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MULTISPECIES: LysR family transcriptional regulator [Enterobacter]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 1.51e-78

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: 236.57  E-value: 1.51e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFFAGQS-WHFLTPEGEsLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGE-VEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1016941181 249 GLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08422   160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 4.78e-16

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 4.78e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1016941181   8 QVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 1.51e-78

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: 236.57  E-value: 1.51e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFFAGQS-WHFLTPEGEsLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGE-VEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1016941181 249 GLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08422   160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-291 5.57e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 5.57e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  12 RICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIEG--QSEKDLPS 89
Cdd:COG0583    11 AVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAelRALRGGPR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPV---SLVGERIDVAVRITDNPEPGMIARRLGECRSVLCAS 166
Cdd:COG0583    91 GTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGEERLVLVAS 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 167 PDYLAQHGTPVSPEelaqhnclhysffagqswhfltpegeslsvavsgnlsasiSSLLMDAAIKHCGIAMLPEREASAAL 246
Cdd:COG0583   171 PDHPLARRAPLVNS----------------------------------------LEALLAAVAAGLGIALLPRFLAADEL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1016941181 247 EQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:COG0583   211 AAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-291 7.21e-41

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 143.75  E-value: 7.21e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   1 MDRVIAAQVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIE 80
Cdd:PRK10632    1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  81 GQ--SEKDLPSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELdVNNHPV-SLVGERIDVAVRITDNPEPGMIARRLG 157
Cdd:PRK10632   81 EQlyAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL-VTGIPApDLIADGLDVVIRVGALQDSSLFSRRLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 158 ECRSVLCASPDYLAQHGTPVSPEELAQHNCLHYSFFAGQSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAML 237
Cdd:PRK10632  160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYV 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1016941181 238 PEREASAALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:PRK10632  240 PLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-291 4.10e-34

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: 123.17  E-value: 4.10e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  89 SGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNN--HPVSLVGE-RIDVAVRITDNPEPGMIARRLGECRSVLCA 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 166 SPDYLAQHGTPVSPEELAQHNCLHYSFFAGQSWHFLTpEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAA 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDR-ALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1016941181 246 LEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 4.78e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 4.78e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1016941181   8 QVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10341 PRK10341
transcriptional regulator TdcA;
9-86 8.00e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.56  E-value: 8.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   9 VYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQK----TRTLSQISQEIEGQSE 84
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRsesiTREMKNMVNEINGMSS 93


                  ..
gi 1016941181  85 KD 86
Cdd:PRK10341   94 EA 95
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-78 5.14e-07

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 47.51  E-value: 5.14e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1016941181  12 RICELGSLSAAARALGISRpmvSR---YLEQMEKWAGTRLVNRST--RK---LTLTAAGEKVLQKTRTLSQISQE 78
Cdd:COG2005    29 AIDETGSISAAAKAMGMSY---KRawdLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRLEAEAQR 100
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 1.51e-78

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: 236.57  E-value: 1.51e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFFAGQS-WHFLTPEGEsLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGE-VEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1016941181 249 GLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08422   160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-286 4.50e-57

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: 182.28  E-value: 4.50e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  88 PSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLG-ECRSVLCAS 166
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVAS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 167 PDYLAQHGTPVSPEELAQHNCLHYSF-FAGQ--SWHFlTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREAS 243
Cdd:cd08474    81 PAYLARHGTPEHPRDLLNHRCIRYRFpTSGAlyRWEF-ERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1016941181 244 AALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08474   160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-284 3.35e-54

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: 174.73  E-value: 3.35e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFFAGQS-WHFLTPEGESlSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08477    81 LARHGTPTTPEDLARHECLGFSYWRARNrWRLEGPGGEV-KVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1016941181 249 GLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLD 284
Cdd:cd08477   160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFID 195
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-291 5.57e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 5.57e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  12 RICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIEG--QSEKDLPS 89
Cdd:COG0583    11 AVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAelRALRGGPR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPV---SLVGERIDVAVRITDNPEPGMIARRLGECRSVLCAS 166
Cdd:COG0583    91 GTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGEERLVLVAS 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 167 PDYLAQHGTPVSPEelaqhnclhysffagqswhfltpegeslsvavsgnlsasiSSLLMDAAIKHCGIAMLPEREASAAL 246
Cdd:COG0583   171 PDHPLARRAPLVNS----------------------------------------LEALLAAVAAGLGIALLPRFLAADEL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1016941181 247 EQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:COG0583   211 AAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-286 1.73e-51

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: 167.73  E-value: 1.73e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  88 PSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPE--PGMIARRLGECRSVLCA 165
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLedSSLVMRVLGQSRQRLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 166 SPDYLAQHGTPVSPEELAQHNCLHYSFFAG-QSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASA 244
Cdd:cd08473    81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGrHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1016941181 245 ALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08473   161 ALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-284 4.37e-51

