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Conserved domains on  [gi|15597613|ref|NP_251107|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK14997 super family cl33055
LysR family transcriptional regulator; Provisional
8-305 3.14e-107

LysR family transcriptional regulator; Provisional


The actual alignment was detected with superfamily member PRK14997:

Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 314.24  E-value: 3.14e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    8 DLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDV 87
Cdd:PRK14997   3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   88 IEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDSDLVMKVLAR 167
Cdd:PRK14997  83 IAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSDLVMRVLAD 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  168 SPQVLVASPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGL 247
Cdd:PRK14997 163 RGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQL 242
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597613  248 PLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFADAAQ 305
Cdd:PRK14997 243 PVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYARMVE 300
 
Name Accession Description Interval E-value
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
8-305 3.14e-107

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 314.24  E-value: 3.14e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    8 DLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDV 87
Cdd:PRK14997   3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   88 IEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDSDLVMKVLAR 167
Cdd:PRK14997  83 IAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSDLVMRVLAD 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  168 SPQVLVASPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGL 247
Cdd:PRK14997 163 RGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQL 242
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597613  248 PLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFADAAQ 305
Cdd:PRK14997 243 PVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYARMVE 300
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-296 8.47e-102

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: 296.77  E-value: 8.47e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  95 PCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDSDLVMKVLARSPQVLVA 174
Cdd:cd08473   1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDSSLVMRVLGQSRQRLVA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 175 SPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSR 254
Cdd:cd08473  81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597613 255 DLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08473 161 ALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-302 6.37e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.89  E-value: 6.37e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   7 FDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAED 86
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  87 VIEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFN--RRVDVIAEGyDISLSLRFPPLEDSDLVMKV 164
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDALLEG-ELDLAIRLGPPPDPGLVARP 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 165 LARSPQVLVASPEL-LARYRPpelpadlsampyvgwersrldgslrlvgadgssaalnlrpqlLSDDLGTLRQAVLEGVG 243
Cdd:COG0583 160 LGEERLVLVASPDHpLARRAP------------------------------------------LVNSLEALLAAVAAGLG 197
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15597613 244 IGGLPLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFAD 302
Cdd:COG0583 198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
97-301 5.61e-30

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: 112.77  E-value: 5.61e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGyDISLSLRFPPLEDSDLVMKVLARSPQVLVA 174
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEG-ELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   175 SPEL-LARYRPPElPADLSAMPYVGWERSRldGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVS 253
Cdd:pfam03466  81 PPDHpLARGEPVS-LEDLADEPLILLPPGS--GLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 15597613   254 RDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFA 301
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
8-305 3.14e-107

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 314.24  E-value: 3.14e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    8 DLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDV 87
Cdd:PRK14997   3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   88 IEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDSDLVMKVLAR 167
Cdd:PRK14997  83 IAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSDLVMRVLAD 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  168 SPQVLVASPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGL 247
Cdd:PRK14997 163 RGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQL 242
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597613  248 PLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFADAAQ 305
Cdd:PRK14997 243 PVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYARMVE 300
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-296 8.47e-102

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: 296.77  E-value: 8.47e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  95 PCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDSDLVMKVLARSPQVLVA 174
Cdd:cd08473   1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDSSLVMRVLGQSRQRLVA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 175 SPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSR 254
Cdd:cd08473  81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15597613 255 DLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08473 161 ALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
97-296 2.80e-61

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: 193.43  E-value: 2.80e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFD--LAIRIGELPDSSLVARRLGPVRRVLVASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSsAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDL 256
Cdd:cd08422  79 AYLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGE-VEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15597613 257 AERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08422 158 ASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-302 6.37e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.89  E-value: 6.37e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   7 FDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAED 86
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  87 VIEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFN--RRVDVIAEGyDISLSLRFPPLEDSDLVMKV 164
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDALLEG-ELDLAIRLGPPPDPGLVARP 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 165 LARSPQVLVASPEL-LARYRPpelpadlsampyvgwersrldgslrlvgadgssaalnlrpqlLSDDLGTLRQAVLEGVG 243
Cdd:COG0583 160 LGEERLVLVASPDHpLARRAP------------------------------------------LVNSLEALLAAVAAGLG 197
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15597613 244 IGGLPLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFAD 302
Cdd:COG0583 198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-296 5.98e-38

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: 133.51  E-value: 5.98e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08477   1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFD--AAFRIGELADSSLVARPLAPYRMVLCASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSSAALnLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDL 256
Cdd:cd08477  79 DYLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVP-VSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15597613 257 AERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08477 158 ASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-305 1.88e-36

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 132.58  E-value: 1.88e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    9 LNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVI 88
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   89 EQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDIslSLRFPPLEDSDLVMKVLARS 168
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDV--VIRVGALQDSSLFSRRLGAM 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  169 PQVLVASPELLARYRPPELPADLSAMPYVGWErSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLP 248
Cdd:PRK10632 162 PMVVCAAKSYLAQYGTPEKPADLSSHSWLEYS-VRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVP 240
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15597613  249 LCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFADAAQ 305
Cdd:PRK10632 241 LMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFVEVAK 297
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
100-296 4.81e-35

