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Conserved domains on  [gi|488138641|ref|WP_002209849|]
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MULTISPECIES: LysR family transcriptional regulator [Yersinia pseudotuberculosis complex]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-287 1.22e-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: 237.34  E-value: 1.22e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYFGESL-WHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488138641 251 ELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 1.54e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.72  E-value: 1.54e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488138641    8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGE 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 ...
 92-287 1.22e-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: 237.34  E-value: 1.22e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYFGESL-WHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488138641 251 ELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
8-290 6.01e-54

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 177.92  E-value: 6.01e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQES 87
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  88 EELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCA 167
Cdd:PRK09801  92 TRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 168 SPAYLSVSGIPESPQDLTVHNCLTYSY--FGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAP 245
Cdd:PRK09801 172 APEYLQKYPQPQSLQELSRHDCLVTKErdMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVLP 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 488138641 246 YIARGELIKLLPDYQpQAMGIYGVYASRRQMPTTLRTMLDFLVEW 290
Cdd:PRK09801 252 FLESGKLVQVLPEYA-QSANIWAVYREPLYRSMKLRVCVEFLAAW 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 2.80e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.97  E-value: 2.80e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   1 MDrITAAEVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMD 80
Cdd:COG0583    1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  81 LAEGQESEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNN--RAIN-LVEERIDLALRITNELDPNLIARP 157
Cdd:COG0583   80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 158 LSTCYSVVCASPAYLSVSGIPESpqdltvhncltysyfgeslwhfdqsgvkssvavsgnlsaNESVVLLSGALEGAGITL 237
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488138641 238 QPIYSVAPYIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:COG0583  201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 5.81e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.08  E-value: 5.81e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   91 RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNN--RAINLVEE-RIDLALRITNELDPNLIARPLSTCYSVVCA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  168 SPAYLSVSGIPESPQDLTVHNCLTYSYFGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYI 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 488138641  248 ARGELIKL-LPDYQPQaMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:pfam03466 161 ADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 1.54e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.72  E-value: 1.54e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488138641    8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-79 9.55e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 9.55e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDM 79
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESM 79
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-95 4.66e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 39.03  E-value: 4.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  12 AIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTT--RK---LSLTHAGEATLERCRRMlEFAQDMDLAEgqE 86
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRL-EAEAQRALAA--L 105


                 ....*....
gi 488138641  87 SEELRGLLR 95
Cdd:COG2005  106 FEELFALLR 114
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-287 1.22e-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: 237.34  E-value: 1.22e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYFGESL-WHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLrWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488138641 251 ELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 7.55e-64

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: 199.76  E-value: 7.55e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYF-GESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08477   81 LARHGTPTTPEDLARHECLGFSYWrARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488138641 251 ELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08477  161 RLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 3.90e-56

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: 180.10  E-value: 3.90e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYFGE--SLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIAR 249
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRENDEdfGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488138641 250 GELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08479  161 GRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 9.68e-55

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: 176.35  E-value: 9.68e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSyfgESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARGE 251
Cdd:cd08470   81 LERHGTPHSLADLDRHNCLLGT---SDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAGR 157

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488138641 252 LIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVE 289
Cdd:cd08470  158 LVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PRK09801 PRK09801
LysR family transcriptional regulator;
8-290 6.01e-54

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 177.92  E-value: 6.01e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQES 87
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  88 EELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCA 167
Cdd:PRK09801  92 TRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 168 SPAYLSVSGIPESPQDLTVHNCLTYSY--FGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAP 245
Cdd:PRK09801 172 APEYLQKYPQPQSLQELSRHDCLVTKErdMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVLP 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 488138641 246 YIARGELIKLLPDYQpQAMGIYGVYASRRQMPTTLRTMLDFLVEW 290
Cdd:PRK09801 252 FLESGKLVQVLPEYA-QSANIWAVYREPLYRSMKLRVCVEFLAAW 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 2.80e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.97  E-value: 2.80e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   1 MDrITAAEVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMD 80
Cdd:COG0583    1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  81 LAEGQESEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNN--RAIN-LVEERIDLALRITNELDPNLIARP 157
Cdd:COG0583   80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 158 LSTCYSVVCASPAYLSVSGIPESpqdltvhncltysyfgeslwhfdqsgvkssvavsgnlsaNESVVLLSGALEGAGITL 237
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488138641 238 QPIYSVAPYIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:COG0583  201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-287 1.01e-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 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: 161.09  E-value: 1.01e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  91 RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLS--TCYSVVcAS 168
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGppLRMAVV-AS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 169 PAYLSVSGIPESPQDLTVHNCLTYsYFGES----LWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVA 244
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRY-RFPTSgalyRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488138641 245 PYIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08474  160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 2.80e-47

