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Conserved domains on  [gi|15596935|ref|NP_250429|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444115)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic binding proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  19047729|8257110
SCOP:  4000316|3000083

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-293 8.43e-105

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: 304.00  E-value: 8.43e-105
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDLRLAIVAT 171
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 172 PAYFRRQGRPGSPEELLGHRCIGWRKVSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAE 251
Cdd:cd08474  81 PAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596935 252 HLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08474 161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.02e-21

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 1.02e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935     9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGE 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-293 8.43e-105

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: 304.00  E-value: 8.43e-105
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDLRLAIVAT 171
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 172 PAYFRRQGRPGSPEELLGHRCIGWRKVSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAE 251
Cdd:cd08474  81 PAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596935 252 HLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08474 161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-294 7.72e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.52  E-value: 7.72e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDS 84
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  85 LNRFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVA---DEGFANIVEAGFDAGIRLGEDLQHGMRAVRVG 161
Cdd:COG0583  82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnsDRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 162 PDlRLAIVATPAYFRRQGRPgspeellghrcigwrkvssgelykwqfskgtkalsvamsgplVLDDPRLMLQAALADVGI 241
Cdd:COG0583 162 EE-RLVLVASPDHPLARRAP------------------------------------------LVNSLEALLAAVAAGLGI 198
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 15596935 242 AFAIEEEVAEHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLLR 294
Cdd:COG0583 199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
3-293 2.41e-33

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 123.95  E-value: 2.41e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    3 KPDLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAAL 82
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   83 DSLNRFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRL-GEDLQHGMRAVRVG 161
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrPRPFEDSDLVMRVL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  162 PDLRLAIVATPAYFRRQGRPGSPEELlgHRCIGWRKVSSGELYKWQFS--KGTKAlSVAMSGPLVLDDPRLMLQAALADV 239
Cdd:PRK14997 161 ADRGHRLFASPDLIARMGIPSAPAEL--SHWPGLSLASGKHIHRWELYgpQGARA-EVHFTPRMITTDMLALREAAMAGV 237
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15596935  240 GIAFAIEEEVAEHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:PRK14997 238 GLVQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFL 291
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.02e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 1.02e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935     9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGE 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-294 1.24e-21

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: 90.43  E-value: 1.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    93 HGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVAD--EGFANIVEAG-FDAGIRLGEDLQHGMRAVRVGPDlRLAIV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGnsEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEE-PLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   170 ATPAYFRRQGRPGSPEELLGHRCIGWRKVSSgelYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEV 249
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSG---LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 15596935   250 AEHLAAGRL-ERVLADWCAPFPgFHLYYPNRRNHPAALSAVINLLR 294
Cdd:pfam03466 157 ARELADGRLvALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-104 2.51e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 74.62  E-value: 2.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRtTRNVSPTEAGEHLLAHLDpafediAAAL-- 82
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLR------QVALle 75
                         90       100
                 ....*....|....*....|...
gi 15596935   83 -DSLNRFRETPHGLVRINAPRNA 104
Cdd:PRK13348  76 aDLLSTLPAERGSPPTLAIAVNA 98
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
28-86 1.97e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.19  E-value: 1.97e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935     28 LGVTPPTLSHTLRELETQlgiRLLNRT-------TRNVSPTEAGEHLLAHLDPAF-EDIAAALDSLN 86
Cdd:smart00347  34 LGVSPSTVTRVLDRLEKK---GLVRREpspedrrSVLVSLTEEGRELIEQLLEARsETLAELLAGLT 97
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
25-82 5.19e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.49  E-value: 5.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596935  25 AATLGVTPPTLSHTLRELEtQLGirLLNRTT-------RNVSPTEAGEHLLAHLDPAFEDIAAAL 82
Cdd:COG1846  59 AERLGLTKSTVSRLLDRLE-EKG--LVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAEL 120
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-293 8.43e-105