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: 125.82  E-value: 4.81e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 100 RLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLslRFPPLEDSDLVMKVLARSPQVLVASPELL 179
Cdd:cd08476   2 RLRVSLPLVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVI--RTGELPDSRLMSRRLGSFRMVLVASPDYL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 180 ARYRPPELPADLSAMPYVgweRSRLDGSLRL----VGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRD 255
Cdd:cd08476  80 ARHGTPETPADLAEHACL---RYRFPTTGKLepwpLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREA 156
                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15597613 256 LAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08476 157 LADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-299 1.57e-34

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: 124.34  E-value: 1.57e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08470   1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFD--LAIRLGRLTDSSLMARRLASRRHYVCASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAM-----PYVGWeRSRLDGSLRLVGADG----SSAAlnlrpqllsddlgTLRQAVLEGVGIGGL 247
Cdd:cd08470  79 AYLERHGTPHSLADLDRHncllgTSDHW-RFQENGRERSVRVQGrwrcNSGV-------------ALLDAALKGMGLAQL 144
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15597613 248 PLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAG 299
Cdd:cd08470 145 PDYYVDEHLAAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-296 4.40e-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 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: 123.48  E-value: 4.40e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLslRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08479   1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDI--RVGDLPDSSLIARKLAPNRRILCASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMP-YVGWERSRLDGSLRLVGADGSsAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRD 255
Cdd:cd08479  79 AYLERHGAPASPEDLARHDcLVIRENDEDFGLWRLRNGDGE-ATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPY 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15597613 256 LAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08479 158 LRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
112-296 4.21e-33

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 120.74  E-value: 4.21e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVkTFN-RRVDVIAEGYDisLSLRFPPLEDS-DLVMKVLARSPQVLVASPELLARYRPPELPA 189
Cdd:cd08475  16 VAPLLLELARRHPELELEL-SFSdRFVDLIEEGID--LAVRIGELADStGLVARRLGTQRMVLCASPAYLARHGTPRTLE 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 190 DLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVRVLPEWT 269
Cdd:cd08475  93 DLAEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELA 172
                       170       180
                ....*....|....*....|....*..
gi 15597613 270 PVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08475 173 PEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-296 1.27e-31

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 116.79  E-value: 1.27e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  95 PCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLslRFPPLEDSDLV-MKVLARSPQVLV 173
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGI--RLGESVEKDMVaVPLGPPLRMAVV 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 174 ASPELLARYRPPELPADLSAMPYVGWeRSRLDGSL------RlvgaDGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGL 247
Cdd:cd08474  79 ASPAYLARHGTPEHPRDLLNHRCIRY-RFPTSGALyrwefeR----GGRELEVDVEGPLILNDSDLMLDAALDGLGIAYL 153
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 15597613 248 PLCVVSRDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08474 154 FEDLVAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-298 1.48e-30

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 114.15  E-value: 1.48e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08472   1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVD--CVIRVGELADSSLVARRLGELRMVTCASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMPYVGW--ERSRLDGSLRLVgADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSR 254
Cdd:cd08472  79 AYLARHGTPRHPEDLERHRAVGYfsARTGRVLPWEFQ-RDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRP 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597613 255 DLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAA 298
Cdd:cd08472 158 HLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
97-301 5.61e-30

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: 112.77  E-value: 5.61e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGyDISLSLRFPPLEDSDLVMKVLARSPQVLVA 174
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEG-ELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   175 SPEL-LARYRPPElPADLSAMPYVGWERSRldGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVS 253
Cdd:pfam03466  81 PPDHpLARGEPVS-LEDLADEPLILLPPGS--GLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 15597613   254 RDLAERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGFA 301
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09801 PRK09801
LysR family transcriptional regulator;
12-311 1.22e-28

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 112.05  E-value: 1.22e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   12 LFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVIEQN 91
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   92 RSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEgyDISLSLRFPPLEDSDLVMKVLARSPQV 171
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQD--NIDLDIRINDEIPDYYIAHLLTKNKRI 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  172 LVASPELLARYRPPELPADLSAMP-YVGWERSRLDGSLRLvGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLC 250
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDcLVTKERDMTHGIWEL-GNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEW 247
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597613  251 VVSRDLAERRLVRVLPEWTPVEGM-VVAMFPSRRGLlpSVRALIDFLAAGfadaAQRQYPEP 311
Cdd:PRK09801 248 DVLPFLESGKLVQVLPEYAQSANIwAVYREPLYRSM--KLRVCVEFLAAW----CQQRLGKP 303
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-296 1.21e-25