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: 157.29  E-value: 2.80e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHncLTYSYF----GESL-WHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPY 246
Cdd:cd08472   81 LARHGTPRHPEDLERH--RAVGYFsartGRVLpWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPH 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488138641 247 IARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVE 289
Cdd:cd08472  159 LASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 3.17e-47

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: 157.30  E-value: 3.17e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYS-YFGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08471   81 LARHGTPKHPDDLADHDCIAFTgLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAG 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488138641 251 ELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVE 289
Cdd:cd08471  161 RLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVP 199
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-292 9.63e-47

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 159.16  E-value: 9.63e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   1 MDRITAAEVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMD 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  81 LAEGQESEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLST 160
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 161 CYSVVCASPAYLSVSGIPESPQDLTVHNCLTYSYFGESlwHFD---QSGVKSSVAVSGNLSANESVVLLSGALEGAGITL 237
Cdd:PRK10632 161 MPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDN--EFEliaPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAY 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488138641 238 QPIYSVAPYIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:PRK10632 239 VPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-287 5.88e-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 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: 151.17  E-value: 5.88e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  91 RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNEL--DPNLIARPLSTCYSVVCAS 168
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPleDSSLVMRVLGQSRQRLVAS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 169 PAYLSVSGIPESPQDLTVHNCLTYSYF-GESLWH-FDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPY 246
Cdd:cd08473   82 PALLARLGRPRSPEDLAGLPTLSLGDVdGRHSWRlEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCREA 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488138641 247 IARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08473  162 LRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-292 2.68e-43

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 150.14  E-value: 2.68e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQESEE 89
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  90 LRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNEL--DPNLIARPLSTCYSVVCA 167
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADRGHRLFA 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 168 SPAYLSVSGIPESPQDLTVHNCLTYSYfGESL--WH-FDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVA 244
Cdd:PRK14997 170 SPDLIARMGIPSAPAELSHWPGLSLAS-GKHIhrWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVK 248

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 488138641 245 PYIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:PRK14997 249 EQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYA 296
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 2.22e-39

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 136.70  E-value: 2.22e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYF-GESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGFNFRrALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAAG 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488138641 251 ELIKLLPDYQP-QAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08480  161 RLVPVLEEYNPgDREPIHAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 2.00e-36

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: 129.21  E-value: 2.00e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDP-NLIARPLSTCYSVVCASPA 170
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 171 YLSVSGIPESPQDLTVHNCLTYSYFGESL-WHF-DQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIA 248
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLpWRLaDEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488138641 249 RGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08475  161 RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 5.81e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.08  E-value: 5.81e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   91 RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNN--RAINLVEE-RIDLALRITNELDPNLIARPLSTCYSVVCA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  168 SPAYLSVSGIPESPQDLTVHNCLTYSYFGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYI 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 488138641  248 ARGELIKL-LPDYQPQaMGIYGVYASRRQMPTTLRTMLDFLVEWFA 292
Cdd:pfam03466 161 ADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 2.02e-30

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 113.49  E-value: 2.02e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  92 GLLRISCSqsLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAY 171
Cdd:cd08476    1 GRLRVSLP--LVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 172 LSVSGIPESPQDLTVHNCLTYSYFGESL---WHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIA 248
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRFPTTGKlepWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488138641 249 RGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08476  159 DGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-287 5.81e-29

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: 109.74  E-value: 5.81e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  91 RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPA 170
Cdd:cd08478    2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 171 YLSVSGIPESPQDLTVHNCLTYSYFGE-SLW---HFDQSGVKssvaVSGNLSANESVVLLSGALEGAGITLQPIYSVAPY 246
Cdd:cd08478   82 YLARHGTPQSIEDLAQHQLLGFTEPASlNTWpikDADGNLLK----IQPTITASSGETLRQLALSGCGIACLSDFMTDKD 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488138641 247 IARGELIKLLPDYQ-PQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08478  158 IAEGRLIPLFAEQTsDVRQPINAVYYRNTALSLRIRCFIDFL 199
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 1.54e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.72  E-value: 1.54e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488138641    8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-287 2.87e-15

