 98
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-292 9.08e-63

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: 196.89  E-value: 9.08e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGEL-PDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2324969454 252 GRLQRIFPDWQASPGAanssINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08422   160 GRLVRVLPDWRPPPLP----IYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-297 2.53e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.27  E-value: 2.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   6 AMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIAD 85
Cdd:COG0583     5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  86 RGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGF 162
Cdd:COG0583    85 LRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRlelREGNSDRLVDALLEGELDLAIRLGPP-PDPGLVARPLGEE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 163 QRWLVASPAY-LAGREPLqhpqelldhaclrfrygqkarpwrltcgqdsleldvsgplrSANADMLRETALAGSGIALLA 241
Cdd:COG0583   164 RLVLVASPDHpLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2324969454 242 DWLVREDVLAGRLQRI-FPDWqaspgAANSSINALYMPNHRGSRRVNAFIDFCENLL 297
Cdd:COG0583   203 RFLAADELAAGRLVALpLPDP-----PPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 6.04e-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 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: 148.53  E-value: 6.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDeLVCRRLGGFQRWLVASPA 171
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSS-LVARPLAPYRMVLCASPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08477    80 YLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2324969454 252 GRLQRIFPDWQASPgaanSSINALYMPNHRGSRRVNAFIDFC 293
Cdd:cd08477   160 GRLVELLPDYLPPP----RPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-292 2.59e-42

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: 144.53  E-value: 2.59e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDeLVCRRLGGFQRWL-VA 168
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKD-MVAVPLGPPLRMAvVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 169 SPAYLAGREPLQHPQELLDHACLRFRYGQKARP--WRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVR 246
Cdd:cd08474    80 SPAYLARHGTPEHPRDLLNHRCIRYRFPTSGALyrWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2324969454 247 EDVLAGRLQRIFPDWQASPgaanSSINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08474   160 EHLASGRLVRVLEDWSPPF----PGGYLYYPSRRRVPPALRAFIDF 201
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 3.80e-41

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: 141.20  E-value: 3.80e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDL-PDSSLIARKLAPNRRILCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARP-WRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVL 250
Cdd:cd08479    80 YLERHGAPASPEDLARHDCLVIRENDEDFGlWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2324969454 251 AGRLQRIFPDWQASPgaANssINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08479   160 SGRLVRVLPDWQLPD--AD--IWAVYPSRLSRSARVRVFVDF 197
PRK09801 PRK09801
LysR family transcriptional regulator;
7-276 2.01e-36

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 132.47  E-value: 2.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   7 MKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADR 86
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  87 GEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPnDELVCRRLGGFQRWL 166
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIP-DYYIAHLLTKNKRIL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 167 VASPAYLAGREPLQHPQELLDHACLRFRYGQKARP-WRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLV 245
Cdd:PRK09801  170 CAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGiWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDV 249

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2324969454 246 REDVLAGRLQRIFPDWqaspgAANSSINALY 276
Cdd:PRK09801  250 LPFLESGKLVQVLPEY-----AQSANIWAVY 275
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 1.00e-33

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: 122.24  E-value: 1.00e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGEL-ADSSLVARRLGELRMVTCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKAR--PWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDV 249
Cdd:cd08472    80 YLARHGTPRHPEDLERHRAVGYFSARTGRvlPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2324969454 250 LAGRLQRIFPDWQASPgaanSSINALYMPNHRGSRRVNAFID 291
Cdd:cd08472   160 ASGRLVEVLPDWRPPP----LPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 1.44e-33

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: 121.58  E-value: 1.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFgrRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08476     1 GRLRVSLPLVG--GLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGEL-PDSRLMSRRLGSFRMVLVASPD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRY--GQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDV 249
Cdd:cd08476    78 YLARHGTPETPADLAEHACLRYRFptTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2324969454 250 LAGRLQRIFPDWQASPGaansSINALYmPNHRG-SRRVNAFIDF 292
Cdd:cd08476   158 ADGRLVTVLDDYVEERG----QFRLLW-PSSRHlSPKLRVFVDF 196
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 1.14e-31

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: 116.89  E-value: 1.14e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSL-ELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVL 250
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEQGRLvRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2324969454 251 AGRLQRIFPDwQASPGAAnssINALYMPNHRGSRRVNAFID 291
Cdd:cd08475   161 RGELVEVLPE-LAPEGLP---IHAVWPRTRHLPPKVRAAVD 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-292 1.17e-31