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: 101.26  E-value: 1.21e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  97 GMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLslRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd08480   1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAI--RVGPLPDSSLVARKLGESRRVIVASP 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMPYVGW--ERSRLDGSLRlvgADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSR 254
Cdd:cd08480  79 SYLARHGTPLTPQDLARHNCLGFnfRRALPDWPFR---DGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVAD 155
                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15597613 255 DLAERRLVRVLPEWTPVEGMVV-AMFPSRRGLLPSVRALIDFL 296
Cdd:cd08480 156 DIAAGRLVPVLEEYNPGDREPIhAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
95-296 1.41e-25

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: 100.88  E-value: 1.41e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  95 PCGMVRLTCSTP-LLHFeLAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLslRFPPLEDSDLVMKVLARSPQVLV 173
Cdd:cd08478   1 PSGLLRVDAATPfVLHL-LAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAI--RIGELTDSTLHARPLGKSRLRIL 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 174 ASPELLARYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGSsaALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVS 253
Cdd:cd08478  78 ASPDYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGN--LLKIQPTITASSGETLRQLALSGCGIACLSDFMTD 155
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597613 254 RDLAERRLVRVLPEWT-PVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08478 156 KDIAEGRLIPLFAEQTsDVRQPINAVYYRNTALSLRIRCFIDFL 199
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
100-300 8.74e-21

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: 87.97  E-value: 8.74e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 100 RLTCSTPLL--HFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASPE 177
Cdd:cd08471   2 LLTVTAPVLfgRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVD--VAVRIGHLPDSSLVATRVGSVRRVVCASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 178 LLARYRPPELPADLSAMPYVGWERSRLDGSLRLvGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLA 257
Cdd:cd08471  80 YLARHGTPKHPDDLADHDCIAFTGLSPAPEWRF-REGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158
                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15597613 258 ERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFLAAGF 300
Cdd:cd08471 159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
112-296 3.92e-18

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 80.70  E-value: 3.92e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDIslSLRFPPLEDSDLVMKVLARSPQVLVASPELLARYRPPElPADL 191
Cdd:cd08432  15 LIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDL--AIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLS-PADL 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 192 SAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLlsDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVRVLPEWTPV 271
Cdd:cd08432  92 ARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRF--DDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPS 169
                       170       180
                ....*....|....*....|....*
gi 15597613 272 EGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08432 170 GGAYYLVYPPGRAESPAVAAFRDWL 194
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
99-296 3.07e-17

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: 78.41  E-value: 3.07e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  99 VRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGyDISLSLRFPPLEDSDLVMKVLARSPQVLVASP 176
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSelLEALLEG-ELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 177 ELLARYRPPELPADLSAMPYVGweRSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVsRDL 256
Cdd:cd05466  81 DHPLAKRKSVTLADLADEPLIL--FERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAV-EEL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15597613 257 AERRLVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd05466 158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
9-267 5.59e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.81  E-value: 5.59e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    9 LNALfiyaKVVE----HGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHC-VAMTVEAEA 83
Cdd:PRK11139   8 LNAL----RAFEaaarHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIrEIFDQLAEA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   84 AEDVIEQNRSEpcgmvRLTCSTP---LLHFeLAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDIslSLRFPPLEDSDL 160
Cdd:PRK11139  84 TRKLRARSAKG-----ALTVSLLpsfAIQW-LVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDV--AIRYGRGNWPGL 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  161 VMKVLARSPQVLVASPELLARYRPPELPADLSAMPYVgwersRLDGS------LRLVGADGssaaLNLRPQLLSDDLGTL 234
Cdd:PRK11139 156 RVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLL-----HDDSRedwrawFRAAGLDD----LNVQQGPIFSHSSMA 226
                        250       260       270
                 ....*....|....*....|....*....|...
gi 15597613  235 RQAVLEGVGIGGLPLCVVSRDLAERRLVRVLPE 267
Cdd:PRK11139 227 LQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDT 259
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 3.05e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.95  E-value: 3.05e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613     9 LNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQ 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
18-197 1.56e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 66.90  E-value: 1.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   18 VVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAE----DVIEQNRs 93
Cdd:PRK11242  12 VAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRraihDVADLSR- 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   94 epcGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNR----------RVDViAEGYDISLSlrfPPLEDSDLVMK 163
Cdd:PRK11242  91 ---GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQeriealladdELDV-GIAFAPVHS---PEIEAQPLFTE 163
                        170       180       190
                 ....*....|....*....|....*....|....
gi 15597613  164 VLArspqVLVASPELLARYRPPELPADLSAMPYV 197
Cdd:PRK11242 164 TLA----LVVGRHHPLAARRKALTLDELADEPLV 193
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
16-267 4.76e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 65.38  E-value: 4.76e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   16 AKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRsTRQFQVTEIGQAYYRHCVAMTV-EAeaaeDVIEQNRSE 94
Cdd:PRK13348  11 AAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALlEA----DLLSTLPAE 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   95 PCGMVRL-------TCSTPLLhfelaPMLARFMAQyPNVELyvktfnrrvDVIAEGYDISLSLrfppLEDSDlVMKVLAR 167
Cdd:PRK13348  86 RGSPPTLaiavnadSLATWFL-----PALAAVLAG-ERILL---------ELIVDDQDHTFAL----LERGE-VVGCVST 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  168 SPQ---------------VLVASPELLARYRPPEL-PADLSAMPYVGWER--SRLDGSLRLVGADGSSaalNLRPQLLSD 229
Cdd:PRK13348 146 QPKpmrgclaeplgtmryRCVASPAFAARYFAQGLtRHSALKAPAVAFNRkdTLQDSFLEQLFGLPVG---AYPRHYVPS 222
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 15597613  230 DLGTLRqAVLEGVGIGGLPLCVVSRDLAERRLVRVLPE 267
Cdd:PRK13348 223 THAHLA-AIRHGLGYGMVPELLIGPLLAAGRLVDLAPG 259
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-182 1.75e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.87  E-value: 1.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    7 FDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYrHCVAMTVEAEAAEd 86
Cdd:PRK10086  14 WQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF-WALKSSLDTLNQE- 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   87 VIEQNRSEPCGmvRLTCSTP--LLHFELAPMLARFMAQYPNVELYVKTFNRRVDViaEGYDISLSLRFPPLEDSDLVMKV 164
Cdd:PRK10086  92 ILDIKNQELSG--TLTVYSRpsIAQCWLVPRLADFTRRYPSISLTILTGNENVNF--QRAGIDLAIYFDDAPSAQLTHHF 167
                        170
                 ....*....|....*...
gi 15597613  165 LARSPQVLVASPELLARY 182
Cdd:PRK10086 168 LMDEEILPVCSPEYAERH 185
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
112-296 1.70e-10