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: 304.00  E-value: 8.43e-105
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDLRLAIVAT 171
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 172 PAYFRRQGRPGSPEELLGHRCIGWRKVSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAE 251
Cdd:cd08474  81 PAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596935 252 HLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08474 161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
94-293 7.66e-65

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: 202.29  E-value: 7.66e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPdLRLAIVATPA 173
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGP-VRRVLVASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIGWRkvSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08422  80 YLARHGTPQTPEDLARHRCLGYR--LPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596935 254 AAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08422 158 ASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-294 7.72e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.52  E-value: 7.72e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDS 84
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  85 LNRFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVA---DEGFANIVEAGFDAGIRLGEDLQHGMRAVRVG 161
Cdd:COG0583  82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnsDRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 162 PDlRLAIVATPAYFRRQGRPgspeellghrcigwrkvssgelykwqfskgtkalsvamsgplVLDDPRLMLQAALADVGI 241
Cdd:COG0583 162 EE-RLVLVASPDHPLARRAP------------------------------------------LVNSLEALLAAVAAGLGI 198
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 15596935 242 AFAIEEEVAEHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLLR 294
Cdd:COG0583 199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-291 1.52e-37

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: 132.25  E-value: 1.52e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGpDLRLAIVATPA 173
Cdd:cd08472   1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLG-ELRMVTCASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIGWRKVSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08472  80 YLARHGTPRHPEDLERHRAVGYFSARTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159
                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15596935 254 AAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVIN 291
Cdd:cd08472 160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-293 2.18e-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 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: 126.58  E-value: 2.18e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPdLRLAIVATPA 173
Cdd:cd08477   1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAP-YRMVLCASPD 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIG---WRKVSSgelykWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVA 250
Cdd:cd08477  80 YLARHGTPTTPEDLARHECLGfsyWRARNR-----WRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLA 154
                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15596935 251 EHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08477 155 EDLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
3-293 2.41e-33

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 123.95  E-value: 2.41e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    3 KPDLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAAL 82
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   83 DSLNRFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRL-GEDLQHGMRAVRVG 161
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrPRPFEDSDLVMRVL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  162 PDLRLAIVATPAYFRRQGRPGSPEELlgHRCIGWRKVSSGELYKWQFS--KGTKAlSVAMSGPLVLDDPRLMLQAALADV 239
Cdd:PRK14997 161 ADRGHRLFASPDLIARMGIPSAPAEL--SHWPGLSLASGKHIHRWELYgpQGARA-EVHFTPRMITTDMLALREAAMAGV 237
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15596935  240 GIAFAIEEEVAEHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:PRK14997 238 GLVQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFL 291
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-294 4.38e-32

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 118.01  E-value: 4.38e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGpDLRLAIVATPA 173
Cdd:cd08471   1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVG-SVRRVVCASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIGWRKVSSGElyKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08471  80 YLARHGTPKHPDDLADHDCIAFTGLSPAP--EWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEEL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596935 254 AAGRLERVLADW-CAPFPgFHLYYPNRRNHPAALSAVINLLR 294
Cdd:cd08471 158 AAGRLQRVLEDFePPPLP-VHLVHPEGRLAPAKVRAFVDFAV 198
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-293 1.41e-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 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: 113.85  E-value: 1.41e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDLRLaIVATPA 173
Cdd:cd08479   1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRI-LCASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIGWRKVSSGELYkWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08479  80 YLERHGAPASPEDLARHDCLVIRENDEDFGL-WRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYL 158
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596935 254 AAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08479 159 RSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-293 1.04e-29

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 111.49  E-value: 1.04e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRnAIG-LVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQH-GMRAVRVGPDlRLAIVAT 171
Cdd:cd08475   1 GRLRIDLPV-AFGrLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQ-RMVLCAS 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 172 PAYFRRQGRPGSPEELLGHRCIGWRKvsSGELYKWQFSKGTKAL-SVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVA 250
Cdd:cd08475  79 PAYLARHGTPRTLEDLAEHQCIAYGR--GGQPLPWRLADEQGRLvRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVA 156
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15596935 251 EHLAAGRLERVLADwCAPFP-GFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08475 157 DHLQRGELVEVLPE-LAPEGlPIHAVWPRTRHLPPKVRAAVDAL 199
PRK09801 PRK09801
LysR family transcriptional regulator;
9-265 3.70e-29