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 119.71  E-value: 1.17e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADRGEE 89
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLgDPSP--NDELVCRRLGGFQRWLV 167
Cdd:PRK14997   90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRV-RPRPfeDSDLVMRVLADRGHRLF 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 168 ASPAYLAGREPLQHPQELLDHACLRFRYGQKARPWRLtCGQDSLELDVSGPLRSANADM--LRETALAGSGIALLADWLV 245
Cdd:PRK14997  169 ASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWEL-YGPQGARAEVHFTPRMITTDMlaLREAAMAGVGLVQLPVLMV 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2324969454 246 REDVLAGRLQRIFPDWQASpgaaNSSINALYmPNHRG-SRRVNAFIDF 292
Cdd:PRK14997  248 KEQLAAGELVAVLEEWEPR----REVIHAVF-PSRRGlLPSVRALVDF 290
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-289 2.88e-31

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 118.41  E-value: 2.88e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   4 LLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASI 83
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  84 ADRGEEpvGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPS-PNdeLVCRRLggF 162
Cdd:PRK11139   88 RARSAK--GALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNwPG--LRVEKL--L 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 163 QRWL--VASPAYLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDvSGPLRSaNADMLRETALAGSGIALL 240
Cdd:PRK11139  162 DEYLlpVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQ-QGPIFS-HSSMALQAAIHGQGVALG 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2324969454 241 ADWLVREDVLAGRLQRIFPDWQASPgaanssiNALYMPNHRGSR---RVNAF 289
Cdd:PRK11139  240 NRVLAQPEIEAGRLVCPFDTVLPSP-------NAFYLVCPDSQAelpKVAAF 284
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 1.32e-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 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: 113.97  E-value: 1.32e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGdPSPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVG-PLPDSSLVARKLGESRRVIVASPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08480    80 YLARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2324969454 252 GRLQRIFPDWqaSPGAAnSSINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08480   160 GRLVPVLEEY--NPGDR-EPIHAVYVGGGRLPARVRAFLDF 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 2.72e-29

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: 110.69  E-value: 2.72e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGdPSPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIG-HLPDSSLVATRVGSVRRVVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLA 251
Cdd:cd08471    80 YLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2324969454 252 GRLQRIFPDWQASPgaanSSINALYMPNHRGSRRVNAFIDFC 293
Cdd:cd08471   160 GRLQRVLEDFEPPP----LPVHLVHPEGRLAPAKVRAFVDFA 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-292 8.13e-28

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: 106.49  E-value: 8.13e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPND-ELVCRRLGGFQRWLVA 168
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDsSLVMRVLGQSRQRLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 169 SPAYLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQ-DSLELDVSGPLRSANADMLRETALAGSGIALLADWLVRE 247
Cdd:cd08473    81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDgESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2324969454 248 DVLAGRLQRIFPDWQASPGaansSINALYmPNHRG-SRRVNAFIDF 292
Cdd:cd08473   161 ALRAGRLVRVLPDWTPPRG----IVHAVF-PSRRGlLPAVRALIDF 201
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-265 5.16e-26

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 104.46  E-value: 5.16e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   1 MDKLLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEAD 80
Cdd:PRK10632    1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  81 ASIADRGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDpSPNDELVCRRLG 160
Cdd:PRK10632   81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGA-LQDSSLFSRRLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 161 GFQRWLVASPAYLAGREPLQHPQELLDHACLRFRyGQKARPWRLTCGQD-SLELDVSGPLRSANADMLRETALAGSGIAL 239
Cdd:PRK10632  160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYS-VRPDNEFELIAPEGiSTRLIPQGRFVTNDPQTLVRWLTAGAGIAY 238

                         250       260
                  ....*....|....*....|....*.
gi 2324969454 240 LADWLVREDVLAGRLQRIFPDWQASP 265
Cdd:PRK10632  239 VPLMWVIDEINRGELEILFPRYQSDP 264
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 3.22e-24