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: 59.43  E-value: 1.70e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGyDISLSLRFPPLEDSDLVMKVLARSPQVLVASPEL-LARyRPPELP 188
Cdd:cd08420  15 LPRLLARFRKRYPEVRVSLTIGNTEeiAERVLDG-EIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHpLAG-RKEVTA 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 189 ADLSAMPYVGWE-----RSRLDGSLRLVGADGssaaLNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVR 263
Cdd:cd08420  93 EELAAEPWILREpgsgtREVFERALAEAGLDG----LDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVA 168
                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15597613 264 VlpewtPVEGMVVAM-----FPSRRGLLPSVRALIDFL 296
Cdd:cd08420 169 L-----PVEGLRLTRpfsliYHKDKYLSPAAEAFLEFL 201
PRK09791 PRK09791
LysR family transcriptional regulator;
9-130 2.39e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.46  E-value: 2.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    9 LNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVI 88
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 15597613   89 EQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYV 130
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
112-296 5.24e-09

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: 54.99  E-value: 5.24e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRF----PPLEDSDLVMkvlaRSPQVLVASPELLARyRPPEL 187
Cdd:cd08481  15 LIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFD--AAIHFgdpvWPGAESEYLM----DEEVVPVCSPALLAG-RALAA 87
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 188 PADLSAMPYV-------GWERsrldgSLRLVGADGSSAALNLRPQLLSddlgTLRQAVLEGVGIGGLPLCVVSRDLAERR 260
Cdd:cd08481  88 PADLAHLPLLqqttrpeAWRD-----WFEEVGLEVPTAYRGMRFEQFS----MLAQAAVAGLGVALLPRFLIEEELARGR 158
                       170       180       190
                ....*....|....*....|....*....|....*.
gi 15597613 261 LVRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08481 159 LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
9-264 6.62e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 6.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    9 LNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTveaEAAEDvI 88
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL---EQAVE-I 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   89 EQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRvDVIAEGYD--ISLSLRFPPLEDSDLVMKVLA 166
Cdd:PRK10837  81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQ-DVINAVLDfrVDIGLIEGPCHSPELISEPWL 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  167 RSPQVLVASPELLARYRPPELpADLSAMPYVGWERsrldGSlrlvgadGSSAALN--LRPQL----LSDDLG---TLRQA 237
Cdd:PRK10837 160 EDELVVFAAPDSPLARGPVTL-EQLAAAPWILRER----GS-------GTREIVDylLLSHLprfeLAMELGnseAIKHA 227
                        250       260
                 ....*....|....*....|....*..
gi 15597613  238 VLEGVGIGGLPLCVVSRDLAERRLVRV 264
Cdd:PRK10837 228 VRHGLGISCLSRRVIADQLQAGTLVEV 254
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-267 1.50e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.78  E-value: 1.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    7 FDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRsTRQFQVTEIGQAYYRHC--VAMtVEAEAA 84
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHArqVRL-LEAELL 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   85 EDVieqnRSEPCGMVRLTC-------STPLLhfelaPMLARFMAQYPnVELyvktfnrrvDVIAEGYDISLSLrfppLED 157
Cdd:PRK03635  80 GEL----PALDGTPLTLSIavnadslATWFL-----PALAPVLARSG-VLL---------DLVVEDQDHTAEL----LRR 136
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  158 SDlVMKVLARSPQ---------------VLVASPELLARYRPPEL-PADLSAMPYVGWerSRLDGS-----LRLVGADGS 216
Cdd:PRK03635 137 GE-VVGAVTTEPQpvqgcrvdplgamryLAVASPAFAARYFPDGVtAEALAKAPAVVF--NRKDDLqdrflRQAFGLPPG 213
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 15597613  217 SAALNLRPQllSDDLGtlrQAVLEGVGIGGLPLCVVSRDLAERRLVRVLPE 267
Cdd:PRK03635 214 SVPCHYVPS--SEAFV---RAALAGLGWGMIPELQIEPELASGELVDLTPG 259
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
112-263 3.29e-08