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 113.21  E-value: 3.70e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRF 88
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   89 RETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDLRLaI 168
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI-L 169
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  169 VATPAYFRRQGRPGSPEELLGHRCI--GWRKVSSGelyKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIE 246
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRHDCLvtKERDMTHG---IWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSE 246
                        250
                 ....*....|....*....
gi 15596935  247 EEVAEHLAAGRLERVLADW 265
Cdd:PRK09801 247 WDVLPFLESGKLVQVLPEY 265
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-293 1.47e-28

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 108.49  E-value: 1.47e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPrnAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPdLRLAIVATPA 173
Cdd:cd08476   1 GRLRVSLP--LVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGS-FRMVLVASPD 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIGWRKVSSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08476  78 YLARHGTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596935 254 AAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08476 158 ADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
4-264 7.62e-26

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 103.77  E-value: 7.62e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    4 PDLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALD 83
Cdd:PRK11139   6 PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATR 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   84 SLNRFRETPHglVRINAPRNAIGLVLAPRFGELARDYPGITLE---VVADEGFANiveAGFDAGIRLGEDLQHGMRAVRV 160
Cdd:PRK11139  86 KLRARSAKGA--LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRlkaVDRLEDFLR---DDVDVAIRYGRGNWPGLRVEKL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  161 GPDlRLAIVATPAYFRRQGRPGSPEELLGHRCIgwrKVSSGELYK-WQFSKGTKALSVAmSGPLvLDDPRLMLQAALADV 239
Cdd:PRK11139 161 LDE-YLLPVCSPALLNGGKPLKTPEDLARHTLL---HDDSREDWRaWFRAAGLDDLNVQ-QGPI-FSHSSMALQAAIHGQ 234
                        250       260
                 ....*....|....*....|....*
gi 15596935  240 GIAFAIEEEVAEHLAAGRLERVLAD 264
Cdd:PRK11139 235 GVALGNRVLAQPEIEAGRLVCPFDT 259
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-294 8.23e-24

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 98.54  E-value: 8.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    6 LAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALdsL 85
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEI--L 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   86 NRFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGeDLQHGMRAVRVGPDLR 165
Cdd:PRK10086  94 DIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFD-DAPSAQLTHHFLMDEE 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  166 LAIVATPAYFRRQGRPGSPEEL----LGHRCIGWRKVSSGElyKWQFSKGTKALSVAMSGP-LVLDDPRLMLQAALADVG 240
Cdd:PRK10086 173 ILPVCSPEYAERHALTGNPDNLrhctLLHDRQAWSNDSGTD--EWHSWAQHFGVNLLPPSSgIGFDRSDLAVIAAMNHIG 250
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596935  241 IAFAIEEEVAEHLAAGRLervladwCAPFPGF-----HLYY----PNRrnHPAALSAVINLLR 294
Cdd:PRK10086 251 VAMGRKRLVQKRLASGEL-------VAPFGDMevkchQHYYvttlPGR--QWPKIEAFIDWLK 304
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-294 3.67e-23

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: 94.30  E-value: 3.67e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDlRLAIVATPA 173
Cdd:cd08470   1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASR-RHYVCASPA 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 174 YFRRQGRPGSPEELLGHRCIgwrkvsSGELYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHL 253
Cdd:cd08470  80 YLERHGTPHSLADLDRHNCL------LGTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHL 153
                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15596935 254 AAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLLR 294
Cdd:cd08470 154 AAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLA 194
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
92-280 4.50e-22

