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Conserved domains on  [gi|2546352544|ref|WP_301334555|]
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LysR family transcriptional regulator [Variovorax dokdonensis]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-293 2.38e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 2.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   5 EAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLveltQRLDDARTEV 84
Cdd:COG0583     7 RAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIL----AELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  85 QDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPG---SLSPEEADCYVCAAPPDSQQLVLKSIGQ 161
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 162 LGFGLYASPSYlaragapdtpdALAEHDAIVlhdalgrgdltllrgrahalirpraafstNDHWVMKTLCLDGLGIALMP 241
Cdd:COG0583   163 ERLVLVASPDH-----------PLARRAPLV-----------------------------NSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2546352544 242 DYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMARCV 293
Cdd:COG0583   203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-293 2.38e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 2.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   5 EAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLveltQRLDDARTEV 84
Cdd:COG0583     7 RAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIL----AELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  85 QDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPG---SLSPEEADCYVCAAPPDSQQLVLKSIGQ 161
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 162 LGFGLYASPSYlaragapdtpdALAEHDAIVlhdalgrgdltllrgrahalirpraafstNDHWVMKTLCLDGLGIALMP 241
Cdd:COG0583   163 ERLVLVASPDH-----------PLARRAPLV-----------------------------NSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2546352544 242 DYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMARCV 293
Cdd:COG0583   203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-289 5.88e-45

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: 151.44  E-value: 5.88e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY 172
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 173 LARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELRHQ 252
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2546352544 253 GLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08422   161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-290 8.46e-29

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 112.01  E-value: 8.46e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   7 FVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVEltqrLDDARTEVQD 86
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVE----AQAAQDAIAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  87 LSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADC--YVCAAPPDSQQLVLKSIGQLGF 164
Cdd:PRK14997   86 LQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVaiRVRPRPFEDSDLVMRVLADRGH 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 165 GLYASPSYLARAGAPDTPDALAEHDAIVLHDA--LGRGDLTLLRG-RAHALIRPRaaFSTNDHWVMKTLCLDGLGIALMP 241
Cdd:PRK14997  166 RLFASPDLIARMGIPSAPAELSHWPGLSLASGkhIHRWELYGPQGaRAEVHFTPR--MITTDMLALREAAMAGVGLVQLP 243

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2546352544 242 DYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMA 290
Cdd:PRK14997  244 VLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLT 292
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-291 3.30e-26

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: 102.75  E-value: 3.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  92 TGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPG---SLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEElldLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 169 SPSYLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHAlIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPE 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAG-LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2546352544 249 LRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMAR 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
13-79 4.82e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.03  E-value: 4.82e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2546352544   13 SGSLTRAE--QSSGMSKASLSRHLAQLEaslGAELIQRG-------SRHLRPTEAGRAFFARCEPMLVELTQRLDD 79
Cdd:smart00347  22 EGPLSVSElaKRLGVSPSTVTRVLDRLE---KKGLVRREpspedrrSVLVSLTEEGRELIEQLLEARSETLAELLA 94
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-293 2.38e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 2.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   5 EAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLveltQRLDDARTEV 84
Cdd:COG0583     7 RAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIL----AELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  85 QDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPG---SLSPEEADCYVCAAPPDSQQLVLKSIGQ 161
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 162 LGFGLYASPSYlaragapdtpdALAEHDAIVlhdalgrgdltllrgrahalirpraafstNDHWVMKTLCLDGLGIALMP 241
Cdd:COG0583   163 ERLVLVASPDH-----------PLARRAPLV-----------------------------NSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2546352544 242 DYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMARCV 293
Cdd:COG0583   203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-289 5.88e-45

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: 151.44  E-value: 5.88e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY 172
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 173 LARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELRHQ 252
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2546352544 253 GLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08422   161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 3.00e-31

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 115.79  E-value: 3.00e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY 172
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 173 LARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELRHQ 252
Cdd:cd08477    81 LARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2546352544 253 GLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVD 287
Cdd:cd08477   161 RLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFID 195
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 1.08e-29

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 111.84  E-value: 1.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY 172
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 173 LARAGAPDTPDALAEHDAI--VLHDALGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELR 250
Cdd:cd08472    81 LARHGTPRHPEDLERHRAVgyFSARTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLA 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2546352544 251 HQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVD 287
Cdd:cd08472   161 SGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-290 8.46e-29

