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Conserved domains on  [gi|2532407933|ref|WP_289914101|]
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MULTISPECIES: LysR family transcriptional regulator [unclassified Janthinobacterium]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444120)

LysR family transcriptional regulator may function as a transcriptional activator or repressor 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, among others

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 6.12e-100

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: 291.42  E-value: 6.12e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08479    81 LERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2532407933 255 GKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08479   161 GRLVRVLPDWQlPDADIWAVYPSRLSRSARVRVFVDFL 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 2.09e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 2.09e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGE 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 6.12e-100

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: 291.42  E-value: 6.12e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08479    81 LERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2532407933 255 GKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08479   161 GRLVRVLPDWQlPDADIWAVYPSRLSRSARVRVFVDFL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
5-298 1.35e-97

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 289.63  E-value: 1.35e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   5 PLLEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGE 84
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  85 AVAQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASN 164
Cdd:PRK09801   86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 165 QRVLCAAPAYLARRGTPDTLAQLREHDCIVIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRS 244
Cdd:PRK09801  166 KRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRS 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2532407933 245 AWDVESSLAQGKLVRILPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQAR 298
Cdd:PRK09801  246 EWDVLPFLESGKLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQR 299
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-297 5.43e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 5.43e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELL--DRPVD-LLGEGFDLDIRIGVVHEPDLIAHRIAS 163
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDaLLEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 164 NQRVLCAAPAYLARRGTPDTlaqlrehdcivirerdqdgrrwklqgpqgvetvkvdgplsaNNGEIVHQWALDGHGIILR 243
Cdd:COG0583   163 ERLVLVASPDHPLARRAPLV-----------------------------------------NSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2532407933 244 SAWDVESSLAQGKLVRI-LPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQA 297
Cdd:COG0583   202 PRFLAADELAAGRLVALpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-296 1.10e-31

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: 117.00  E-value: 1.10e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  94 QGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLD--RPVDLLGEG-FDLDIRIGVVHEPDLIAHRIASNQRVLCA 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 171 APAYLARRGTPDTLAQLREHDCIVIreRDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVES 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILL--PPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2532407933 251 SLAQGKLVRI-LPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQ 296
Cdd:pfam03466 159 ELADGRLVALpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 2.09e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 2.09e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGE 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-93 5.03e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.19  E-value: 5.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  10 LRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRtTRRVSVTDHGEIVRQWAQRIledveQMGEAVAQS 89
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-----ALLEADLLS 80


                  ....
gi 2532407933  90 KLQP 93
Cdd:PRK13348   81 TLPA 84
 
Name Accession Description Interval E-value
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 6.12e-100

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: 291.42  E-value: 6.12e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08479    81 LERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2532407933 255 GKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08479   161 GRLVRVLPDWQlPDADIWAVYPSRLSRSARVRVFVDFL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
5-298 1.35e-97

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 289.63  E-value: 1.35e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   5 PLLEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGE 84
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  85 AVAQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASN 164
Cdd:PRK09801   86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 165 QRVLCAAPAYLARRGTPDTLAQLREHDCIVIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRS 244
Cdd:PRK09801  166 KRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRS 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2532407933 245 AWDVESSLAQGKLVRILPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQAR 298
Cdd:PRK09801  246 EWDVLPFLESGKLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQR 299
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-291 3.68e-77

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: 233.49  E-value: 3.68e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIRERDQdGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGR-PLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2532407933 255 GKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08422   160 GRLVRVLPDWRpPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-297 5.43e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 5.43e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELL--DRPVD-LLGEGFDLDIRIGVVHEPDLIAHRIAS 163
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDaLLEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 164 NQRVLCAAPAYLARRGTPDTlaqlrehdcivirerdqdgrrwklqgpqgvetvkvdgplsaNNGEIVHQWALDGHGIILR 243
Cdd:COG0583   163 ERLVLVASPDHPLARRAPLV-----------------------------------------NSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2532407933 244 SAWDVESSLAQGKLVRI-LPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQA 297
Cdd:COG0583   202 PRFLAADELAAGRLVALpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 4.15e-53