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: 91.25  E-value: 4.50e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGpDLRLAIVAT 171
Cdd:cd08478   1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLG-KSRLRILAS 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 172 PAYFRRQGRPGSPEELLGHRCIGWRKVSSgeLYKWQFSKGTKALSVAMSGpLVLDDPRLMLQAALADVGIAFAIEEEVAE 251
Cdd:cd08478  80 PDYLARHGTPQSIEDLAQHQLLGFTEPAS--LNTWPIKDADGNLLKIQPT-ITASSGETLRQLALSGCGIACLSDFMTDK 156
                       170       180       190
                ....*....|....*....|....*....|...
gi 15596935 252 HLAAGRLERVLA----DWCAPFPGfhLYYPNRR 280
Cdd:cd08478 157 DIAEGRLIPLFAeqtsDVRQPINA--VYYRNTA 187
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.02e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 1.02e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935     9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGE 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-294 1.24e-21

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: 90.43  E-value: 1.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    93 HGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVAD--EGFANIVEAG-FDAGIRLGEDLQHGMRAVRVGPDlRLAIV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGnsEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEE-PLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   170 ATPAYFRRQGRPGSPEELLGHRCIGWRKVSSgelYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEV 249
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSG---LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 15596935   250 AEHLAAGRL-ERVLADWCAPFPgFHLYYPNRRNHPAALSAVINLLR 294
Cdd:pfam03466 157 ARELADGRLvALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-293 2.47e-20

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: 86.84  E-value: 2.47e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRL-GEDLQHGMRAVRVGPDLRLAIVA 170
Cdd:cd08473   1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVrFPPLEDSSLVMRVLGQSRQRLVA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 171 TPAYFRRQGRPGSPEELLGHRCIGWRkvSSGELYKWQF--SKGTKAlSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEE 248
Cdd:cd08473  81 SPALLARLGRPRSPEDLAGLPTLSLG--DVDGRHSWRLegPDGESI-TVRHRPRLVTDDLLTLRQAALAGVGIALLPDHL 157
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 15596935 249 VAEHLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08473 158 CREALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-293 4.80e-20

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 88.28  E-value: 4.80e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    6 LAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGE-------HLLAHLDPAFEDI 78
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRiyyqgcrRMLHEVQDVHEQL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   79 AAaldslnrFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAV 158
Cdd:PRK10632  84 YA-------FNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSR 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  159 RVGpDLRLAIVATPAYFRRQGRPGSPEELLGHRCIGW--RKVSSGELykwqFSKGTKALSVAMSGPLVLDDPRLMLQAAL 236
Cdd:PRK10632 157 RLG-AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYsvRPDNEFEL----IAPEGISTRLIPQGRFVTNDPQTLVRWLT 231
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596935  237 ADVGIAFAIEEEVAEHLAAGRLERVLADW-CAPFPGFHLyYPNRRNHPAALSAVINLL 293
Cdd:PRK10632 232 AGAGIAYVPLMWVIDEINRGELEILFPRYqSDPRPVYAL-YTEKDKLPLKVQVCINYL 288
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-293 5.22e-18

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: 80.46  E-value: 5.22e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  94 GLVRINA--PRNAIGLV-LAPRFGELardYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGpDLRLAIVA 170
Cdd:cd08480   1 GRLRVNAsvPFGTHFLLpLLPAFLAR---YPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLG-ESRRVIVA 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 171 TPAYFRRQGRPGSPEELLGHRCIGWRKVSSgeLYKWQFSKGTKALSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVA 250
Cdd:cd08480  77 SPSYLARHGTPLTPQDLARHNCLGFNFRRA--LPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVA 154
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15596935 251 EHLAAGRLERVLADWCapfPG----FHLYYPNRRNHPAALSAVINLL 293
Cdd:cd08480 155 DDIAAGRLVPVLEEYN---PGdrepIHAVYVGGGRLPARVRAFLDFL 198
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
109-288 4.02e-17