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: 72.61  E-value: 2.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  94 LRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPL-STCYSVVCaSPAYL 172
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLmDEELVPVC-SPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 173 SVSGiPESPQDLTVHNCLTYSYFGESLWHFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARGEL 252
Cdd:cd08432   81 AGLP-LLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 488138641 253 IKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-289 1.01e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 73.11  E-value: 1.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   9 VFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGE---ATLERcrRMLEFAQDM-DLAeg 84
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKrvfWALKS--SLDTLNQEIlDIK-- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  85 qeSEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSV 164
Cdd:PRK10086  97 --NQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEIL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 165 -VCaSPAYLSVSGIPESPQDL----TVHNCLTYSY-FGESLWHF--DQSGVkSSVAVSGNLSANESVVLLSGALEGAGIT 236
Cdd:PRK10086 175 pVC-SPEYAERHALTGNPDNLrhctLLHDRQAWSNdSGTDEWHSwaQHFGV-NLLPPSSGIGFDRSDLAVIAAMNHIGVA 252

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488138641 237 LQPIYSVAPYIARGELIKLLPDYQ-PQAMGIYGVYASRRQMPtTLRTMLDFLVE 289
Cdd:PRK10086 253 MGRKRLVQKRLASGELVAPFGDMEvKCHQHYYVTTLPGRQWP-KIEAFIDWLKE 305
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-258 1.48e-13

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 69.49  E-value: 1.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  18 SMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLefaqdMDLAEGqeSEELR-----G 92
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF-----DQLAEA--TRKLRarsakG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  93 LLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAYL 172
Cdd:PRK11139  95 ALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 173 SVSGIPESPQDLTVHNCLTYSyfGESLWH--FDQSGVkSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARG 250
Cdd:PRK11139 175 NGGKPLKTPEDLARHTLLHDD--SREDWRawFRAAGL-DDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAG 251


                 ....*...
gi 488138641 251 ELIKLLPD 258
Cdd:PRK11139 252 RLVCPFDT 259
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-153 3.12e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.89  E-value: 3.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   9 VFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQD-----MDLAE 83
Cdd:CHL00180  12 ILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEEtcralEDLKN 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488138641  84 GQeseelRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMN-NRAI--NLVEERIDLALrITNELDPNL 153
Cdd:CHL00180  92 LQ-----RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHsTRRIawNVANGQIDIAI-VGGEVPTEL 158
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-287 7.46e-13

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: 66.08  E-value: 7.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  94 LRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNN--RAINLVEE-RIDLALRITNELDPNLIARPLSTCYSVVCASPA 170
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGssELLEALLEgELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 171 YLSVSGIPESPQDLTVHNCLT----YSYFGESLWHFDQSGVKSSVAV-SGNLSAnesvvLLSGALEGAGITLQPiYSVAP 245
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILfergSGLRRLLDRAFAEAGFTPNIALeVDSLEA-----IKALVAAGLGIALLP-ESAVE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488138641 246 YIARGELIKLLPDYQPQAMGIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd05466  156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 94-290 3.13e-12

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: 64.29  E-value: 3.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  94 LRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAYLS 173
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 174 VSGIpESPQDLTVHNCL-TYSYFGESLWHFDQSGVKSSVAVSGNLSANesvVLLSGALEGAGITLQPIYSVAPYIARGEL 252
Cdd:cd08483   82 DRKV-DSLADLAGLPWLqERGTNEQRVWLASMGVVPDLERGVTFLPGQ---LVLEAARAGLGLSIQARALVEPDIAAGRL 157

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488138641 253 IKLLPDyQPQAMGIYGVyasrrQMPTTLRTMLDFLVEW 290
Cdd:cd08483  158 TVLFEE-EEEGLGYHIV-----TRPGVLRPAAKAFVRW 189
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-158 3.90e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 62.67  E-value: 3.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEfaqdmDLAEGQ---- 85
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ-----DLEAGRraih 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488138641  86 ESEEL-RGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQ-MNNRAIN--LVEERIDLALRITNELDPNLIARPL 158
Cdd:PRK11242  84 DVADLsRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIReMSQERIEalLADDELDVGIAFAPVHSPEIEAQPL 160
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-250 1.40e-09