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: 166.92  E-value: 4.37e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYsFFAGQ----SWHFlTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAA 245
Cdd:cd08472    81 LARHGTPRHPEDLERHRAVGY-FSARTgrvlPWEF-QRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPH 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1016941181 246 LEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLD 284
Cdd:cd08472   159 LASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-284 1.46e-48

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: 160.38  E-value: 1.46e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRV-ACAHFTAMHlIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPD 168
Cdd:cd08471     1 GLLTVtAPVLFGRLH-VLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 169 YLAQHGTPVSPEELAQHNCLHYS-FFAGQSWHFlTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALE 247
Cdd:cd08471    80 YLARHGTPKHPDDLADHDCIAFTgLSPAPEWRF-REGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1016941181 248 QGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLD 284
Cdd:cd08471   159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVD 195
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-290 5.75e-47

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: 155.93  E-value: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLhysffAGQS--WHFLTpEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALE 247
Cdd:cd08470    81 LERHGTPHSLADLDRHNCL-----LGTSdhWRFQE-NGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1016941181 248 QGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYL 290
Cdd:cd08470   155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADAL 197
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 3.17e-45

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 151.55  E-value: 3.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRI--TDNPEpGMIARRLGECRSVLCASP 167
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIgeLADST-GLVARRLGTQRMVLCASP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 168 DYLAQHGTPVSPEELAQHNCLHYSFFAG-QSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAAL 246
Cdd:cd08475    80 AYLARHGTPRTLEDLAEHQCIAYGRGGQpLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1016941181 247 EQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08475   160 QRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 3.44e-44

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 148.90  E-value: 3.44e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAH-FTAMHlIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPD 168
Cdd:cd08479     1 GLLRVNASFgFGRRH-IAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 169 YLAQHGTPVSPEELAQHNCL-----HYSFFAgqsWHFlTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREAS 243
Cdd:cd08479    80 YLERHGAPASPEDLARHDCLvirenDEDFGL---WRL-RNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1016941181 244 AALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08479   156 PYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 1.04e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 147.87  E-value: 1.04e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFF-AGQSWHFLTPeGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08480    81 LARHGTPLTPQDLARHNCLGFNFRrALPDWPFRDG-GRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1016941181 249 GLLVPVLEALEPKPL-AIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08480   160 GRLVPVLEEYNPGDRePIHAVYVGGGRLPARVRAFLDFL 198
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-291 7.21e-41

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 143.75  E-value: 7.21e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   1 MDRVIAAQVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIE 80
Cdd:PRK10632    1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  81 GQ--SEKDLPSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELdVNNHPV-SLVGERIDVAVRITDNPEPGMIARRLG 157
Cdd:PRK10632   81 EQlyAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL-VTGIPApDLIADGLDVVIRVGALQDSSLFSRRLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 158 ECRSVLCASPDYLAQHGTPVSPEELAQHNCLHYSFFAGQSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAML 237
Cdd:PRK10632  160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYV 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1016941181 238 PEREASAALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:PRK10632  240 PLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-284 4.08e-40

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 138.53  E-value: 4.08e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACAHftAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDY 169
Cdd:cd08476     1 GRLRVSLPL--VGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 170 LAQHGTPVSPEELAQHNCLHYSFFAG---QSWHFLTPEGESL----SVAVSGNLSAsisslLMDAAIKHCGIAMLPEREA 242
Cdd:cd08476    79 LARHGTPETPADLAEHACLRYRFPTTgklEPWPLRGDGGDPElrlpTALVCNNIEA-----LIEFALQGLGIACLPDFSV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1016941181 243 SAALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLD 284
Cdd:cd08476   154 REALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVD 195
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 12-287 1.39e-36

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 132.42  E-value: 1.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  12 RICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSqisqeIEGQSEKDL---- 87
Cdd:PRK14997   12 HVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAML-----VEAQAAQDAiaal 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  88 ---PSGTLRVACAhFTAMHL-IAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNP--EPGMIARRLGECRS 161
Cdd:PRK14997   87 qvePRGIVKLTCP-VTLLHVhIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADRGH 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 162 VLCASPDYLAQHGTPVSPEELAQHNCLhySFFAGQ---SWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLP 238
Cdd:PRK14997  166 RLFASPDLIARMGIPSAPAELSHWPGL--SLASGKhihRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLP 243

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1016941181 239 EREASAALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELS 287
Cdd:PRK14997  244 VLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLT 292
PRK09801 PRK09801
LysR family transcriptional regulator;
8-281 5.94e-36

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 130.93  E-value: 5.94e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   8 QVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKT-RTLSQISQEIEGQSE-K 85
Cdd:PRK09801   12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHAlEILTQYQRLVDDVTQiK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  86 DLPSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCA 165
Cdd:PRK09801   92 TRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCA 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 166 SPDYLAQHGTPVSPEELAQHNCL--HYSFFAGQSWHfLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREAS 243
Cdd:PRK09801  172 APEYLQKYPQPQSLQELSRHDCLvtKERDMTHGIWE-LGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVL 250