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: 77.62  E-value: 4.02e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 109 LAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGPDlRLAIVATPAYFRRqGRPGSPEELL 188
Cdd:cd08432  15 LIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDE-ELVPVCSPALLAG-LPLLSPADLA 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 189 GHRCIgwRKVSSGELYKWQFSKGTKALSVAMSGPlVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRLervladwCAP 268
Cdd:cd08432  93 RHTLL--HDATRPEAWQWWLWAAGVADVDARRGP-RFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL-------VRP 162
                       170       180
                ....*....|....*....|....*..
gi 15596935 269 FP-------GFHLYYPNRRNHPAALSA 288
Cdd:cd08432 163 FDlplpsggAYYLVYPPGRAESPAVAA 189
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-104 2.51e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 74.62  E-value: 2.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRtTRNVSPTEAGEHLLAHLDpafediAAAL-- 82
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLR------QVALle 75
                         90       100
                 ....*....|....*....|...
gi 15596935   83 -DSLNRFRETPHGLVRINAPRNA 104
Cdd:PRK13348  76 aDLLSTLPAERGSPPTLAIAVNA 98
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
12-127 7.09e-15

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 73.45  E-value: 7.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   12 FVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRFRET 91
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15596935   92 PHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEV 127
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTI 124
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-100 3.07e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 68.68  E-value: 3.07e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLdpafEDIAAALDSLnrf 88
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA----RDWLSWLESM--- 79
                         90
                 ....*....|..
gi 15596935   89 retPHGLVRINA 100
Cdd:PRK10094  80 ---PSELQQVND 88
PRK09986 PRK09986
LysR family transcriptional regulator;
5-124 3.92e-12

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 65.51  E-value: 3.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFediAAALDS 84
Cdd:PRK09986   8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---DNAEQS 84
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15596935   85 LNRFREtphgLVRINAPRNAIGLV-------LAPRFGELARDYPGIT 124
Cdd:PRK09986  85 LARVEQ----IGRGEAGRIEIGIVgtalwgrLRPAMRHFLKENPNVE 127
rbcR CHL00180
LysR transcriptional regulator; Provisional
9-127 7.60e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 64.66  E-value: 7.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAF---EDIAAALDSL 85
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILalcEETCRALEDL 89
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15596935   86 nrfRETPHGLVRINAPRnAIGLVLAPRFGEL-ARDYPGITLEV 127
Cdd:CHL00180  90 ---KNLQRGTLIIGASQ-TTGTYLMPRLIGLfRQRYPQINVQL 128
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-72 6.12e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 61.71  E-value: 6.12e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRtTRNVSPTEAGEHLLAHLD 72
Cdd:PRK03635   3 DYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHAR 69
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
5-70 1.27e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 60.94  E-value: 1.27e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAH 70
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQD 67
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
13-64 2.67e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 60.04  E-value: 2.67e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 15596935   13 VAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAG 64
Cdd:PRK11151  10 VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PRK09791 PRK09791
LysR family transcriptional regulator;
9-149 1.61e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.85  E-value: 1.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRF 88
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596935   89 RETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANIVEagfdagIRLGE 149
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINE------LRQGE 144
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
9-125 1.43e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.07  E-value: 1.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRF 88
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNV 85
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15596935   89 RETPHGLVRIN-APRNAIGLVLAPRFGELARDYPGITL 125
Cdd:PRK11233  86 GQALSGQVSIGlAPGTAASSLTMPLLQAVRAEFPGIVL 123
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
109-288 1.51e-08

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: 53.84  E-value: 1.51e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 109 LAPRFGELARDYPGITLEVVA-DEGFANIvEAGFDAGIRLGEDLQHGMRAVRVgPDLRLAIVATPAYFRRQGrPGSPEEL 187
Cdd:cd08481  15 LIPRLPDFLARHPDITVNLVTrDEPFDFS-QGSFDAAIHFGDPVWPGAESEYL-MDEEVVPVCSPALLAGRA-LAAPADL 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 188 LG-------HRCIGWRkvssgelyKWQFSKGTKALSvAMSGPLVlDDPRLMLQAALADVGIA----FAIEEEvaehLAAG 256
Cdd:cd08481  92 AHlpllqqtTRPEAWR--------DWFEEVGLEVPT-AYRGMRF-EQFSMLAQAAVAGLGVAllprFLIEEE----LARG 157
                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15596935 257 RL-----ERVLADWcapfpGFHLYYPNRRNHPAALSA 288
Cdd:cd08481 158 RLvvpfnLPLTSDK-----AYYLVYPEDKAESPPVQA 189
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
109-258 4.02e-08