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: 56.80  E-value: 1.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  93 LLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRA--INLVEER-IDLALRITNELDPNLIARPLSTCySVVCASP 169
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSStvVEAVLSGqADLGLASLPLDHPGLESEPLASG-RAVCVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 170 AYLSVSGIPE-SPQDLTVHNCLTYSY---FGESLWH-FDQSGVKSSVAVsgnlSANESVVLLSGALEGAGITLqpiysVA 244
Cdd:cd08415   80 PGHPLARKDVvTPADLAGEPLISLGRgdpLRQRVDAaFERAGVEPRIVI----ETQLSHTACALVAAGLGVAI-----VD 150


                 ....*.
gi 488138641 245 PYIARG 250
Cdd:cd08415  151 PLTAAG 156
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-170 3.08e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.01  E-value: 3.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDlaegQES 87
Cdd:PRK10837   9 EVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE----QLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  88 EELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNR--AINLVEE-RIDLALRITNELDPNLIARPLSTCYSV 164
Cdd:PRK10837  85 REDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSqdVINAVLDfRVDIGLIEGPCHSPELISEPWLEDELV 164


                 ....*.
gi 488138641 165 VCASPA 170
Cdd:PRK10837 165 VFAAPD 170
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-79 9.55e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 9.55e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDM 79
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESM 79
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 111-266 1.83e-08

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: 53.30  E-value: 1.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 111 VADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTcysvvcaspAYLSVSGIPE------SPQDL 184
Cdd:cd08488   19 LADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFE---------APLSPLCTPElarqlrEPADL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 185 TVHNCLTySYFGE--SLWhFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARGELIkllpdyQPQ 262
Cdd:cd08488   90 ARHTLLR-SYRADewPQW-FEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV------QPF 161


                 ....
gi 488138641 263 AMGI 266
Cdd:cd08488  162 ATTL 165
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
34-143 4.41e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 53.28  E-value: 4.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  34 TRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQESEELRGLLRISCSQSLGQSALAIAVAD 113
Cdd:PRK11716   9 SRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPILDR 88

                         90       100       110
                 ....*....|....*....|....*....|...
gi 488138641 114 YLRRYPQVAVDLQMNN--RAINLVE-ERIDLAL 143
Cdd:PRK11716  89 FRAEHPLVEIKLTTGDaaDAVEKVQsGEADLAI 121
PRK12680 PRK12680
LysR family transcriptional regulator;
4-126 1.81e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.55  E-value: 1.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   4 ITAAEVFVAIVDRGSMIA-AAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKL-SLTHAGEATLERCRRMLEFAQDMDL 81
Cdd:PRK12680   3 LTQLRYLVAIADAELNITlAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRT 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 488138641  82 AEGQESEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQ 126
Cdd:PRK12680  83 YAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQ 127
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 112-254 1.87e-07

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 50.45  E-value: 1.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 112 ADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPL-STCYSVVCASPAYLSVSgipeSPQDLTVHNCL 190
Cdd:cd08484   20 AEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLfEAPLSPLCTPELARRLS----EPADLANETLL 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488138641 191 TySYFGE--SLWhFDQSGVkSSVAVSGNLsANESVVLLSGALEGAGITLQPIYSVAPYIARGELIK 254
Cdd:cd08484   96 R-SYRADewPQW-FEAAGV-PPPPINGPV-FDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQ 157
PRK09791 PRK09791
LysR family transcriptional regulator;
10-123 2.72e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 2.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLE---FAQDmDLAegQE 86
Cdd:PRK09791  13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEelrAAQE-DIR--QR 89

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 488138641  87 SEELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAV 123
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKV 126
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 20-96 8.50e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 49.38  E-value: 8.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  20 IAAAESLEMSRAMATRYLAQ---------MEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQESEEL 90
Cdd:PRK09906  10 VAVAEELNFTKAAEKLHTAQpslsqqikdLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQED 89