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1016941181 244 AALEQGLLVPVLEALePKPLAIHGIYQSREYQPAALRV 281
Cdd:PRK09801  251 PFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRV 287
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-291 4.10e-34

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: 123.17  E-value: 4.10e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  89 SGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNN--HPVSLVGE-RIDVAVRITDNPEPGMIARRLGECRSVLCA 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 166 SPDYLAQHGTPVSPEELAQHNCLHYSFFAGQSWHFLTpEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAA 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDR-ALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1016941181 246 LEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDELSRYLA 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 88-286 4.76e-33

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: 120.14  E-value: 4.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  88 PSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASP 167
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 168 DYLAQHGTPVSPEELAQHNCLHYSFFAG-QSWHFLTPEGESLSvaVSGNLSASISSLLMDAAIKHCGIAMLPEREASAAL 246
Cdd:cd08478    81 DYLARHGTPQSIEDLAQHQLLGFTEPASlNTWPIKDADGNLLK--IQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1016941181 247 EQGLLVPVL-EALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd08478   159 AEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 91-284 1.72e-24

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: 97.27  E-value: 1.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDYL 170
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 171 AQHGtPVSPEELAQHNCLHySFFAGQSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQGL 250
Cdd:cd08432    81 AGLP-LLSPADLARHTLLH-DATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGR 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1016941181 251 LVPVLEALEPKPLAIHGIYQSREYQPAALRVFLD 284
Cdd:cd08432   159 LVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
18-252 5.69e-21

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 90.45  E-value: 5.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  18 SLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQK-TRTLSQISQEIEGQSEKDLpSGTLRVAC 96
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWAlKSSLDTLNQEILDIKNQEL-SGTLTVYS 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  97 AHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDYLAQHGTP 176
Cdd:PRK10086  109 RPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAERHALT 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 177 VSPEELAQHNCLHysffAGQSWHF--LTPEGESLSVAVSGNLSASISSLLMD-------AAIKHCGIAMLPEREASAALE 247
Cdd:PRK10086  189 GNPDNLRHCTLLH----DRQAWSNdsGTDEWHSWAQHFGVNLLPPSSGIGFDrsdlaviAAMNHIGVAMGRKRLVQKRLA 264


                  ....*
gi 1016941181 248 QGLLV 252
Cdd:PRK10086  265 SGELV 269
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 1.51e-18

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: 81.49  E-value: 1.51e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPV---SLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASP 167
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSElleALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 168 DYLAQHGTPVSPEELAQHNCLHY---SFFAGQSWHFLTPEGESLSVAVSGNLSASIssllMDAAIKHCGIAMLPEReASA 244
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFergSGLRRLLDRAFAEAGFTPNIALEVDSLEAI----KALVAAGLGIALLPES-AVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1016941181 245 ALEQGLLVPVLEALEPKPLAIHGIYQSREYQPAALRVFLDEL 286
Cdd:cd05466   156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 4.78e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 4.78e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1016941181   8 QVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
17-252 8.20e-15

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 73.13  E-value: 8.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  17 GSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQ-KTRTLSQISQEIEGQSEkdlPSGT-LRV 94
Cdd:PRK15421   17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQlANQVLPQISQALQACNE---PQQTrLRI 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  95 ACAHFTAMHLIAPVLPGLLSRYPQlrIELDVNN------HPVSLVGErIDVAVRITDNPEPGMIARRLGECRSVLCASPD 168
Cdd:PRK15421   94 AIECHSCIQWLTPALENFHKNWPQ--VEMDFKSgvtfdpQPALQQGE-LDLVMTSDILPRSGLHYSPMFDYEVRLVLAPD 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 169 YLAQHGTPVSPEELAQHNCLHYSFFAGQ--SW-HFLTPEGeslsvaVSGNLSASISSLLMDAAIK-HCGIAMLPEREASA 244
Cdd:PRK15421  171 HPLAAKTRITPEDLASETLLIYPVQRSRldVWrHFLQPAG------VSPSLKSVDNTLLLIQMVAaRMGIAALPHWVVES 244


                  ....*...
gi 1016941181 245 ALEQGLLV 252
Cdd:PRK15421  245 FERQGLVV 252
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
13-255 6.65e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 67.30  E-value: 6.65e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  13 ICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRsTRKLTLTAAGEKVLQKTRTLSQisQEIEGQSE-KDLPSGT 91
Cdd:PRK13348   13 VVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVAL--LEADLLSTlPAERGSP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  92 LRVACAhFTAMHLIAPVLPGLLSRYPQLRIELDV------NNHPVSLVGERIDvAVRITDNPEPGMIARRLGECRSVLCA 165
Cdd:PRK13348   90 PTLAIA-VNADSLATWFLPALAAVLAGERILLELivddqdHTFALLERGEVVG-CVSTQPKPMRGCLAEPLGTMRYRCVA 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 166 SPDYLAQHGTP-VSPEELAQ--------HNCLHYSFFAGqswHFLTPEGeslsvAVSGNLSASISSLLMdAAIKHCGIAM 236
Cdd:PRK13348  168 SPAFAARYFAQgLTRHSALKapavafnrKDTLQDSFLEQ---LFGLPVG-----AYPRHYVPSTHAHLA-AIRHGLGYGM 238