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 172.03  E-value: 4.15e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIvIRERDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08477    81 LARHGTPTTPEDLARHECL-GFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2532407933 255 GKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08477   160 GRLVELLPDYLpPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 2.15e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 147.32  E-value: 2.15e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEP-DLIAHRIASNQRVLCAAPA 173
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 174 YLARRGTPDTLAQLREHDCIVIRERDQDGrRWKLQGPQGVET-VKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSL 252
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAYGRGGQPL-PWRLADEQGRLVrFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHL 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2532407933 253 AQGKLVRILPAY-QQAADVWAVTTSRLSNSAKVRACV 288
Cdd:cd08475   160 QRGELVEVLPELaPEGLPIHAVWPRTRHLPPKVRAAV 196
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-295 1.08e-42

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: 145.15  E-value: 1.08e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIrerDQDGRRWKLQGPQgvETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSLAQ 254
Cdd:cd08470    81 LERHGTPHSLADLDRHNCLLG---TSDHWRFQENGRE--RSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2532407933 255 GKLVRILPAYQQAAD-VWAVTTSRLSNSAKVRACVQFLEQWL 295
Cdd:cd08470   156 GRLVPVLEDYRPPDEgIWALYPHNRHLSPKVRLLVDYLADAL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-298 3.60e-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 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: 144.19  E-value: 3.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHdcIVIRERDQDGRR---WKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESS 251
Cdd:cd08472    81 LARHGTPRHPEDLERH--RAVGYFSARTGRvlpWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPH 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2532407933 252 LAQGKLVRILPAYQQAA-DVWAVTTSRLSNSAKVRAcvqFLEqWLQAR 298
Cdd:cd08472   159 LASGRLVEVLPDWRPPPlPVSLLYPHRRHLSPRVRV---FVD-WVAEL 202
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-291 2.09e-40

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: 139.52  E-value: 2.09e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  93 PQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLC-AA 171
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVvAS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 172 PAYLARRGTPDTLAQLREHDCIVIReRDQDGR--RWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVE 249
Cdd:cd08474    81 PAYLARHGTPEHPRDLLNHRCIRYR-FPTSGAlyRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2532407933 250 SSLAQGKLVRILPAYQ-QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08474   160 EHLASGRLVRVLEDWSpPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 6.77e-39

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 135.73  E-value: 6.77e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGvvHEPD--LIAHRIASNQRVLCAAP 172
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIG--HLPDssLVATRVGSVRRVVCASP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 173 AYLARRGTPDTLAQLREHDCIVIRERDQdGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSL 252
Cdd:cd08471    79 AYLARHGTPKHPDDLADHDCIAFTGLSP-APEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEEL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2532407933 253 AQGKLVRILPAYQQAA-DVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08471   158 AAGRLQRVLEDFEPPPlPVHLVHPEGRLAPAKVRAFVDFA 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-293 4.69e-37

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 133.58  E-value: 4.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:PRK14997    4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRI--GVVHEPDLIAHRIASN 164
Cdd:PRK14997   84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVLADR 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 165 QRVLCAAPAYLARRGTPDTLAQLREHDCIVIRErDQDGRRWKLQGPQGVET-VKVDGPLSANNGEIVHQWALDGHGIILR 243
Cdd:PRK14997  164 GHRLFASPDLIARMGIPSAPAELSHWPGLSLAS-GKHIHRWELYGPQGARAeVHFTPRMITTDMLALREAAMAGVGLVQL 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2532407933 244 SAWDVESSLAQGKLVRILPAYQQAADV-WAVTTSRLSNSAKVRACVQFLEQ 293
Cdd:PRK14997  243 PVLMVKEQLAAGELVAVLEEWEPRREViHAVFPSRRGLLPSVRALVDFLTE 293
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
7-294 4.11e-36

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 131.42  E-value: 4.11e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQR 166
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPM 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 167 VLCAAPAYLARRGTPDTLAQLREHDCIVIRER-DQDgrrWKLQGPQGVET-VKVDGPLSANNGEIVHQWALDGHGIILRS 244
Cdd:PRK10632  164 VVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRpDNE---FELIAPEGISTrLIPQGRFVTNDPQTLVRWLTAGAGIAYVP 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2532407933 245 AWDVESSLAQGKLVRILPAYQQAA-DVWAVTTSRLSNSAKVRACVQFLEQW 294
Cdd:PRK10632  241 LMWVIDEINRGELEILFPRYQSDPrPVYALYTEKDKLPLKVQVCINYLTDY 291
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 8.66e-34