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 112.01  E-value: 8.46e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   7 FVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVEltqrLDDARTEVQD 86
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVE----AQAAQDAIAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  87 LSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADC--YVCAAPPDSQQLVLKSIGQLGF 164
Cdd:PRK14997   86 LQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVaiRVRPRPFEDSDLVMRVLADRGH 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 165 GLYASPSYLARAGAPDTPDALAEHDAIVLHDA--LGRGDLTLLRG-RAHALIRPRaaFSTNDHWVMKTLCLDGLGIALMP 241
Cdd:PRK14997  166 RLFASPDLIARMGIPSAPAELSHWPGLSLASGkhIHRWELYGPQGaRAEVHFTPR--MITTDMLALREAAMAGVGLVQLP 243

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2546352544 242 DYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMA 290
Cdd:PRK14997  244 VLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLT 292
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-291 3.30e-26

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: 102.75  E-value: 3.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  92 TGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPG---SLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEElldLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 169 SPSYLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHAlIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPE 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAG-LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2546352544 249 LRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMAR 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-289 1.88e-25

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 100.36  E-value: 1.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYV-CAAPPDSQqLVLKSIGQLGFGLYASPS 171
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIrVGDLPDSS-LIARKLAPNRRILCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 172 YLARAGAPDTPDALAEHDAIVLHDALGRGDL-TLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELR 250
Cdd:cd08479    80 YLERHGAPASPEDLARHDCLVIRENDEDFGLwRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2546352544 251 HQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08479   160 SGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-290 8.19e-24

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: 96.06  E-value: 8.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAP-PDSQqLVLKSIGQLGFGLYASPS 171
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHlPDSS-LVATRVGSVRRVVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 172 YLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELRH 251
Cdd:cd08471    80 YLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAA 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2546352544 252 QGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMA 290
Cdd:cd08471   160 GRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAV 198
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-274 1.42e-22

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: 93.00  E-value: 1.42e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  92 TGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADC--YVCAAPPDSQQLVLKSIGQLGFGLYAS 169
Cdd:cd08473     2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDValRVRFPPLEDSSLVMRVLGQSRQRLVAS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 170 PSYLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLR--GRAHAL-IRPRaaFSTNDHWVMKTLCLDGLGIALMPDYFVQ 246
Cdd:cd08473    82 PALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGpdGESITVrHRPR--LVTDDLLTLRQAALAGVGIALLPDHLCR 159

                         170       180       190
                  ....*....|....*....|....*....|
gi 2546352544 247 PELRHQGLVPVLPEWKPAPRRIHCAF--RR 274
Cdd:cd08473   160 EALRAGRLVRVLPDWTPPRGIVHAVFpsRR 189
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 168-289 5.06e-21

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 88.67  E-value: 5.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 168 ASPSYLARAGAPDTPDALAEHDAIVL----HDALGRGDLTllRGRAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDY 243
Cdd:cd08474    79 ASPAYLARHGTPEHPRDLLNHRCIRYrfptSGALYRWEFE--RGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFED 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2546352544 244 FVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08474   157 LVAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-289 3.58e-19

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: 83.54  E-value: 3.58e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRM----DIAGMPGslspEEADCYVCAAPPDSQQLVLKSIGQLGFGLYA 168
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLsltdEVVDLLA----ERTDVAIRVGPLPDSSLVARKLGESRRVIVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 169 SPSYLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGrAHALIRP-RAAFSTNDHWVMKTLCLDGLGIALMPDYFVQP 247
Cdd:cd08480    77 SPSYLARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDG-GRIVALPvSGNILVNDGEALRRLALAGAGLARLALFHVAD 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2546352544 248 ELRHQGLVPVLPEWKPAPRR-IHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08480   156 DIAAGRLVPVLEEYNPGDREpIHAVYVGGGRLPARVRAFLDFL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
2-290 3.83e-19

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 85.86  E-value: 3.83e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   2 KSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRaffaRCEPMLVELTQRLDDAR 81
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQ----RCYEHALEILTQYQRLV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  82 TEVQDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPE--EADCYVCAAPPDS--QQLVLK 157
Cdd:PRK09801   85 DDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDniDLDIRINDEIPDYyiAHLLTK 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 158 SIGQlgfgLYASPSYLARAGAPDTPDALAEHDAIVLHDA-LGRGDLTLLRGRAHALIRPRAAFSTNDHWVMKTLCLDGLG 236
Cdd:PRK09801  165 NKRI----LCAAPEYLQKYPQPQSLQELSRHDCLVTKERdMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKG 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2546352544 237 IALMPDYFVQPELRHQGLVPVLPEWKPAPrRIHCAFRRQRYAGSKLRDFVDLMA 290
Cdd:PRK09801  241 IMLRSEWDVLPFLESGKLVQVLPEYAQSA-NIWAVYREPLYRSMKLRVCVEFLA 293
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-291 6.92e-19