                         250
                  ....*....|....*....
gi 1016941181 237 LPEREASAALEQGLLVPVL 255
Cdd:PRK13348  239 VPELLIGPLLAAGRLVDLA 257
rbcR CHL00180
LysR transcriptional regulator; Provisional
 17-141 5.55e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 61.96  E-value: 5.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  17 GSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQ-KTRTLS---QISQEIEgqSEKDLPSGTL 92
Cdd:CHL00180   20 GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRyGNRILAlceETCRALE--DLKNLQRGTL 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1016941181  93 RVACAHFTAMHLIaPVLPGLLS-RYPQLRIELDVNNHPV---SLVGERIDVAV 141
Cdd:CHL00180   98 IIGASQTTGTYLM-PRLIGLFRqRYPQINVQLQVHSTRRiawNVANGQIDIAI 149
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-256 4.39e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 59.09  E-value: 4.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  18 SLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRT-LSQISQEIEGQSEKDlPSGTLRVAC 96
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREiFDQLAEATRKLRARS-AKGALTVSL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  97 AHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDYLAQHGTP 176
Cdd:PRK11139  101 LPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKPL 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 177 VSPEELAQHNCLHYS--------FFAGQSWHFLTPEGeslsvavsgnLSASISSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:PRK11139  181 KTPEDLARHTLLHDDsredwrawFRAAGLDDLNVQQG----------PIFSHSSMALQAAIHGQGVALGNRVLAQPEIEA 250


                  ....*...
gi 1016941181 249 GLLVPVLE 256
Cdd:PRK11139  251 GRLVCPFD 258
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
15-255 5.88e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 59.02  E-value: 5.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  15 ELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRsTRKLTLTAAGEKVLQKTRTLSQISQEIEGQSeKDLPSGTLRV 94
Cdd:PRK03635   15 REGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGEL-PALDGTPLTL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  95 AcahftamhlIA-----------PVLPGLLSRyPQLRIELDVNNHPVSLvgERI---DV--AVRITDNPEPGMIARRLGE 158
Cdd:PRK03635   93 S---------IAvnadslatwflPALAPVLAR-SGVLLDLVVEDQDHTA--ELLrrgEVvgAVTTEPQPVQGCRVDPLGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 159 CRSVLCASPDYLAQH---GtpVSPEELA--------QHNCLHYSFFAgqsWHFLTPEGESLSVAVSGnlsasiSSLLMDA 227
Cdd:PRK03635  161 MRYLAVASPAFAARYfpdG--VTAEALAkapavvfnRKDDLQDRFLR---QAFGLPPGSVPCHYVPS------SEAFVRA 229

                         250       260
                  ....*....|....*....|....*...
gi 1016941181 228 AIKHCGIAMLPEREASAALEQGLLVPVL 255
Cdd:PRK03635  230 ALAGLGWGMIPELQIEPELASGELVDLT 257
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 101-279 1.04e-09

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: 56.61  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 101 AMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGEC-RSVLCaSPDyLAQHGTpvSP 179
Cdd:cd08484    11 AVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEApLSPLC-TPE-LARRLS--EP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 180 EELAQHNCLHySFFAGQ--SWhfltpegesLSVA-VSGNLSASI---SSLLM-DAAIKHCGIAMLPEREASAALEQGLLV 252
Cdd:cd08484    87 ADLANETLLR-SYRADEwpQW---------FEAAgVPPPPINGPvfdSSLLMvEAALQGAGVALAPPSMFSRELASGALV 156

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1016941181 253 pvlealEPKPLAIH-GIY-----QSREYQPAAL 279
Cdd:cd08484   157 ------QPFKITVStGSYwltrlKSKPETPAMS 183
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 107-252 7.51e-09

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: 54.46  E-value: 7.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 107 PVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECR-SVLCaSPDyLAQhgTPVSPEELAQH 185
Cdd:cd08488    17 PRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPlSPLC-TPE-LAR--QLREPADLARH 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1016941181 186 NCLHySFFAGQSWHFLTPEGESLSVAVSGNLSASISSLLMDAAIKHCGIAMLPEREASAALEQGLLV 252
Cdd:cd08488    93 TLLR-SYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV 158
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 15-184 1.18e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 54.96  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  15 ELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRtlsQISQEIE-GQSE----KDLPS 89
Cdd:PRK11242   14 EHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYAR---RALQDLEaGRRAihdvADLSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 GTLRVACA-HFTAmHLIAPVLPGLLSRYPQLRIELDVNNH---PVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCA 165
Cdd:PRK11242   91 GSLRLAMTpTFTA-YLIGPLIDAFHARYPGITLTIREMSQeriEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVV 169