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: 121.97  E-value: 8.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRnrLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08476     1 GRLRVSLPLVGGL--LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCIVIReRDQDGR--RWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSL 252
Cdd:cd08476    79 LARHGTPETPADLAEHACLRYR-FPTTGKlePWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2532407933 253 AQGKLVRILPAYQQAADV----WAvtTSRlSNSAKVRACVQFL 291
Cdd:cd08476   158 ADGRLVTVLDDYVEERGQfrllWP--SSR-HLSPKLRVFVDFM 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-291 1.43e-32

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: 119.20  E-value: 1.43e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  93 PQGVLRI-CSSSGFgRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRI--GVVHEPDLIAHRIASNQRVLC 169
Cdd:cd08473     1 PRGTVRVsCPPALA-QELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVrfPPLEDSSLVMRVLGQSRQRLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 170 AAPAYLARRGTPDTLAQLREHDCIVIRERDQDGrRWKLQGPQG-VETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDV 248
Cdd:cd08473    80 ASPALLARLGRPRSPEDLAGLPTLSLGDVDGRH-SWRLEGPDGeSITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2532407933 249 ESSLAQGKLVRILPAYQQAAD-VWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08473   159 REALRAGRLVRVLPDWTPPRGiVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 1.59e-32

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: 118.98  E-value: 1.59e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  95 GVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRGTPDTLAQLREHDCI---VIRERDQdgrrWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESS 251
Cdd:cd08480    81 LARHGTPLTPQDLARHNCLgfnFRRALPD----WPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADD 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2532407933 252 LAQGKLVRILPAYQ--QAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08480   157 IAAGRLVPVLEEYNpgDREPIHAVYVGGGRLPARVRAFLDFL 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-296 1.10e-31

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: 117.00  E-value: 1.10e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  94 QGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLD--RPVDLLGEG-FDLDIRIGVVHEPDLIAHRIASNQRVLCA 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 171 APAYLARRGTPDTLAQLREHDCIVIreRDQDGRRWKLQGPQGVETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVES 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILL--PPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2532407933 251 SLAQGKLVRI-LPAYQQAADVWAVTTSRLSNSAKVRACVQFLEQWLQ 296
Cdd:pfam03466 159 ELADGRLVALpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 93-291 9.00e-28

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: 106.27  E-value: 9.00e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  93 PQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAP 172
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 173 AYLARRGTPDTLAQLREHDCIVIRErDQDGRRWKLQGPQGvETVKVDGPLSANNGEIVHQWALDGHGIILRSAWDVESSL 252
Cdd:cd08478    81 DYLARHGTPQSIEDLAQHQLLGFTE-PASLNTWPIKDADG-NLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2532407933 253 AQGKLV-----RILPAYQqaaDVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd08478   159 AEGRLIplfaeQTSDVRQ---PINAVYYRNTALSLRIRCFIDFL 199
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-299 2.25e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 91.44  E-value: 2.25e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   5 PLLEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGeivRQWAQRILEDVEQMGE 84
Cdd:PRK11139    6 PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG---QRYFLDIREIFDQLAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  85 AVAQSK-LQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIAS 163
Cdd:PRK11139   83 ATRKLRaRSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLD 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 164 NQRVLCAAPAYLARRGTPDTLAQLREHDCIvireRDQDGRRWKLQGPQ-GVETVKVDGPLSANNGEIVHQWALDGHGIIL 242
Cdd:PRK11139  163 EYLLPVCSPALLNGGKPLKTPEDLARHTLL----HDDSREDWRAWFRAaGLDDLNVQQGPIFSHSSMALQAAIHGQGVAL 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2532407933 243 rsawdVESSLAQ-----GKLVRILP-AYQQAADVWAVTTSRLSNSAKVRAcvqfLEQWLQARA 299
Cdd:PRK11139  239 -----GNRVLAQpeieaGRLVCPFDtVLPSPNAFYLVCPDSQAELPKVAA----FRQWLLAEA 292
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 96-295 3.23e-21