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: 97.00  E-value: 3.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPsPNDELVCRRLGGFQRWLVASPA 171
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRL-TDSSLMARRLASRRHYVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 172 YLAGREPLQHPQELLDHACL-------RFRYGQKARPWRltcgqdsleldVSGPLRSANADMLRETALAGSGIALLADWL 244
Cdd:cd08470    80 YLERHGTPHSLADLDRHNCLlgtsdhwRFQENGRERSVR-----------VQGRWRCNSGVALLDAALKGMGLAQLPDYY 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2324969454 245 VREDVLAGRLQRIFPDWQASPGAanssINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08470   149 VDEHLAAGRLVPVLEDYRPPDEG----IWALYPHNRHLSPKVRLLVDY 192
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-292 3.25e-23

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: 94.33  E-value: 3.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGdPSPNDELVCRRLGGFQRWLVAS 169
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIG-ELTDSTLHARPLGKSRLRILAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 170 PAYLAGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLeLDVSGPLRSANADMLRETALAGSGIALLADWLVREDV 249
Cdd:cd08478    80 PDYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGNL-LKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2324969454 250 LAGRLQRIFPDwQASPGaaNSSINALYMPNHRGSRRVNAFIDF 292
Cdd:cd08478   159 AEGRLIPLFAE-QTSDV--RQPINAVYYRNTALSLRIRCFIDF 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 1.01e-22

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 93.12  E-value: 1.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  92 GVLRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSIRLGDPSPnDELVCRRLGGFQRWLVA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVElelTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 169 SPAY-LAGREPLqHPQELLDHACLRFRYGQKAR-PWRLTCGQDSLELDVSgpLRSANADMLRETALAGSGIALLADWLVR 246
Cdd:pfam03466  81 PPDHpLARGEPV-SLEDLADEPLILLPPGSGLRdLLDRALRAAGLRPRVV--LEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2324969454 247 EDVLAGRLQRI-FPDWQASpgaanSSINALYMPNHRGSRRVNAFIDFC 293
Cdd:pfam03466 158 RELADGRLVALpLPEPPLP-----RELYLVWRKGRPLSPAVRAFIEFL 200
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-291 6.61e-18

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: 79.93  E-value: 6.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  93 VLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDeLVCRRLGGFQRWLVASPAY 172
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPG-LEAERLMDEELVPVCSPAL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 173 LAGREPLQhPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPlRSANADMLRETALAGSGIALLADWLVREDVLAG 252
Cdd:cd08432    80 LAGLPLLS-PADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGP-RFDDSSLALQAAVAGLGVALAPRALVADDLAAG 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2324969454 253 RLQRIFPDWQASPGAAnssiNALYMPNHRGSRRVNAFID 291
Cdd:cd08432   158 RLVRPFDLPLPSGGAY----YLVYPPGRAESPAVAAFRD 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.49e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.65  E-value: 2.49e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2324969454   4 LLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 102-291 1.84e-15

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: 73.10  E-value: 1.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 102 FGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDElVCRRLGGFQRWLVASPAYLAGRePLQH 181
Cdd:cd08481    10 FGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGA-ESEYLMDEEVVPVCSPALLAGR-ALAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 182 PQELLDHACLRfrygQKARP--WRltcgQ--DSLELDVSGPLRSANAD---MLRETALAGSGIALLADWLVREDVLAGRL 254
Cdd:cd08481    88 PADLAHLPLLQ----QTTRPeaWR----DwfEEVGLEVPTAYRGMRFEqfsMLAQAAVAGLGVALLPRFLIEEELARGRL 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2324969454 255 QRIFPDWQASPGAAnssinALYMPNHR-GSRRVNAFID 291
Cdd:cd08481   160 VVPFNLPLTSDKAY-----YLVYPEDKaESPPVQAFRD 192
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-291 3.75e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 62.71  E-value: 3.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIadRGEE 89
Cdd:PRK10086   22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI--KNQE 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDpSPNDELVCRRLGGFQRWLVAS 169
Cdd:PRK10086  100 LSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDD-APSAQLTHHFLMDEEILPVCS 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 170 PAY-----LAGR-EPLQHPQELLDHAClrFRYGQKARPWRLTCGQDSLELDVS----GPLRSanaDMLRETALAGSGIAL 239
Cdd:PRK10086  179 PEYaerhaLTGNpDNLRHCTLLHDRQA--WSNDSGTDEWHSWAQHFGVNLLPPssgiGFDRS---DLAVIAAMNHIGVAM 253