                         170       180
                  ....*....|....*....|
gi 1016941181 166 SPDY-LAQHGTPVSPEELAQ 184
Cdd:PRK11242  170 GRHHpLAARRKALTLDELAD 189
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-197 1.50e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 54.61  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  19 LSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLT--------LTAAGEKVLQKTRTLSQISQEIEGQSekdlpSG 90
Cdd:PRK12682   19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgltepgkaVLDVIERILREVGNIKRIGDDFSNQD-----SG 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDvNNHPVSLVG----ERIDVAV---RITDNPEpgMIARRLGECRSVL 163
Cdd:PRK12682   94 TLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLH-QGSPDEIARmvisGEADIGIateSLADDPD--LATLPCYDWQHAV 170

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1016941181 164 CASPDY-LAQHGtPVSPEELAQHNCLHYSF-FAGQS 197
Cdd:PRK12682  171 IVPPDHpLAQEE-RITLEDLAEYPLITYHPgFTGRS 205
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 20-129 2.52e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 54.01  E-value: 2.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  20 SAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTR-TLSQISQEIEGQSEKDLPSGTLRVACAH 98
Cdd:PRK09906   19 TKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARaILEQAEKAKLRARKIVQEDRQLTIGFVP 98

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1016941181  99 FTAMHLIAPVLPGLLSRYPQLRIELDVNNHP 129
Cdd:PRK09906   99 SAEVNLLPKVLPMFRLRHPDTLIELVSLITT 129
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
18-259 3.45e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.52  E-value: 3.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  18 SLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQ----EIEGQSekDLPSGTLR 93
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLEsnlaELRGGS--DYAQRKIK 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  94 VACAHFTAMHLiapvLPGLLSRYPQL---RIE-LDVNNHPVSLVGERIDVAVRITDNP--EPGMIARRLGECRSV-LCAS 166
Cdd:PRK10082  105 IAAAHSLSLGL----LPSIISQMPPLftwAIEaIDVDEAVDKLREGQSDCIFSFHDEDllEAPFDHIRLFESQLFpVCAS 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 167 PdylaQHGTPVSPEELAQHNCLHY---SFFAGQSWHFLTPEGEslsVAVSGNLSASISSLLMDAAIKHCGIAMLPEREAS 243
Cdd:PRK10082  181 D----EHGEALFNLAQPHFPLLNYsrnSYMGRLINRTLTRHSE---LSFSTFFVSSMSELLKQVALDGCGIAWLPEYAIQ 253

                         250
                  ....*....|....*.
gi 1016941181 244 AALEQGLLVpVLEALE 259
Cdd:PRK10082  254 QEIRSGQLV-VLNRDE 268
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 106-284 5.96e-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: 51.91  E-value: 5.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 106 APVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDYLAQHGtPVSPEELAQH 185
Cdd:cd08481    16 IPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAPADLAHL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 186 NCLHYSFFAGQSWHFLTPEGESLSVAVSGNLSASIsSLLMDAAIKHCGIAMLPEREASAALEQGLLVPVLEALEPKPLAI 265
Cdd:cd08481    95 PLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQF-SMLAQAAVAGLGVALLPRFLIEEELARGRLVVPFNLPLTSDKAY 173

                         170
                  ....*....|....*....
gi 1016941181 266 HGIYQSREYQPAALRVFLD 284
Cdd:cd08481   174 YLVYPEDKAESPPVQAFRD 192
PRK10341 PRK10341
transcriptional regulator TdcA;
9-86 8.00e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.56  E-value: 8.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   9 VYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQK----TRTLSQISQEIEGQSE 84
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRsesiTREMKNMVNEINGMSS 93


                  ..
gi 1016941181  85 KD 86
Cdd:PRK10341   94 EA 95
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-123 1.23e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 51.90  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   3 RVIAAQVYNricelgsLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLT-LTAAG-------EKVLQKTRTLSQ 74
Cdd:PRK12684   10 REAVRQNFN-------LTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGriilasvERILQEVENLKR 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1016941181  75 ISQEIEGQSekdlpSGTLRVACAHFTAMHLIAPVLPGLLSRYPQLRIEL 123
Cdd:PRK12684   83 VGKEFAAQD-----QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSI 126
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 19-197 4.48e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 50.43  E-value: 4.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  19 LSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLT-LTAAG-------EKVLQKTRTLSQISQEIEGQSekdlpSG 90
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGkellqivERMLLDAENLRRLAEQFADRD-----SG 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDvNNHPVSLV-----GER-IDVAVRITDNpEPGMIARRLGECRSVLC 164
Cdd:PRK12683   94 HLTVATTHTQARYALPKVVRQFKEVFPKVHLALR-QGSPQEIAemllnGEAdIGIATEALDR-EPDLVSFPYYSWHHVVV 171