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 52.76  E-value: 3.29e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFP----PLEDSdlvmKVLARSPQVLVASPELLARYRPpel 187
Cdd:cd08484  15 LLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLD--FAIRFGegawPGTDA----TRLFEAPLSPLCTPELARRLSE--- 85
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597613 188 PADLSAMPYVgweRS-RLDGSLRLVGADGSSAALNLRPqlLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVR 263
Cdd:cd08484  86 PADLANETLL---RSyRADEWPQWFEAAGVPPPPINGP--VFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQ 157
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
112-266 1.45e-07

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: 50.99  E-value: 1.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASPELLARYRPpelPADL 191
Cdd:cd08488  15 LLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLD--YAIRFGSGAWHGIDATRLFEAPLSPLCTPELARQLRE---PADL 89
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597613 192 SAMPYVgweRS-RLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVRVLP 266
Cdd:cd08488  90 ARHTLL---RSyRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPFA 162
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
115-296 4.42e-07

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 49.43  E-value: 4.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 115 MLARFMAQYPNVELYVKTFNRR--VDVIAEG-YDISLSLRfPPlEDSDLVMKVLARSPQVLVASPE--LLARYRPPelPA 189
Cdd:cd08419  17 LLGAFCRRHPGVEVSLRVGNREqvLERLADNeDDLAIMGR-PP-EDLDLVAEPFLDNPLVVIAPPDhpLAGQKRIP--LE 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 190 DLSAMPYVGWERsrldGSlrlvgadGSSAA---------LNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERR 260
Cdd:cd08419  93 RLAREPFLLREP----GS-------GTRLAmerffaehgVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELATGR 161
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 15597613 261 LVrVLpewtPVEGmvvamFP--------SRRG--LLPSVRALIDFL 296
Cdd:cd08419 162 LA-VL----DVEG-----FPirrqwyvvHRKGkrLSPAAQAFLDFL 197
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-128 8.55e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 8.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   36 STISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVIEQNRSEPCGMVRLTCSTPLLHFELAPM 115
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPI 85
                         90
                 ....*....|...
gi 15597613  116 LARFMAQYPNVEL 128
Cdd:PRK11716  86 LDRFRAEHPLVEI 98
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
112-262 1.45e-06

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: 47.72  E-value: 1.45e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASPELLaRYRPPELPADL 191
Cdd:cd08483  15 LMPRLGSFWAKHPEIELSLLPSADLVDLRPDGID--VAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL-GDRKVDSLADL 91
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597613 192 SAMPyvgWERSRLDGSLRLVGAD-GSSAALNLRPQLLSDDLgtLRQAVLEGVGIGGLPLCVVSRDLAERRLV 262
Cdd:cd08483  92 AGLP---WLQERGTNEQRVWLASmGVVPDLERGVTFLPGQL--VLEAARAGLGLSIQARALVEPDIAAGRLT 158
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
112-263 2.28e-06

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 47.15  E-value: 2.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDisLSLRFPPLEDSDLVMKVLARSPQVLVASPELLaryRPPELPADL 191
Cdd:cd08487  15 LLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLD--FAIRFGEGLWPATHNERLLDAPLSVLCSPEIA---KRLSHPADL 89
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597613 192 SAMPYVgweRS-RLDGSLRLVGADGSSAALNLRPQLLSDDLgtLRQAVLEGVGIGGLPLCVVSRDLAERRLVR 263
Cdd:cd08487  90 INETLL---RSyRTDEWLQWFEAANMPPIKIRGPVFDSSRL--MVEAAMQGAGVALAPAKMFSREIENGQLVQ 157
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
15-248 7.30e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.60  E-value: 7.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   15 YAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVIEQNRSE 94
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQA 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   95 PCGMVRLTCSTPLLHFELA-PMLARFMAQYPNVELYV----------KTFNRRVD--VIAEGYDISlSLRFPPLEDSDLV 161
Cdd:PRK11233  89 LSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLhensgatlneKLMNGQLDmaVIYEHSPVA-GLSSQPLLKEDLF 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  162 MkVLARS------PQVLVASPELLaryrppeLPADLSAMpyvgweRSRLDGSLRLVGadgssaalnLRPQLLS--DDLGT 233
Cdd:PRK11233 168 L-VGTQDcpgqsvDLAAVAQMNLF-------LPRDYSAV------RLRVDEAFSLRR---------LTAKVIGeiESIAT 224
                        250
                 ....*....|....*
gi 15597613  234 LRQAVLEGVGIGGLP 248
Cdd:PRK11233 225 LTAAIASGMGVTVLP 239
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
99-296 1.34e-05