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: 82.74  E-value: 6.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGMPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY 172
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 173 LARAGAPDTPDALAEHDAIvlhdaLGRGDLTLLR--GRAHAlIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELR 250
Cdd:cd08470    81 LERHGTPHSLADLDRHNCL-----LGTSDHWRFQenGRERS-VRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2546352544 251 HQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMAR 291
Cdd:cd08470   155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 147-288 1.49e-18

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 81.83  E-value: 1.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 147 APPDSQQLVLKSIGQLGFGLYASPSYLARAGAPDTPDALAEHDAIvlhdALGRGDLTL------LRGRAHAlIRPRAAFS 220
Cdd:cd08475    56 ELADSTGLVARRLGTQRMVLCASPAYLARHGTPRTLEDLAEHQCI----AYGRGGQPLpwrladEQGRLVR-FRPAPRLQ 130

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2546352544 221 TNDHWVMKTLCLDGLGIALMPDYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDL 288
Cdd:cd08475   131 FDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDA 198
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-289 4.11e-18

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 80.72  E-value: 4.11e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  94 TLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAGmpgslSPE--------EADCYVCAAPPDSQQLVLKSIGQLGFG 165
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGG-----SSElleallegELDLAIVALPVDDPGLESEPLFEEPLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 166 LYASPSYLARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRaHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFV 245
Cdd:cd05466    76 LVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFA-EAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2546352544 246 QpELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd05466   155 E-ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 148-289 2.80e-17

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: 78.44  E-value: 2.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 148 PPDSQqLVLKSIGQLGFGLYASPSYLARAGAPDTPDALAEHDAIvLHDALGRGDL---TLLRGRAHALIRPRAAFSTNDH 224
Cdd:cd08476    55 LPDSR-LMSRRLGSFRMVLVASPDYLARHGTPETPADLAEHACL-RYRFPTTGKLepwPLRGDGGDPELRLPTALVCNNI 132

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2546352544 225 WVMKTLCLDGLGIALMPDYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08476   133 EALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-60 4.68e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 4.68e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   1 MKSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGR 60
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-275 4.88e-15

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 74.03  E-value: 4.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   1 MKSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQrlddA 80
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQD----V 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  81 RTEVQDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMdIAGMPG-SLSPEEADCYVCAAPPDSQQLVLKSI 159
Cdd:PRK10632   80 HEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL-VTGIPApDLIADGLDVVIRVGALQDSSLFSRRL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 160 GQLGFGLYASPSYLARAGAPDTPDALAEHdAIVLHDALGRGDLTLLRGRAHAL-IRPRAAFSTNDHWVMKTLCLDGLGIA 238
Cdd:PRK10632  159 GAMPMVVCAAKSYLAQYGTPEKPADLSSH-SWLEYSVRPDNEFELIAPEGISTrLIPQGRFVTNDPQTLVRWLTAGAGIA 237

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2546352544 239 LMPDYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQ 275
Cdd:PRK10632  238 YVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEK 274
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 93-289 1.31e-14

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: 71.22  E-value: 1.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVLADPQFGTAFVCQVVRLYMASYPgvHCRMDIAGMPG--SLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASP 170
Cdd:cd08478     3 GLLRVDAATPFVLHLLAPLIAKFRERYP--DIELELVSNEGiiDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 171 SYLARAGAPDTPDALAEHDAI------VLHD-ALGRGDLTLLRgrahalIRPRAAFSTNDhwVMKTLCLDGLGIALMPDY 243
Cdd:cd08478    81 DYLARHGTPQSIEDLAQHQLLgftepaSLNTwPIKDADGNLLK------IQPTITASSGE--TLRQLALSGCGIACLSDF 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2546352544 244 FVQPELRHQGLVPVL-PEWKPAPRRIHCAFRRQRYAGSKLRDFVDLM 289
Cdd:cd08478   153 MTDKDIAEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 14-289 1.08e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 67.29  E-value: 1.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  14 GSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELT--QRlddARTEVQDLSAGR 91
Cdd:PRK11242   16 GNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagRR---AIHDVADLSRGS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  92 tgtLRVLADPQFGTAFVCQVVRLYMASYPGVHcrMDIAGMP-----GSLSPEEADCYVCAAPP-----DSQQLVLKSIgq 161
Cdd:PRK11242   93 ---LRLAMTPTFTAYLIGPLIDAFHARYPGIT--LTIREMSqerieALLADDELDVGIAFAPVhspeiEAQPLFTETL-- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 162 lgfGLYASPSY-LARAGAPDTPDALAEHDAIVLHDALGRGDLTLLRGRAHAlIRPRAAFSTNDHWVMKTLCLDGLGIALM 240
Cdd:PRK11242  166 ---ALVVGRHHpLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHG-VTPRVAIEANSISAVLEIVRRGRLATLL 241