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1016941181 165 ASPDYLAQHGTPVSPEELAQHNCLHY-SFFAGQS 197
Cdd:PRK12683  172 VPKGHPLTGRENLTLEAIAEYPIITYdQGFTGRS 205
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-78 5.14e-07

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 47.51  E-value: 5.14e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1016941181  12 RICELGSLSAAARALGISRpmvSR---YLEQMEKWAGTRLVNRST--RK---LTLTAAGEKVLQKTRTLSQISQE 78
Cdd:COG2005    29 AIDETGSISAAAKAMGMSY---KRawdLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRLEAEAQR 100
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-184 9.63e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.30  E-value: 9.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181   8 QVYNRICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIEGQSEKDL 87
Cdd:PRK10837    9 EVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLFREDN 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  88 psGTLRVACAHFTAMHLiapvLPGLLSRY----PQLRIELDVNNHP--VSLVGE-RIDVAvrITDNP--EPGMIARRLGE 158
Cdd:PRK10837   89 --GALRIYASSTIGNYI----LPAMIARYrrdyPQLPLELSVGNSQdvINAVLDfRVDIG--LIEGPchSPELISEPWLE 160

                         170       180
                  ....*....|....*....|....*..
gi 1016941181 159 CRSVLCASPDY-LAQHgtPVSPEELAQ 184
Cdd:PRK10837  161 DELVVFAAPDSpLARG--PVTLEQLAA 185
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-265 1.12e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 49.03  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  12 RICELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRT-----------LSQISQEIE 80
Cdd:PRK10094   12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDwlswlesmpseLQQVNDGVE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  81 GQSE---KDL---PSGTLR-VACAH----FTAMHLIAPVLPGLLSrypqlrieldvnnhpvSLVGERIDVAVRITDNpEP 149
Cdd:PRK10094   92 RQVNiviNNLlynPQAVAQlLAWLNerypFTQFHISRQIYMGVWD----------------SLLYEGFSLAIGVTGT-EA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 150 ---GMIARRLGECRSVLCASPDY-LAQHGTPVSPEELAQHNCLHysffagqswhfLTPEGESLSVAVSGNLSASISSLLM 225
Cdd:PRK10094  155 lanTFSLDPLGSVQWRFVMAADHpLANVEEPLTEAQLRRFPAVN-----------IEDSARTLTKRVAWRLPGQKEIIVP 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1016941181 226 D------AAIKHCGIAMLPEREASAALEQGLLVP--VLEALEPKPLAI 265
Cdd:PRK10094  224 DmetkiaAHLAGVGIGFLPKSLCQSMIDNQQLVSrvIPTMRPPSPLSL 271
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-286 2.26e-06

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 47.10  E-value: 2.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 108 VLPGLLS----RYPQLRIELDVNN--HPVSLVGE-RIDVAVRITDNPEPGMIARRLGECRSVLCASPDY-LAQHGtPVSP 179
Cdd:cd08420    14 LLPRLLArfrkRYPEVRVSLTIGNteEIAERVLDgEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHpLAGRK-EVTA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 180 EELAQHNclhysffagqsW--------------HFLTPEGESLSvavSGNLSASISSLlmdAAIKHC-----GIAMLPER 240
Cdd:cd08420    93 EELAAEP-----------WilrepgsgtrevfeRALAEAGLDGL---DLNIVMELGST---EAIKEAveaglGISILSRL 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1016941181 241 EASAALEQGLLVPV-LEALEPK-PLAIhgIYQSREYQPAALRVFLDEL 286
Cdd:cd08420   156 AVRKELELGRLVALpVEGLRLTrPFSL--IYHKDKYLSPAAEAFLEFL 201
cysB PRK12681
HTH-type transcriptional regulator CysB;
20-128 3.92e-06

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 47.59  E-value: 3.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  20 SAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLT-LTAAGEKV-------LQKTRTLSQISQEIEGQSEkdlpsGT 91
Cdd:PRK12681   20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIiriareiLSKVESIKSVAGEHTWPDK-----GS 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1016941181  92 LRVACAHFTAMHLIAPVLPGLLSRYPqlrielDVNNH 128
Cdd:PRK12681   95 LYIATTHTQARYALPPVIKGFIERYP------RVSLH 125
PBP2_IciA_ArgP cd08428
The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), ...
 105-252 4.00e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176119 [Multi-domain]  Cd Length: 195  Bit Score: 46.47  E-value: 4.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 105 IAPVLPgllsrypQLRIELDVN----NHPVSLV--GERIDvAVRITDNPEPGMIARRLGECRSVLCASPDYLAQHGtP-- 176
Cdd:cd08428    19 LAPVLK-------RERILLDLIvddeDRTHDLLrdGEVVG-CISTQAQPMQGCRSDYLGSMDYLLVASPDFAARYF-Png 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 177 VSPEELA--------QHNCLHYSFFAGqswHFLTPEGESLSVAVSGnlsasiSSLLMDAAIKHCGIAMLPEREASAALEQ 248
Cdd:cd08428    90 LTREALLkapavafnRKDDLHQSFLQQ---HFGLPPGSYPCHYVPS------SEAFVDLAAQGLAYGMIPELQIEPELAS 160