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 45.21  E-value: 1.34e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  99 VRLTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGY-DISLSLRFPPLEdsDLVMKVLARSPQVLVAS 175
Cdd:cd08421   2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSAdiVRAVAEGRaDLGIVAGNVDAA--GLETRPYRTDRLVVVVP 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 176 PE-LLARYRPPELpADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDlgTLRQAVLEGVGIGGLPLCVVSR 254
Cdd:cd08421  80 RDhPLAGRASVAF-ADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFD--AVCRMVAAGLGIGIVPESAARR 156
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597613 255 DLAERRLVRV-LPE-WTPVEGMVVAMfpSRRGLLPSVRALIDFL 296
Cdd:cd08421 157 YARALGLRVVpLDDaWARRRLLLCVR--SFDALPPAARALVDHL 198
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
99-296 1.43e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 44.99  E-value: 1.43e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  99 VRLTCSTPLLHFELAPMLARFMAQYPNV--ELYVKTFNRRVDVIAEG-YDISLSLRFPPLEDsdlvMKVLARSP---QVL 172
Cdd:cd08426   2 VRVATGEGLAAELLPSLIARFRQRYPGVffTVDVASTADVLEAVLSGeADIGLAFSPPPEPG----IRVHSRQPapiGAV 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 173 VASPELLARYRPPELpADLSAMPYVGWERSRldgSLR-LVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCV 251
Cdd:cd08426  78 VPPGHPLARQPSVTL-AQLAGYPLALPPPSF---SLRqILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELA 153
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 15597613 252 VSRDLAERRLVRV-----LPEWTPVEGMVVAmfpsRRGLLPSVRALIDFL 296
Cdd:cd08426 154 VRREIRRGQLVAVpladpHMNHRQLELQTRA----GRQLPAAASAFLQLL 199
PRK12680 PRK12680
LysR family transcriptional regulator;
38-297 3.33e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.00  E-value: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   38 ISRKVAQLEARLGVRLVQRSTRQFQ-VTEIGQAYYRHCVAMTVEAEAAEDVIEQNRSEPCGMVRLTCSTPLLHFELAPML 116
Cdd:PRK12680  33 LSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAV 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  117 ARFMAQYPNVELYVKTFNRR--VDVIAEGydislslrfppleDSDL-VMKVLARSPQVLVASPelLARYR---------- 183
Cdd:PRK12680 113 AQIKQAYPQVSVHLQQAAESaaLDLLGQG-------------DADIaIVSTAGGEPSAGIAVP--LYRWRrlvvvprgha 177
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  184 ------PPELPAdLSAMPYVGWERS-RLDGSLRLvgadgSSAALNLRPQ--LLSDDLGTLRQAVLEGVGIGGLPLCVVSr 254
Cdd:PRK12680 178 ldtprrAPDMAA-LAEHPLISYESStRPGSSLQR-----AFAQLGLEPSiaLTALDADLIKTYVRAGLGVGLLAEMAVN- 250
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 15597613  255 dlAERRLVRVLPEWTPV-EGMVVAMFPSRRGLLPSVRALIDFLA 297
Cdd:PRK12680 251 --ANDEDLRAWPAPAPIaECIAWAVLPRDRVLRDYALELVHVLA 292
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
101-262 3.91e-05

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: 43.54  E-value: 3.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 101 LTCSTPLLHFELAPMLARFMAQYPNVELYVKTFNRRVDVIAEGYDISLSLRFPPLEDsDLVMKVLARSPQVLVASPELLA 180
Cdd:cd08482   4 LSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPA-GMQVIELFPERVGPVCSPSLAP 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 181 RYRPPELPADLSAMPYVGWERSRLDGSLRLVGADGsSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERR 260
Cdd:cd08482  83 TVPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQG-LAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161

                ..
gi 15597613 261 LV 262
Cdd:cd08482 162 LV 163
rbcR CHL00180
LysR transcriptional regulator; Provisional
4-151 4.64e-05