                 ....*.
gi 488138641  91 RgLLRI 96
Cdd:PRK09906  90 R-QLTI 94
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-258 4.00e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 47.27  E-value: 4.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   7 AEVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRtTRKLSLTHAGEATLERCRRMlefaqDMdlaegQE 86
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-----AL-----LE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  87 SEELRGLLRiscsQSLGQSALAIAV-ADYLRRY--PQVAVDLQMNNRAINLVEERIDLALR----------ITNELDP-- 151
Cdd:PRK13348  76 ADLLSTLPA----ERGSPPTLAIAVnADSLATWflPALAAVLAGERILLELIVDDQDHTFAllergevvgcVSTQPKPmr 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 152 NLIARPLSTCYSVVCASPAY--------LSVSGIPESP-----QDLTVHNCLTYSYFGESLWHFDQSGVKSSVAvsgnls 218
Cdd:PRK13348 152 GCLAEPLGTMRYRCVASPAFaaryfaqgLTRHSALKAPavafnRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHA------ 225

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 488138641 219 anesvvLLSGALEGAGITLQPIYSVAPYIARGELIKLLPD 258
Cdd:PRK13348 226 ------HLAAIRHGLGYGMVPELLIGPLLAAGRLVDLAPG 259
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 113-287 5.47e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 46.13  E-value: 5.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 113 DYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIARPLSTCYSVVCASPAYLSVSGIpESPQDLtVHNCLTY 192
Cdd:cd08481   21 DFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRAL-AAPADL-AHLPLLQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 193 SYFGESLWH--FDQSGVKSSVAVSGNLSANESVVlLSGALEGAGITLQPIYSVAPYIARGELIKLLPDYQPQAMGIYGVY 270
Cdd:cd08481   99 QTTRPEAWRdwFEEVGLEVPTAYRGMRFEQFSML-AQAAVAGLGVALLPRFLIEEELARGRLVVPFNLPLTSDKAYYLVY 177

                        170
                 ....*....|....*..
gi 488138641 271 ASRRQMPTTLRTMLDFL 287
Cdd:cd08481  178 PEDKAESPPVQAFRDWL 194
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-250 9.77e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 46.55  E-value: 9.77e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   1 MDRITAAEVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRML-EFAQdm 79
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLpQISQ-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  80 DLAEGQESEELRGLLRISCSQSLgqSALAIAVADYLRRYPQVAVDLQMN---NRAINLVEERIDLALriTNELDP--NLI 154
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCI--QWLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLVM--TSDILPrsGLH 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 155 ARPLSTCYSVVCASPAYLSVSGIPESPQDLTVHNCLTYSYFGESL--W-HFDQSGvkssvAVSGNL-SANESVVLLSGAL 230
Cdd:PRK15421 155 YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLdvWrHFLQPA-----GVSPSLkSVDNTLLLIQMVA 229

                        250       260
                 ....*....|....*....|
gi 488138641 231 EGAGITLQPIYSVAPYIARG 250
Cdd:PRK15421 230 ARMGIAALPHWVVESFERQG 249
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 8-124 1.23e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.14  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCR-------RMLEFAQDM- 79
Cdd:PRK11013  10 EIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQrsyygldRIVSAAESLr 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 488138641  80 DLAEGQeseelrglLRISCSQSLGQSALAIAVADYLRRYPQVAVD 124
Cdd:PRK11013  90 EFRQGQ--------LSIACLPVFSQSLLPGLCQPFLARYPDVSLN 126
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 201-287 7.84e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 42.68  E-value: 7.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 201 HFDQSGVKSSVAVSGNLSANESVVLLSGALEGAGITLQPIYSVAPYIARGELIKL-LPDYQPQAMGIYGVYASRRQMPTT 279
Cdd:cd08426  112 ILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQLVAVpLADPHMNHRQLELQTRAGRQLPAA 191


                 ....*...
gi 488138641 280 LRTMLDFL 287
Cdd:cd08426  192 ASAFLQLL 199
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 111-254 3.26e-04