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: 52.40  E-value: 4.02e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 109 LAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGE-DLQHGMRAVRVGPDlRLAIVATPAYFRRQGRPGSPEEL 187
Cdd:cd08482  15 LIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDaPWPAGMQVIELFPE-RVGPVCSPSLAPTVPLRQAPAAA 93
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15596935 188 LGH--------RCIGWRkvssgelyKWQFSKGTKALSVAMSgpLVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRL 258
Cdd:cd08482  94 LLGapllhtrsRPQAWP--------DWAAAQGLAPEKLGTG--QSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRL 162
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
104-260 9.40e-08

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: 51.39  E-value: 9.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 104 AIGLVLaPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVgPDLRLAIVATPAYFRRQGRpgs 183
Cdd:cd08487  11 AVGWLL-PRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERL-LDAPLSVLCSPEIAKRLSH--- 85
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935 184 PEELLGHRCIgwRKVSSGELYKWqFSKGTKAlSVAMSGPlVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRLER 260
Cdd:cd08487  86 PADLINETLL--RSYRTDEWLQW-FEAANMP-PIKIRGP-VFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ 157
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
14-69 1.10e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.25  E-value: 1.10e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15596935   14 AIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLA 69
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVK 67
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
104-258 2.01e-07

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: 50.45  E-value: 2.01e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 104 AIGLVLaPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRVGpDLRLAIVATPAYFRRQGRpgs 183
Cdd:cd08484  11 AVGWLL-PRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLF-EAPLSPLCTPELARRLSE--- 85
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596935 184 PEELLGHRCIgwRKVSSGELYKWQFSKGTKALSVAmsGPlVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRL 258
Cdd:cd08484  86 PADLANETLL--RSYRADEWPQWFEAAGVPPPPIN--GP-VFDSSLLMVEAALQGAGVALAPPSMFSRELASGAL 155
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-68 3.11e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 3.11e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLL 68
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
96-293 4.70e-07

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: 49.52  E-value: 4.70e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935  96 VRINAPRNAIGLVLAPRFGELARDYPGITLEVVADEGFANI--VEAG-FDAGIRLGEDLQHGMRAVRVGPDlRLAIVATP 172
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLeaLLEGeLDLAIVALPVDDPGLESEPLFEE-PLVLVVPP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 173 AYFRRQGRPGSPEELLGHRCIGWRKVSS-GELYKWQFSKGTKALSVAMsgplVLDDPRLMLQAALADVGIAFaIEEEVAE 251
Cdd:cd05466  81 DHPLAKRKSVTLADLADEPLILFERGSGlRRLLDRAFAEAGFTPNIAL----EVDSLEAIKALVAAGLGIAL-LPESAVE 155
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596935 252 HLAAGRLERVLADWCAPFPGFHLYYPNRRNHPAALSAVINLL 293
Cdd:cd05466 156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
4-69 1.59e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 48.71  E-value: 1.59e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596935    4 PDLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLA 69
Cdd:PRK10341   7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
104-258 2.86e-06

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: 47.14  E-value: 2.86e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 104 AIGLVLaPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVRV--GPdlrLAIVATPAyFRRQGRp 181
Cdd:cd08488  11 AVGWLL-PRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLfeAP---LSPLCTPE-LARQLR- 84
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935 182 gSPEELLGHRCIgwRKVSSGELYKWQFSKGTKALSVAMSGpLVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRL 258
Cdd:cd08488  85 -EPADLARHTLL--RSYRADEWPQWFEAAGVGHPCGLPNS-IMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGAL 157
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
109-285 1.45e-05