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 44.24  E-value: 4.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    4 ELVFDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEA 83
Cdd:CHL00180   2 DLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEE 81
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15597613   84 AEDVIEQNRSEPCGMVRLTCSTPLLHFELAPMLARFMAQYP--NVELYV--------KTFNRRVDVIAEGYDISLSLR 151
Cdd:CHL00180  82 TCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPqiNVQLQVhstrriawNVANGQIDIAIVGGEVPTELK 159
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
112-296 8.72e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 42.56  E-value: 8.72e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFN-----RRVDviAEGYDISLSLRFPPLEDSDLVMKVLARSPQVLVASPElLARYRPPE 186
Cdd:cd08427  15 LPRALARLRRRHPDLEVHIVPGLsaellARVD--AGELDAAIVVEPPFPLPKDLVWTPLVREPLVLIAPAE-LAGDDPRE 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 187 LpadLSAMPYVGWERSRLDGslRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPL-CVVSRDLAERRLVRvL 265
Cdd:cd08427  92 L---LATQPFIRYDRSAWGG--RLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDiAVPLPAGPRVRVLP-L 165
                       170       180       190
                ....*....|....*....|....*....|...
gi 15597613 266 PEWTPVE--GMVVamfPSRRGLLPSVRALIDFL 296
Cdd:cd08427 166 GDPAFSRrvGLLW---RRSSPRSRLIQALLEAL 195
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
113-296 9.52e-05

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 42.58  E-value: 9.52e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 113 APMLARFMAQYPNVELYvktfnrrvdvIAEGY-----------DISLSLRFPPLEDSDLVMKVLARSPQVLVASPELLAR 181
Cdd:cd08433  16 VPLLRAVRRRYPGIRLR----------IVEGLsghllewllngRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLP 85
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 182 yRPPELP-ADLSAMPYVgwERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERR 260
Cdd:cd08433  86 -RGAPVPlAELARLPLI--LPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGR 162
                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15597613 261 L-VRVLPEWTPVEGMVVAMfPSRRGLLPSVRALIDFL 296
Cdd:cd08433 163 LvAAPIVDPALTRTLSLAT-PRDRPLSPAALAVRDLL 198
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
112-296 1.89e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 41.82  E-value: 1.89e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRRV---DVIAEGYDIS-LSLRFPPLEdsDLVMKVLARSPQVLVASPE-LLARYRPPE 186
Cdd:cd08436  15 LPELLARFHRRHPGVDIRLRQAGSDDllaAVREGRLDLAfVGLPERRPP--GLASRELAREPLVAVVAPDhPLAGRRRVA 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 187 LpADLSAMPYV----GWE-RSRLDGSLRlvgadgsSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVsRDLAERRL 261
Cdd:cd08436  93 L-ADLADEPFVdfppGTGaRRQVDRAFA-------AAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVA-ARLPGLAA 163
                       170       180       190
                ....*....|....*....|....*....|....*
gi 15597613 262 VRVLPEWTPVEGMVVAMFPSRrgllPSVRALIDFL 296
Cdd:cd08436 164 LPLEPAPRRRLYLAWSAPPPS----PAARAFLELL 194
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
22-252 2.03e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 2.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   22 GGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRhcVAMTVEAEAAEDVIEQNRSEPCGM-VR 100
Cdd:PRK15421  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQ--LANQVLPQISQALQACNEPQQTRLrIA 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  101 LTCSTPLLHfeLAPMLARFMAQYPNVELYVK---TFNRRVDVIAEGYDISLS--------LRFPPLEDSDLvmkvlarsp 169
Cdd:PRK15421  95 IECHSCIQW--LTPALENFHKNWPQVEMDFKsgvTFDPQPALQQGELDLVMTsdilprsgLHYSPMFDYEV--------- 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  170 qVLVASPELLARYRPPELPADLSAMPYVGW--ERSRLDGSLRLVGADGSSaalnlrPQLLS-DDLGTLRQAVLEGVGIGG 246
Cdd:PRK15421 164 -RLVLAPDHPLAAKTRITPEDLASETLLIYpvQRSRLDVWRHFLQPAGVS------PSLKSvDNTLLLIQMVAARMGIAA 236

                 ....*.
gi 15597613  247 LPLCVV 252
Cdd:PRK15421 237 LPHWVV 242
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-277 3.09e-04

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 41.72  E-value: 3.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613    7 FDLNALFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAED 86
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   87 VIEQNRSEPCGMVRLTCSTPLLHFE-LAPMLARFMAQYPNVELYvktFNRRV------DVIAEGYDISLSLR-FPPLEDS 158
Cdd:PRK10094  82 ELQQVNDGVERQVNIVINNLLYNPQaVAQLLAWLNERYPFTQFH---ISRQIymgvwdSLLYEGFSLAIGVTgTEALANT 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613  159 DLVMKVLARSPQVLVASPELLARYRPPELPADLSAMPYVGWErsrlDGSLRLVgadgSSAALNLRPQ--LLSDDLGTLRQ 236
Cdd:PRK10094 159 FSLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIE----DSARTLT----KRVAWRLPGQkeIIVPDMETKIA 230
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 15597613  237 AVLEGVGIGGLPLCVVSRDLAERRLV-RVLPEWTPVEGMVVA 277
Cdd:PRK10094 231 AHLAGVGIGFLPKSLCQSMIDNQQLVsRVIPTMRPPSPLSLA 272
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
112-296 6.23e-04