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: 88.79  E-value: 3.23e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  96 VLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAYL 175
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 176 ARRGtPDTLAQLREHDCIVIRERDQDGRRWKLQgpQGVETVKVDGPLSANNGEIVHQWALDGHGI-ILRSAWdVESSLAQ 254
Cdd:cd08432    81 AGLP-LLSPADLARHTLLHDATRPEAWQWWLWA--AGVADVDARRGPRFDDSSLALQAAVAGLGVaLAPRAL-VADDLAA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2532407933 255 GKLVRILPAYQQAA-DVWAVTTSRLSNSAKVRAcvqfLEQWL 295
Cdd:cd08432   157 GRLVRPFDLPLPSGgAYYLVYPPGRAESPAVAA----FRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
1-191 2.60e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 80.43  E-value: 2.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   1 MKHTPL----LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVrQWA-QRI 75
Cdd:PRK10086    6 MRNRLLngwqLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV-FWAlKSS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  76 LEDVEQmgEAVAQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDlkIQLELLDRP--VDLLGEGFDLDIRIGVVHE 153
Cdd:PRK10086   85 LDTLNQ--EILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPS--ISLTILTGNenVNFQRAGIDLAIYFDDAPS 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2532407933 154 PDLIAHRIASNQRVLCAAPAYlARR----GTPDTLAQLRE-HD 191
Cdd:PRK10086  161 AQLTHHFLMDEEILPVCSPEY-AERhaltGNPDNLRHCTLlHD 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 2.09e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 2.09e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGE 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 5-187 1.13e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 64.21  E-value: 1.13e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   5 PLLEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGE 84
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  85 AVAQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELL--DRPVDLLGEGfDLDIRIGV--VHEPDLIAHR 160
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMsqERIEALLADD-ELDVGIAFapVHSPEIEAQP 159

                         170       180
                  ....*....|....*....|....*...
gi 2532407933 161 IASNQRVLCAAPAY-LARRGTPDTLAQL 187
Cdd:PRK11242  160 LFTETLALVVGRHHpLAARRKALTLDEL 187
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-146 2.94e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 62.86  E-value: 2.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQ---MG 83
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKaklRA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2532407933  84 EAVAQSKLQpqgvLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDL--LGEGfDLDI 146
Cdd:PRK09906   83 RKIVQEDRQ----LTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEekLRRG-ELDV 142
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-129 6.94e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 61.96  E-value: 6.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGrNRLGPALSQLARQ-YPDLKIQLE 129
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTG-TYLMPRLIGLFRQrYPQINVQLQ 129
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-198 9.77e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 61.24  E-value: 9.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGeivRQWAQRILEDVEQMGEaV 86
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHG---RLLYPRALALLEQAVE-I 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLElLDRPVDLLGEGFDLDIRIGVV----HEPDLIAHRIA 162
Cdd:PRK10837   81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELS-VGNSQDVINAVLDFRVDIGLIegpcHSPELISEPWL 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2532407933 163 SNQRVLCAAPAY-LARRgtPDTLAQLREHDCIvIRER 198
Cdd:PRK10837  160 EDELVVFAAPDSpLARG--PVTLEQLAAAPWI-LRER 193
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-291 2.55e-09