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: 45.03  E-value: 1.45e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 109 LAPRFGELARDYPGITLEVVADEGFANIVEAGFDAGIRLGEDLQHGMRAVR--VGPdlrLAIVATPAYFRrqGRPG-SPE 185
Cdd:cd08483  15 LMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPltAAP---FVVVAAPGLLG--DRKVdSLA 89
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935 186 ELLGHRcigW-RKVSSGELYKWQFSKGtkaLSVAMSGPLVLDDPRLMLQAALADVGIAFAIEEEVAEHLAAGRLeRVLAD 264
Cdd:cd08483  90 DLAGLP---WlQERGTNEQRVWLASMG---VVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRL-TVLFE 162
                       170       180
                ....*....|....*....|.
gi 15596935 265 WCAPFPGFHLYYPNRRNHPAA 285
Cdd:cd08483 163 EEEEGLGYHIVTRPGVLRPAA 183
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
20-91 2.51e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.01  E-value: 2.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15596935   20 SFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRFRET 91
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQT 89
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-68 5.44e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.04  E-value: 5.44e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 15596935   30 VTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLL 68
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELR 41
nhaR PRK11062
transcriptional activator NhaR; Provisional
12-91 9.33e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 43.46  E-value: 9.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   12 FVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAFEDIAAALDSLNRFRET 91
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMLDIVNYRKES 91
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-87 1.34e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 42.73  E-value: 1.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGE-------HLLAHLDPAFEDIAAA 81
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKifhsqirHLLQQLESNLAELRGG 95

                 ....*.
gi 15596935   82 LDSLNR 87
Cdd:PRK10082  96 SDYAQR 101
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
12-131 9.54e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 9.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935   12 FVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLLAHLDPAF---EDIAAALDSLNRF 88
Cdd:PRK11013  12 FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYyglDRIVSAAESLREF 91
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15596935   89 RETPHGLVRINAPRNAIGLVLAPRFgeLARdYPGITLEVVADE 131
Cdd:PRK11013  92 RQGQLSIACLPVFSQSLLPGLCQPF--LAR-YPDVSLNIVPQE 131
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
28-86 1.97e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.19  E-value: 1.97e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596935     28 LGVTPPTLSHTLRELETQlgiRLLNRT-------TRNVSPTEAGEHLLAHLDPAF-EDIAAALDSLN 86
Cdd:smart00347  34 LGVSPSTVTRVLDRLEKK---GLVRREpspedrrSVLVSLTEEGRELIEQLLEARsETLAELLAGLT 97
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
9-126 2.03e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 39.29  E-value: 2.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    9 LAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHL----LAHLDPAFEdiaaaLDS 84
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLypraLALLEQAVE-----IEQ 82
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 15596935   85 LnrFRETpHGLVRINAPRNAIGLVLAPRFGELARDYPGITLE 126
Cdd:PRK10837  83 L--FRED-NGALRIYASSTIGNYILPAMIARYRRDYPQLPLE 121
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
5-128 4.24e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.09  E-value: 4.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596935    5 DLAGLAAFVAIARERSFRRAAATLGVTPPTLSHTLRELETQLGIRLLNRTTRNVSPTEAGEHLL--AHLDPAFEDIAAAl 82
Cdd:PRK15092  12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLgyARKILRFNDEACS- 90
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 15596935   83 dSLnrFRETPHGLVRINAPRNAIGLVLAPRFGELARDYPGITLEVV 128
Cdd:PRK15092  91 -SL--MYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVR 133
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
25-82 5.19e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.49  E-value: 5.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596935  25 AATLGVTPPTLSHTLRELEtQLGirLLNRTT-------RNVSPTEAGEHLLAHLDPAFEDIAAAL 82
Cdd:COG1846  59 AERLGLTKSTVSRLLDRLE-EKG--LVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAEL 120
 
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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