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2324969454 240 LADWLVREDVLAGRLQRIFPDWQASPgaaNSSINALYMPnHRGSRRVNAFID 291
Cdd:PRK10086  254 GRKRLVQKRLASGELVAPFGDMEVKC---HQHYYVTTLP-GRQWPKIEAFID 301
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-121 4.99e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 62.09  E-value: 4.99e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   7 MKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADAsIADR 86
Cdd:PRK09906    6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL-RARK 84

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2324969454  87 GEEPVGVLRLSLpVEFGRRVIAPHLGP-FLAQHPAL 121
Cdd:PRK09906   85 IVQEDRQLTIGF-VPSAEVNLLPKVLPmFRLRHPDT 119
PRK09791 PRK09791
LysR family transcriptional regulator;
3-119 3.02e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 59.78  E-value: 3.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   3 KLLAMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADAS 82
Cdd:PRK09791    6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2324969454  83 IADRGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHP 119
Cdd:PRK09791   86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHP 122
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-293 3.73e-10

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: 58.38  E-value: 3.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  94 LRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSIrLGDPSPNDELVCRRLGGFQRWLVASP 170
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVElslVEGGSSELLEALLEGELDLAI-VALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 171 AY-LAGREPLqHPQELLDHACLRFRYGQKARPWRLT-CGQDSLELDVSgpLRSANADMLRETALAGSGIALLADWLVREd 248
Cdd:cd05466    81 DHpLAKRKSV-TLADLADEPLILFERGSGLRRLLDRaFAEAGFTPNIA--LEVDSLEAIKALVAAGLGIALLPESAVEE- 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2324969454 249 VLAGRLQRIFPDWQASPgaanSSINALYMPNHRGSRRVNAFIDFC 293
Cdd:cd05466   157 LADGGLVVLPLEDPPLS----RTIGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-119 3.83e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 59.58  E-value: 3.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADRGEE 89
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110
                  ....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLSLPVEFGRRVIAPHLGPFLAQHP 119
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYP 118
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 94-258 6.22e-10

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: 57.74  E-value: 6.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  94 LRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPS-PNDELVCRRLGGFqrWLVASPAY 172
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDwPGLESEPLTAAPF--VVVAAPGL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 173 LAGREPLQhPQELLDHACLRFRYGQKARPWRLTCGqdsLELDVSGPLRSANADMLRETALAGSGIALLADWLVREDVLAG 252
Cdd:cd08483    80 LGDRKVDS-LADLAGLPWLQERGTNEQRVWLASMG---VVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAG 155


                  ....*.
gi 2324969454 253 RLQRIF 258
Cdd:cd08483   156 RLTVLF 161
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-100 1.58e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 57.67  E-value: 1.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRsTRQVSLTEAGARYYQRARGIfeALDEADAsIADRGEE 89
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV--ALLEADL-LSTLPAE 85

                          90
                  ....*....|.
gi 2324969454  90 PVGVLRLSLPV 100
Cdd:PRK13348   86 RGSPPTLAIAV 96
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-77 2.07e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 57.51  E-value: 2.07e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2324969454   6 AMKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALD 77
Cdd:PRK10094    6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
12-121 5.42e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.08  E-value: 5.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  12 ATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRsTRQVSLTEAGARYYQRARGIfeALDEADAsIADRGEEPV 91
Cdd:PRK03635   12 AVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV--RLLEAEL-LGELPALDG 87

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2324969454  92 GVLRLSLPVE-------FgrrviAPHLGPFLAQHPAL 121
Cdd:PRK03635   88 TPLTLSIAVNadslatwF-----LPALAPVLARSGVL 119
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 19-78 4.93e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 44.16  E-value: 4.93e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  19 FSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDE 78
Cdd:PRK11074   19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQE 78
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-109 5.54e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 5.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   7 MKMFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADR 86
Cdd:PRK11233    6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNV 85

                          90       100
                  ....*....|....*....|...
gi 2324969454  87 GEEpvgvlrLSLPVEFGrrvIAP 109
Cdd:PRK11233   86 GQA------LSGQVSIG---LAP 99
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-85 8.76e-05