                  ....
gi 1016941181 249 GLLV 252
Cdd:cd08428   161 GELI 164
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 131-286 8.47e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 45.34  E-value: 8.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 131 SLVGERIDVAVRITDNPEPGMIA-RRLGECRSVLCASPD-YLAQHGTPVSPEELAQHNclhySFFAGQSWHFLTPEG--- 205
Cdd:cd08431    44 ALASGRADLVIGATGELPPGGVKtRPLGEVEFVFAVAPNhPLAKLDGPLDASAIKQYP----AIVVADTSRNLPPRSsgl 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 206 -ESLSVAVSGNLSASIssllmDAAIKHCGIAMLPEREASAALEQGLLVPVLEALEPKPLAIHgiYQSREYQP-AALRVFL 283
Cdd:cd08431   120 lEGQDRIRVPTMQAKI-----DAQVLGLGVGYLPRHLAKPELASGELVEKALEDPRPPQELF--LAWRKDQRgKALAWFV 192


                  ...
gi 1016941181 284 DEL 286
Cdd:cd08431   193 QRL 195
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 92-286 1.88e-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: 44.26  E-value: 1.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  92 LRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASPDYLA 171
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 172 qhGTPV-SPEELAQHnclHYSFFAGQS----W---HFLTPEGESLSVAVSGNLSasissllMDAAIKHCGIAMLPEREAS 243
Cdd:cd08483    82 --DRKVdSLADLAGL---PWLQERGTNeqrvWlasMGVVPDLERGVTFLPGQLV-------LEAARAGLGLSIQARALVE 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1016941181 244 AALEQGLLVpVLEALEPKPLAIHGIYQSREYQPAAlRVFLDEL 286
Cdd:cd08483   150 PDIAAGRLT-VLFEEEEEGLGYHIVTRPGVLRPAA-KAFVRWL 190
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 107-252 2.17e-05

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: 44.46  E-value: 2.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 107 PVLPGLLSRYPQLRIELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECR-SVLCaSPDYlaqhGTPVS-PEELAQ 184
Cdd:cd08487    17 PRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPlSVLC-SPEI----AKRLShPADLIN 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 185 HNCLH-YSFFAGQSWHfltpEGESLS-VAVSGNLSASiSSLLMDAAIKHCGIAMLPEREASAALEQGLLV 252
Cdd:cd08487    92 ETLLRsYRTDEWLQWF----EAANMPpIKIRGPVFDS-SRLMVEAAMQGAGVALAPAKMFSREIENGQLV 156
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-123 5.80e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 43.65  E-value: 5.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  28 ISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQ-KTRTLS---QISQEIEGQSekDLPSGTLRVACAhFTAM- 102
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPfAQQTLLqwqQLRHTLDQQG--PSLSGELSLFCS-VTAAy 79

                          90       100
                  ....*....|....*....|....*.
gi 1016941181 103 -HliapvLPGLLSR----YPQLRIEL 123
Cdd:PRK11716   80 sH-----LPPILDRfraeHPLVEIKL 100
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 17-197 1.82e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  17 GSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAG----EKVLQKTRTLSQISQeiEGQSEKDLPSGTL 92
Cdd:PRK11013   19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfEEVQRSYYGLDRIVS--AAESLREFRQGQL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  93 RVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHPV---SLVGERIDVAVRITDNPEPGMIARRLGECRSVlCASPDy 169
Cdd:PRK11013   97 SIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLleeWLSAQRHDLGLTETLHTPAGTERTELLTLDEV-CVLPA- 174

                         170       180
                  ....*....|....*....|....*...
gi 1016941181 170 laqhGTPvspeeLAQHNCLHYSFFAGQS 197
Cdd:PRK11013  175 ----GHP-----LAAKKVLTPDDFAGEN 193
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 91-186 2.83e-04

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 41.01  E-value: 2.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHP--VSLVGER-IDVAVRITDNPEPGMIARRLGECRSVlCASP 167
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSStvVEAVLSGqADLGLASLPLDHPGLESEPLASGRAV-CVLP 79