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2546352544 241 PDY--FVQPELRhqgLVPVLPewkPAPRRIHCAFRRQ-RYAGSKLRDFVDLM 289
Cdd:PRK11242  242 PAAiaREHDGLC---AIPLDP---PLPQRTAALLRRKgAYRSAAARAFIELA 287
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-129 1.75e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.78  E-value: 1.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   1 MKSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLveltqrldDA 80
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL--------EQ 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2546352544  81 RTEVQDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIA 129
Cdd:PRK10837   77 AVEIEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVG 125
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-265 1.60e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   1 MKSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGsRHLRPTEAGRAFFARCEPMLV---ELTQRL 77
Cdd:PRK13348    4 YKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALleaDLLSTL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  78 DDARTEVQDLSAGrtgtlrVLADpQFGTAF---VCQVVRlymasypGVHCRMDIA-----GMPGSLSPEEADCYVCAAPP 149
Cdd:PRK13348   83 PAERGSPPTLAIA------VNAD-SLATWFlpaLAAVLA-------GERILLELIvddqdHTFALLERGEVVGCVSTQPK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 150 DSQQLVLKSIGQLGFGLYASPSYLAR--AGAPdTPDALAEHDAIV------LHDALGRGDLTLLRGRAhalirPRAAFST 221
Cdd:PRK13348  149 PMRGCLAEPLGTMRYRCVASPAFAARyfAQGL-TRHSALKAPAVAfnrkdtLQDSFLEQLFGLPVGAY-----PRHYVPS 222

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2546352544 222 NDHWVMKtlCLDGLGIALMPDYFVQPELRHQGLVPVLPE-----------WKPAP 265
Cdd:PRK13348  223 THAHLAA--IRHGLGYGMVPELLIGPLLAAGRLVDLAPGhpvdvalywhhWEVES 275
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-128 3.28e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 53.87  E-value: 3.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  10 IMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFF-------ARCEpmlvELTQRLDDART 82
Cdd:CHL00180   16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLrygnrilALCE----ETCRALEDLKN 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2546352544  83 evqdlsaGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDI 128
Cdd:CHL00180   92 -------LQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQV 130
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-122 1.75e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 51.53  E-value: 1.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   4 VEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELtQRLDDArte 83
Cdd:PRK11013    9 IEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGL-DRIVSA--- 84

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2546352544  84 VQDLSAGRTGTLRVLADPQFGTAFVCQVVRLYMASYPGV 122
Cdd:PRK11013   85 AESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDV 123
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 16-286 4.68e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 50.38  E-value: 4.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  16 LTRAEQSSGMSKASLSRHLAQLEASLGAEL-IQRGSRHLRPTEAGRAFFARCEPMLVELTQ--RLDDartevqDLSAGRT 92
Cdd:PRK12682   19 LTEAAKALHTSQPGVSKAIIELEEELGIEIfIRHGKRLKGLTEPGKAVLDVIERILREVGNikRIGD------DFSNQDS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  93 GTLRVlADPQFGTAFVC-QVVRLYMASYPGVHCRM------DIAGMpgsLSPEEADCYVCaappdSQQLVLKSigqlgfG 165
Cdd:PRK12682   93 GTLTI-ATTHTQARYVLpRVVAAFRKRYPKVNLSLhqgspdEIARM---VISGEADIGIA-----TESLADDP------D 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 166 LYASPSY-------------LARAGaPDTPDALAEHDAIVLHDAL-GRGdlTLLRGRAHALIRPRAAFSTNDHWVMKTLC 231
Cdd:PRK12682  158 LATLPCYdwqhavivppdhpLAQEE-RITLEDLAEYPLITYHPGFtGRS--RIDRAFAAAGLQPDIVLEAIDSDVIKTYV 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2546352544 232 LDGLGIALMPDYFVQPElRHQGLV--PVLPEWKPAPRRIhcAFRRqryaGSKLRDFV 286
Cdd:PRK12682  235 RLGLGVGIVAEMAYRPD-RDGDLValPAGHLFGPNTAWV--ALKR----GAYLRNYV 284
PRK09791 PRK09791
LysR family transcriptional regulator;
4-91 6.62e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 49.76  E-value: 6.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   4 VEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQRLDDARtE 83
Cdd:PRK09791   10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIR-Q 88