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 40.33  E-value: 6.23e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPN--VELYVKTFNRRVDVIAEG-YDISLSLRFPPLEDSDLVMKVLARSPQVLVASP-ELLARYRPPEL 187
Cdd:cd08435  15 LPPAIARLLARHPRltVRVVEGTSDELLEGLRAGeLDLAIGRLADDEQPPDLASEELADEPLVVVARPgHPLARRARLTL 94
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 188 pADLSAMPYV-----GWERSRLDGSLRlvgadgsSAALNL-RPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRL 261
Cdd:cd08435  95 -ADLADYPWVlpppgTPLRQRLEQLFA-------AAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDELRAGVL 166
                       170       180       190
                ....*....|....*....|....*....|....*
gi 15597613 262 VRVLPEWTPVEGMVVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08435 167 RELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
115-296 7.35e-04

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 39.83  E-value: 7.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 115 MLARFMAQYPNVELYVKTFNRRV---DVIAEGYDISLSlrFPPLEDSDLVMKVLARSPQVLVASPE-LLARYRPPELpAD 190
Cdd:cd08434  18 LIRAFRKEYPNVTFELHQGSTDElldDLKNGELDLALC--SPVPDEPDIEWIPLFTEELVLVVPKDhPLAGRDSVDL-AE 94
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 191 LSAMPYVGWErsrlDGS-LRLVgADGSSAALNLRPQLL--SDDLGTLRQAVLEGVGIGGLPLcvvsRDLAERRLVRVL-- 265
Cdd:cd08434  95 LADEPFVLLS----PGFgLRPI-VDELCAAAGFTPKIAfeGEEDSTIAGLVAAGLGVAILPE----MTLLNPPGVKKIpi 165
                       170       180       190
                ....*....|....*....|....*....|...
gi 15597613 266 --PEWTPVEGMVVamfPSRRGLLPSVRALIDFL 296
Cdd:cd08434 166 kdPDAERTIGLAW---LKDRYLSPAARRFKDFV 195
PRK10341 PRK10341
transcriptional regulator TdcA;
12-160 1.15e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 40.23  E-value: 1.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   12 LFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEaeaAEDVIEQN 91
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE---MKNMVNEI 88
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597613   92 RSEPCG-MVRLTCSTP-LLHFELAP-MLARFMAQYPNVELYVktfnrrvdviaegYDISLSLRFPPLEDSDL 160
Cdd:PRK10341  89 NGMSSEaVVDVSFGFPsLIGFTFMSdMINKFKEVFPKAQVSM-------------YEAQLSSFLPAIRDGRL 147
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
27-128 1.89e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.20  E-value: 1.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   27 AGRVLGIPKSTISRKVAQLEARLGVRLVQRS-TRQFQVTEIGQAYYRHCVAMTVEAEAAEDVIEQNRSEPCGMVRLTCST 105
Cdd:PRK12682  22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTH 101
                         90       100
                 ....*....|....*....|...
gi 15597613  106 PLLHFELAPMLARFMAQYPNVEL 128
Cdd:PRK12682 102 TQARYVLPRVVAAFRKRYPKVNL 124
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
112-296 5.33e-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: 5.33e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 112 LAPMLARFMAQYPNVELYVKTFNRR--VDVIAEGyDISLSLRFPPLEDSDLVMKVLARSPQVLVASPE-LLARYRPPELp 188
Cdd:cd08414  15 LPRLLRRFRARYPDVELELREMTTAeqLEALRAG-RLDVGFVRPPPDPPGLASRPLLREPLVVALPADhPLAARESVSL- 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613 189 ADLSAMPYVGWERSRLDGSLRLVGADGSSAALNLRPQLLSDDLGTLRQAVLEGVGIGGLPLCVVSRDLAERRLVRVLPEW 268
Cdd:cd08414  93 ADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQRPGVVYRPLADPP 172
                       170       180
                ....*....|....*....|....*...
gi 15597613 269 TPVEgmvVAMFPSRRGLLPSVRALIDFL 296
Cdd:cd08414 173 PRSE---LALAWRRDNASPALRAFLELA 197
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
12-88 5.94e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 37.73  E-value: 5.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597613   12 LFIYAKVVEHGGFAPAGRVLGIPKSTISRKVAQLEARLGVRLVQRSTRQFQVTEIGQAYYRHCVAMTVEAEAAEDVI 88
Cdd:PRK15243   9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEI 85
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
35-128 6.66e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 37.72  E-value: 6.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597613   35 KSTISRKVAQLEARLGVRLVQRSTRQFQ-VTEIGQAYYRHCVAMTVEAEAAEDVIEQNRSEPCGmvRLTCSTPllH---- 109
Cdd:PRK12683  30 QSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSG--HLTVATT--Htqar 105
                         90
                 ....*....|....*....
gi 15597613  110 FELAPMLARFMAQYPNVEL 128
Cdd:PRK12683 106 YALPKVVRQFKEVFPKVHL 124
 
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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