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: 40.99  E-value: 3.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 111 VADYLRRYPQVAVDLQMNNRAINLVEERIDLALRITNELDPNLIA-RPLSTCYSVVCASPAYLSVSgipeSPQDLTVHNC 189
Cdd:cd08487   19 LAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNeRLLDAPLSVLCSPEIAKRLS----HPADLINETL 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488138641 190 LTYSYFGESLWHFDQSGVkSSVAVSGNLsANESVVLLSGALEGAGITLQPIYSVAPYIARGELIK 254
Cdd:cd08487   95 LRSYRTDEWLQWFEAANM-PPIKIRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ 157
PRK09986 PRK09986
LysR family transcriptional regulator;
10-76 3.31e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.63  E-value: 3.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFA 76
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNA 81
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-95 4.66e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 39.03  E-value: 4.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  12 AIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTT--RK---LSLTHAGEATLERCRRMlEFAQDMDLAEgqE 86
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRL-EAEAQRALAA--L 105


                 ....*....
gi 488138641  87 SEELRGLLR 95
Cdd:COG2005  106 FEELFALLR 114
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 10-142 6.41e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 40.82  E-value: 6.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCR---RMLEFAQDMDLAEGQe 86
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARailRQCEQAQLAVHNVGQ- 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  87 seELRGLLRISCSQSLGQSALAIAVADYLR-RYPQVAVDLQMNNRAI---NLVEERIDLA 142
Cdd:PRK11233  88 --ALSGQVSIGLAPGTAASSLTMPLLQAVRaEFPGIVLYLHENSGATlneKLMNGQLDMA 145
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-158 8.63e-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: 39.82  E-value: 8.63e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488138641  93 LLRISCSQSLGQSALAIAVADYLRRYPQVAVDL--QMNNRAINLV-EERIDLALRITNELDPNLIARPL 158
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLrdVSAEQVIEAVrSGEVDFGIGSEPEADPDLEFEPL 69
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-287 2.32e-03

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 38.24  E-value: 2.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  94 LRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAIN---LVEERIDLALRITNELDPNLIARPLSTCYSVVCASPA 170
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIaerVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641 171 YLSVSGIPESPQDLTVHNCL-------TYSYFGESLWHFDQSGVKssVAVSGNLSANESVVllsGALE-GAGITLQPIYS 242
Cdd:cd08420   82 HPLAGRKEVTAEELAAEPWIlrepgsgTREVFERALAEAGLDGLD--LNIVMELGSTEAIK---EAVEaGLGISILSRLA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 488138641 243 VAPYIARGEL----IKLLPDYQPqamgIYGVYASRRQMPTTLRTMLDFL 287
Cdd:cd08420  157 VRKELELGRLvalpVEGLRLTRP----FSLIYHKDKYLSPAAEAFLEFL 201
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-162 2.56e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.80  E-value: 2.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  21 AAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKL-SLTHAGEATLERCRRMLEFAQDMDLAEGQESEELRGLLRISCS 99
Cdd:PRK12684  21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATT 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488138641 100 QSLGQSALAIAVADYLRRYPQVAVDLQMNNR---AINLVEERIDLAlrITNE---LDPNLIARPlstCY 162
Cdd:PRK12684 101 HTQARYALPAAIKEFKKRYPKVRLSILQGSPtqiAEMVLHGQADLA--IATEaiaDYKELVSLP---CY 164
PRK10341 PRK10341
transcriptional regulator TdcA;
9-68 3.99e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 38.30  E-value: 3.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   9 VFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLER 68
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR 73
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-143 5.53e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 37.70  E-value: 5.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  10 FVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQD--MDLAegqeS 87
Cdd:PRK15092  19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEacSSLM----Y 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488138641  88 EELRGLLRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAI---NLVEERIDLAL 143
Cdd:PRK15092  95 SNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFmmeMLESQEVDLAV 153
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 94-143 6.05e-03

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 37.01  E-value: 6.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488138641  94 LRISCSQSLGQSALAIAVADYLRRYPQVAVDLQMNNRAinLVEE-----RIDLAL 143
Cdd:cd08456    2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSP--TVEQwlsaqQCDLGL 54
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-142 6.81e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 37.61  E-value: 6.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641   8 EVFVAIVDRGSMIAAAESLEMSRAMATRYLAQMEQWAGARLLHRTTRKLSLTHAGEATLERCRRMLEFAQDMDLAEGQES 87
Cdd:PRK11074   8 EVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVA 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488138641  88 EELRGLLRISCSQSLGQSALAIAVADYLRRYPQvaVDLQMNNRAIN-----LVEERIDLA 142
Cdd:PRK11074  88 NGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDD--VELIIRQEVFNgvwdaLADGRVDIA 145
 
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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