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: 56.07  E-value: 2.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  97 LRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRP--VDLLGEG-FDLDIRIGVVHEPDLIAHRIASNQRVLCAAPA 173
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSelLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 174 YLARRGTPDTLAQLREHDCIvIRERDQDGRRWKLQ--GPQGVETVKVdgpLSANNGEIVHQWALDGHGIILRSAWDVEsS 251
Cdd:cd05466    82 HPLAKRKSVTLADLADEPLI-LFERGSGLRRLLDRafAEAGFTPNIA---LEVDSLEAIKALVAAGLGIALLPESAVE-E 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2532407933 252 LAQGKLVRI-LPAYQQAADVWAVTTSRLSNSAKVRACVQFL 291
Cdd:cd05466   157 LADGGLVVLpLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-209 5.31e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.35  E-value: 5.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   8 EDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAVA 87
Cdd:PRK10094    5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  88 Q--SKLQPQgVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLElldRPV------DLLGEGFDLdiRIGVV-HEPdlIA 158
Cdd:PRK10094   85 QvnDGVERQ-VNIVINNLLYNPQAVAQLLAWLNERYPFTQFHIS---RQIymgvwdSLLYEGFSL--AIGVTgTEA--LA 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 159 HRIA-----SNQRVLCAAPAY-LARRGTPDTLAQLREHDCIVIRERDQD-GRR--WKLQG 209
Cdd:PRK10094  157 NTFSldplgSVQWRFVMAADHpLANVEEPLTEAQLRRFPAVNIEDSARTlTKRvaWRLPG 216
PRK09791 PRK09791
LysR family transcriptional regulator;
7-128 1.07e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2532407933  87 AQSKLQPQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQL 128
Cdd:PRK09791   87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PRK09986 PRK09986
LysR family transcriptional regulator;
7-195 3.29e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 53.57  E-value: 3.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLQPQG--VLRICSSSGFGRNRlgPALSQLARQYPDLKI---------QLELLDRPvdllgegfDLDI---RIGVVH 152
Cdd:PRK09986   89 EQIGRGEAGriEIGIVGTALWGRLR--PAMRHFLKENPNVEWllrelspsmQMAALERR--------ELDAgiwRMADLE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2532407933 153 -EPDLIAHRIASnQRVLCAAPA--YLARRGTPdTLAQLREHDCIVI 195
Cdd:PRK09986  159 pNPGFTSRRLHE-SAFAVAVPEehPLASRSSV-PLKALRNEYFITL 202
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 97-274 9.00e-07

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: 48.50  E-value: 9.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  97 LRICSSSGFGRNRLGPALSQLARQYPDlkIQLELL--DRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAY 174
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPE--IELSLLpsADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 175 LARRgTPDTLAQLREHDCivIRERDQ-DGRRWKLQgpQGVETVKVDGpLSANNGEIVHQWALDGHGIILRSAWDVESSLA 253
Cdd:cd08483    80 LGDR-KVDSLADLAGLPW--LQERGTnEQRVWLAS--MGVVPDLERG-VTFLPGQLVLEAARAGLGLSIQARALVEPDIA 153

                         170       180
                  ....*....|....*....|.
gi 2532407933 254 QGKLVRILPAYQQAADVWAVT 274
Cdd:cd08483   154 AGRLTVLFEEEEEGLGYHIVT 174
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 105-286 1.42e-06

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: 47.68  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 105 FGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRIASNQRVLCAAPAYLARRG--TPD 182
Cdd:cd08481    10 FGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRAlaAPA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 183 TLAQLrehDCIVIRERDQDGRRWKLQgpQGVEtvkVDGPLSANNGE---IVHQWALDGHGIILRSAWDVESSLAQGKLVR 259
Cdd:cd08481    90 DLAHL---PLLQQTTRPEAWRDWFEE--VGLE---VPTAYRGMRFEqfsMLAQAAVAGLGVALLPRFLIEEELARGRLVV 161

                         170       180
                  ....*....|....*....|....*...
gi 2532407933 260 ILPAYQQAADV-WAVTTSRLSNSAKVRA 286
Cdd:cd08481   162 PFNLPLTSDKAyYLVYPEDKAESPPVQA 189
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
36-128 1.44e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 48.82  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  36 VSKRIGMLEAALQVRLLHRTTRR-VSVTDHGEIVRQWAQRILEDVE---QMGEAVAQsklQPQGVLRICSSSGFGRNRLG 111
Cdd:PRK12684   33 VSKAIIELEDELGVEIFTRHGKRlRGLTEPGRIILASVERILQEVEnlkRVGKEFAA---QDQGNLTIATTHTQARYALP 109