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 43.47  E-value: 8.76e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2324969454  13 TVDAQG-FSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIAD 85
Cdd:CHL00180   15 AIATEGsFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALED 88
PRK10341 PRK10341
transcriptional regulator TdcA;
9-72 3.69e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.39  E-value: 3.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2324969454   9 MFVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGI 72
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI 77
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-83 4.04e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.17  E-value: 4.04e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASI 83
Cdd:PRK15092   19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL 92
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
10-254 4.40e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.19  E-value: 4.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  10 FVATVDAQGFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIadRGEE 89
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAEL--RGGS 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  90 PVGVLRLslpvefgrRVIAPH------LGPFLAQHPALELDIDLS----DRLDDLLDGRYDLSIRLGDP----SPNDELv 155
Cdd:PRK10082   97 DYAQRKI--------KIAAAHslslglLPSIISQMPPLFTWAIEAidvdEAVDKLREGQSDCIFSFHDEdlleAPFDHI- 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 156 crRLGGFQRWLV-ASPAYLAGREPLQHPQ-ELLDHAclrfRYGQKARPWRLTCGQDSlELDVSGPLRSANADMLRETALA 233
Cdd:PRK10082  168 --RLFESQLFPVcASDEHGEALFNLAQPHfPLLNYS----RNSYMGRLINRTLTRHS-ELSFSTFFVSSMSELLKQVALD 240

                         250       260
                  ....*....|....*....|.
gi 2324969454 234 GSGIALLADWLVREDVLAGRL 254
Cdd:PRK10082  241 GCGIAWLPEYAIQQEIRSGQL 261
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
23-79 7.45e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 7.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2324969454  23 ARRLGLATSSVTRLVDALEAslgATLLNRST-------RQVSLTEAGARYYQRARGIFEALDEA 79
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLEE---KGLVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAE 119
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
23-85 7.49e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.34  E-value: 7.49e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2324969454   23 ARRLGLATSSVTRLVDALEaslGATLLNRST-----RQV--SLTEAGARYYQRAR-GIFEALDEADASIAD 85
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLE---KKGLVRREPspedrRSVlvSLTEEGRELIEQLLeARSETLAELLAGLTA 98
PRK12680 PRK12680
LysR family transcriptional regulator;
4-245 2.85e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 38.84  E-value: 2.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454   4 LLAMKMFVATVDAQ-GFSAAARRLGLATSSVTRLVDALEASLGATLLNRSTRQV-SLTEAGARYYQRARGIFEALDEADA 81
Cdd:PRK12680    3 LTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  82 SIADRGEEPVGVLRLSLPVEFGRRVIAPHLGPFLAQHPALE---LDIDLSDRLDDLLDGRYDLSI-RLGDPSPNDELVCR 157
Cdd:PRK12680   83 YAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSvhlQQAAESAALDLLGQGDADIAIvSTAGGEPSAGIAVP 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 158 rlggFQRW--LVASPAylagREPLQHPQELLDHACLR----FRYGQKARPWR-LTCGQDSLELDVSGPLRSANADMLRET 230
Cdd:PRK12680  163 ----LYRWrrLVVVPR----GHALDTPRRAPDMAALAehplISYESSTRPGSsLQRAFAQLGLEPSIALTALDADLIKTY 234

                         250
                  ....*....|....*
gi 2324969454 231 ALAGSGIALLADWLV 245
Cdd:PRK12680  235 VRAGLGVGLLAEMAV 249
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 94-254 2.89e-03

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: 38.15  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  94 LRLSLPVEFGRRVIAPHLGPFLAQHPALELDIDLSDRLDDLLDGRYDLSIRLGDPSPNDELVCRRLGGFQRWLVASPAYl 173
Cdd:cd08482     2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPAGMQVIELFPERVGPVCSPSL- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454 174 AGREPLQHPQELLDHACLRFRYGQKARPWRLTCGQDSLELDVSGPLRS-ANADMLRETALAGSGIALLADWLVREDVLAG 252
Cdd:cd08482    81 APTVPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSfEHFYYLLEAAVAGLGVAIAPWPLVRDDLASG 160


                  ..
gi 2324969454 253 RL 254
Cdd:cd08482   161 RL 162
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-122 7.44e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 37.11  E-value: 7.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2324969454  31 SSVTRLVDALEASLGATLLNRSTRQVSLTEAGARYYQRARGIFEALDEADASIADRGEEPVGVLRL--SlpvefgrrVIA 108
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcS--------VTA 77

                          90       100
                  ....*....|....*....|
gi 2324969454 109 --PHLGP----FLAQHPALE 122
Cdd:PRK11716   78 aySHLPPildrFRAEHPLVE 97
 
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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