                          90       100
                  ....*....|....*....|.
gi 1016941181 168 --DYLAQHGTpVSPEELAQHN 186
Cdd:cd08415    80 pgHPLARKDV-VTPADLAGEP 99
PRK09986 PRK09986
LysR family transcriptional regulator;
21-172 2.85e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.63  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  21 AAARaLGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTL-----------SQISQEIEGQSEKDLPS 89
Cdd:PRK09986   27 AAAR-LNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLldnaeqslarvEQIGRGEAGRIEIGIVG 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  90 ----GTLRVACAHFTAMHLIAPVLPGLLSryPQLRIELdvnnhpvsLVGERIDVAV-RITD-NPEPGMIARRLGEcRSVL 163
Cdd:PRK09986  106 talwGRLRPAMRHFLKENPNVEWLLRELS--PSMQMAA--------LERRELDAGIwRMADlEPNPGFTSRRLHE-SAFA 174

                         170
                  ....*....|.
gi 1016941181 164 CASP--DYLAQ 172
Cdd:PRK09986  175 VAVPeeHPLAS 185
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 91-177 5.05e-04

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 40.01  E-value: 5.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIELDVNNHP---VSLVGERIDVAvrITDNPEPGMIARRLGECRSVLCASP 167
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPrlmEMLERGEVDLA--LITHPPPGASATILRRSPTVWYCAA 78

                          90
                  ....*....|
gi 1016941181 168 DYLAQHGTPV 177
Cdd:cd08439    79 GYILAPGEPL 88
PRK09791 PRK09791
LysR family transcriptional regulator;
17-135 5.28e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.90  E-value: 5.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  17 GSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQ---ISQEiEGQSEKDLPSGTLR 93
Cdd:PRK09791   20 GSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEelrAAQE-DIRQRQGQLAGQIN 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1016941181  94 VACAHFTAMHLIAPVLPGLLSRYPQLRIELdVNNHPVSLVGE 135
Cdd:PRK09791   99 IGMGASIARSLMPAVISRFHQQHPQVKVRI-MEGQLVSMINE 139
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-263 5.69e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 39.96  E-value: 5.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRI---ELDVNNHPVSLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASP 167
Cdd:cd08461     1 TLVIAATDYAQKAILPPLLAALRQEAPGVRVairDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181 168 DYLAQHGtPVSPEELAQHNCLHYSFFAGQswhFLTPEGESLS-VAVSGNLSASISSLLMDAAIKHCG--IAMLPEReasa 244
Cdd:cd08461    81 GHPLLQG-PLSLDQFCALDHIVVSPSGGG---FAGSTDEALAaLGLTRNVVLSVPSFLVVPEILAATdmVAFVPSR---- 152

                         170
                  ....*....|....*....
gi 1016941181 245 aleqglLVPVLEALEPKPL 263
Cdd:cd08461   153 ------LVPNLEGLQEVEL 165
PRK12680 PRK12680
LysR family transcriptional regulator;
15-150 5.91e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.76  E-value: 5.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  15 ELGSLSAAARaLGISRPMVSRYLEQMEKWAGTRLVNRSTRKL-TLTAAGEKVLQKTRTLSQISQEIE--GQSEKDLPSGT 91
Cdd:PRK12680   16 ELNITLAAAR-VHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRtyAANQRRESQGQ 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1016941181  92 LRVACAHFTAMHLIAPVLPGLLSRYPQLRIELD--VNNHPVSLVGE-RIDVAVRITDNPEPG 150
Cdd:PRK12680   95 LTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQqaAESAALDLLGQgDADIAIVSTAGGEPS 156
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-185 8.53e-04

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 39.43  E-value: 8.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  91 TLRVACAHFTAMHLIAPVLPGLLSRYPQLRIEL-DVNNHPV--SLVGERIDVAVRITDNPEPGMIARRLGECRSVLCASP 167
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLrDVSAEQVieAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                          90
                  ....*....|....*....
gi 1016941181 168 DY-LAQHGTpVSPEELAQH 185
Cdd:cd08440    81 DHpLARRRS-VTWAELAGY 98
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 16-72 1.55e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 39.54  E-value: 1.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1016941181  16 LGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTL 72
Cdd:PRK11074   16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSV 72
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 15-177 3.93e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.09  E-value: 3.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  15 ELGSLSAAARALGISRPMVSRYLEQMEKWAGTRLVNRSTRKLTLTAAGEKVLQKTRTLSQISQEIEGQSEKDLPSGTLRV 94
Cdd:PRK15092   24 DLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNLQGVLTI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016941181  95 ACAHFTAmhliAPVLPGLLSR----YPQLRIELDVNNHPV---SLVGERIDVAVrITDNPE--PGMIARR---LGECrsv 162
Cdd:PRK15092  104 GASDDTA----DTILPFLLNRvssvYPKLALDVRVKRNAFmmeMLESQEVDLAV-TTHRPSsfPALNLRTsptLWYC--- 175

                         170
                  ....*....|....*
gi 1016941181 163 lcaSPDYLAQHGTPV 177
Cdd:PRK15092  176 ---AAEYVLQKGEPI 187
 
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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