                          90
                  ....*....|....*..
gi 2532407933 112 PALSQLARQYPDLKIQL 128
Cdd:PRK12684  110 AAIKEFKKRYPKVRLSI 126
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-123 1.67e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 45.66  E-value: 1.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   1 MKhtplLEDLRLFCQVA-HKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVS-VTDHGEIVRQWAQRILED 78
Cdd:PRK12681    1 MK----LQQLRYIVEVVnHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSK 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2532407933  79 VEQMgEAVAQSKLQP-QGVLRICSSSGFGRNRLGPALSQLARQYPD 123
Cdd:PRK12681   77 VESI-KSVAGEHTWPdKGSLYIATTHTQARYALPPVIKGFIERYPR 121
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-93 5.03e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.19  E-value: 5.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  10 LRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRtTRRVSVTDHGEIVRQWAQRIledveQMGEAVAQS 89
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-----ALLEADLLS 80


                  ....
gi 2532407933  90 KLQP 93
Cdd:PRK13348   81 TLPA 84
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-129 6.16e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 43.65  E-value: 6.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  31 ISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAVAQSKLQPQGVLRI-CS---SSGFg 106
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfCSvtaAYSH- 81

                          90       100
                  ....*....|....*....|...
gi 2532407933 107 rnrLGPALSQLARQYPDLKIQLE 129
Cdd:PRK11716   82 ---LPPILDRFRAEHPLVEIKLT 101
PRK10341 PRK10341
transcriptional regulator TdcA;
5-82 6.46e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 43.70  E-value: 6.46e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2532407933   5 PLLEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQM 82
Cdd:PRK10341    7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNM 84
PRK12680 PRK12680
LysR family transcriptional regulator;
36-148 8.39e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 43.46  E-value: 8.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  36 VSKRIGMLEAALQVRLLHRTTRRV-SVTDHGEIVRQWAQRILEDVEQMGEAVAQSKLQPQGVLRICSSSGFGRNRLGPAL 114
Cdd:PRK12680   33 LSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAV 112

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2532407933 115 SQLARQYPDLKIQLELLDRP--VDLLGEGfDLDIRI 148
Cdd:PRK12680  113 AQIKQAYPQVSVHLQQAAESaaLDLLGQG-DADIAI 147
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-128 1.04e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.13  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQmgeav 86
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ----- 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2532407933  87 AQSKLQPQG-VLRICSSSGFGRnrlGPALSQLA--------RQYPDLKIQL 128
Cdd:PRK11233   78 AQLAVHNVGqALSGQVSIGLAP---GTAASSLTmpllqavrAEFPGIVLYL 125
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 97-204 2.15e-04

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 41.39  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  97 LRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRP--VDLLGEG-FDLDIRIGVVHEPDLIAHRIASNQRVlCAAPA 173
Cdd:cd08415     2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSStvVEAVLSGqADLGLASLPLDHPGLESEPLASGRAV-CVLPP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2532407933 174 --YLARRGTPdTLAQLREHDCIVIRERDQDGRR 204
Cdd:cd08415    81 ghPLARKDVV-TPADLAGEPLISLGRGDPLRQR 112
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-258 6.37e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 40.77  E-value: 6.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   1 MKHTPLLEDLRlfcqvaHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVE 80
Cdd:PRK15421    4 VKHLKTLQALR------NCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  81 QMGEAVAQSKlqpQGVLRICSSSGFGRNRLGPALSQLARQYP-----------------------DLKIQLELLDRPVDL 137
Cdd:PRK15421   78 QALQACNEPQ---QTRLRIAIECHSCIQWLTPALENFHKNWPqvemdfksgvtfdpqpalqqgelDLVMTSDILPRSGLH 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 138 LGEGFDLDIRIgvVHEPDliaHRIASNQRVlcaapaylarrgTPDTLAQlrEHDCIVIRERDQ-DGRRWKLQgPQGVE-T 215
Cdd:PRK15421  155 YSPMFDYEVRL--VLAPD---HPLAAKTRI------------TPEDLAS--ETLLIYPVQRSRlDVWRHFLQ-PAGVSpS 214

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 2532407933 216 VKvdgplSANNGEIVHQWALDGHGIILRSAWDVESSLAQGKLV 258
Cdd:PRK15421  215 LK-----SVDNTLLLIQMVAARMGIAALPHWVVESFERQGLVV 252
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 97-260 1.21e-03

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 39.40  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  97 LRICSSSGFGRNRLGPALSQLARQYPDLKIQL------ELLDRPVDllgegFDLDIRI--GVVHEPDLIAHRIASNQRVL 168
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLtignteEIAERVLD-----GEIDLGLveGPVDHPDLIVEPFAEDELVL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 169 CAAPAY-LARRGTPdTLAQLREHDcIVIRE-----RDQDGRRWKLQGPQGvETVKVdgPLSANNGEIVHQWALDGHGIIL 242
Cdd:cd08420    77 VVPPDHpLAGRKEV-TAEELAAEP-WILREpgsgtREVFERALAEAGLDG-LDLNI--VMELGSTEAIKEAVEAGLGISI 151

                         170
                  ....*....|....*...
gi 2532407933 243 RSAWDVESSLAQGKLVRI 260
Cdd:cd08420   152 LSRLAVRKELELGRLVAL 169
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-128 1.29e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.59  E-value: 1.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  25 TALELGISKAVVSKRIGMLEAALQVRLLHRTTRRV-SVTDHGEIVRQWAQRILEDVEQMGEAVAQSKLQPQGVLRICSSS 103
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTH 101

                          90       100
                  ....*....|....*....|....*
gi 2532407933 104 GFGRNRLGPALSQLARQYPDLKIQL 128
Cdd:PRK12682  102 TQARYVLPRVVAAFRKRYPKVNLSL 126
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 31-128 2.36e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 38.86  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  31 ISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAVAQSKLQPQGVLRIcsssGFGRNrL 110
Cdd:PRK11151   27 VSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGPLHI----GLIPT-V 101

                          90       100
                  ....*....|....*....|...
gi 2532407933 111 GPALS-----QLARQYPDLKIQL 128
Cdd:PRK11151  102 GPYLLphiipMLHQTFPKLEMYL 124
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 112-155 2.91e-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: 2.91e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2532407933 112 PALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPD 155
Cdd:cd08482    17 PRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPA 60
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 96-194 4.20e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 37.49  E-value: 4.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  96 VLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELL--DRPVDLLGEGfDLDirIGVVHEPDL---IAHRIASNQRVLCA 170
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMttAEQLEALRAG-RLD--VGFVRPPPDppgLASRPLLREPLVVA 77

                          90       100
                  ....*....|....*....|....*.
gi 2532407933 171 APA--YLARRGTPDtLAQLREHDCIV 194
Cdd:cd08414    78 LPAdhPLAARESVS-LADLADEPFVL 102
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-207 6.39e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 37.70  E-value: 6.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933   7 LEDLRLFCQVAHKTSFAGTALELGISKAVVSKRIGMLEAALQVRLLHRTTRRVSVTDHGEIVRQWAQRILEDVEQMGEAV 86
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  87 AQSKLqpQGVLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRP--VDLLGEG-FDLDIrigVVHEPDLIAHRIAS 163
Cdd:PRK15092   93 MYSNL--QGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAfmMEMLESQeVDLAV---TTHRPSSFPALNLR 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2532407933 164 NQRVL--CAApAYLARRGTPDTLAQLRE---HDCIVIRERDQDGRRWKL 207
Cdd:PRK15092  168 TSPTLwyCAA-EYVLQKGEPIPLVLLDEpspFRDMALATLNAAGIPWRI 215
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 96-295 7.63e-03

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 36.74  E-value: 7.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933  96 VLRICSSSGFGRNRLGPALSQLARQYPDLKIQLELLDRPVDLLGEGFDLDIRIGVVHEPDLIAHRiasnqrvLCAAPayL 175
Cdd:cd08488     1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATR-------LFEAP--L 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2532407933 176 ARRGTPDTLAQLRE----HDCIVIRERDQDgrRWklqgPQGVETVKVDGPLSANNGEI------VHQWALDGHGIILRSA 245
Cdd:cd08488    72 SPLCTPELARQLREpadlARHTLLRSYRAD--EW----PQWFEAAGVGHPCGLPNSIMfdsslgMMEAALQGLGVALAPP 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2532407933 246 WDVESSLAQGKLVRILPAYQQAADVWAVttsRLSNSAKVRACVQFlEQWL 295
Cdd:cd08488   146 SMFSRQLASGALVQPFATTLSTGSYWLT---RLQSRPETPAMSAF-SAWL 191
 
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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