                  ....*...
gi 2546352544  84 VQDLSAGR 91
Cdd:PRK09791   89 RQGQLAGQ 96
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 16-290 2.32e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.12  E-value: 2.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  16 LTRAEQSSGMSKASLSRHLAQLEASLGAEL-IQRGSRHLRPTEAGRAFFARCEPMLVEltqrLDDARTEVQDLSAGRTGT 94
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIfIRRGKRLTGLTEPGKELLQIVERMLLD----AENLRRLAEQFADRDSGH 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  95 LRVLADPQFGTAFVCQVVRLYMASYPGVHCRM------DIAGMpgsLSPEEADCYVCA-APPDSQQLVLKSIGQLGFGLY 167
Cdd:PRK12683   95 LTVATTHTQARYALPKVVRQFKEVFPKVHLALrqgspqEIAEM---LLNGEADIGIATeALDREPDLVSFPYYSWHHVVV 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 168 ASPSYLARAGAPDTPDALAEHDAIVLHdalgrGDLTllrGRAH-------ALIRPRAAFSTNDHWVMKTLCLDGLGIALM 240
Cdd:PRK12683  172 VPKGHPLTGRENLTLEAIAEYPIITYD-----QGFT---GRSRidqafaeAGLVPDIVLTALDADVIKTYVELGMGVGIV 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2546352544 241 PDYFVQPElRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDLMA 290
Cdd:PRK12683  244 AAMAYDPQ-RDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFA 292
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
7-255 7.34e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 46.59  E-value: 7.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   7 FVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQRLDDAR----- 81
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRggsdy 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  82 -------TEVQDLSAGRTGTLRVLADPQFGTAF----VCQVVRL-------YMASY--------PGVHCRMdiagMPGSL 135
Cdd:PRK10082   99 aqrkikiAAAHSLSLGLLPSIISQMPPLFTWAIeaidVDEAVDKlregqsdCIFSFhdedlleaPFDHIRL----FESQL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 136 SPeeadcyVCAAppDSQQLVLKSIGQLGFGL--YASPSYLARagapdtpdalaehdaivlhdALGRgdlTLLRgraHALI 213
Cdd:PRK10082  175 FP------VCAS--DEHGEALFNLAQPHFPLlnYSRNSYMGR--------------------LINR---TLTR---HSEL 220

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2546352544 214 RPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPELRHQGLV 255
Cdd:PRK10082  221 SFSTFFVSSMSELLKQVALDGCGIAWLPEYAIQQEIRSGQLV 262
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-122 8.66e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.60  E-value: 8.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   7 FVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQrlddARTEVQD 86
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ----AQLAVHN 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2546352544  87 LSAGRTGTLRVLADPqfGTAF------VCQVVRlymASYPGV 122
Cdd:PRK11233   85 VGQALSGQVSIGLAP--GTAAssltmpLLQAVR---AEFPGI 121
PRK10341 PRK10341
transcriptional regulator TdcA;
2-90 3.09e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.85  E-value: 3.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544   2 KSVEAFVHIMKSGSLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQRLDDAR 81
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                          90
                  ....*....|...
gi 2546352544  82 TE----VQDLSAG 90
Cdd:PRK10341   90 GMsseaVVDVSFG 102
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 15-267 5.85e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 44.06  E-value: 5.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  15 SLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVEL---TQRLddartevqdLSAGR 91
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLaeaTRKL---------RARSA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  92 TGTLRVLADPQFGTAFVcqVVRLY--MASYPGVHCRMDIAGMPGSLSPEEADCYVcaappdsqqlvlksigQLGFG---- 165
Cdd:PRK11139   93 KGALTVSLLPSFAIQWL--VPRLSsfNEAHPDIDVRLKAVDRLEDFLRDDVDVAI----------------RYGRGnwpg 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 166 LYA------------SPSYLARAGAPDTPDALAEHdaIVLHD-----------ALGRGDLTllrgrahalIRPRAAFSTN 222
Cdd:PRK11139  155 LRVeklldeyllpvcSPALLNGGKPLKTPEDLARH--TLLHDdsredwrawfrAAGLDDLN---------VQQGPIFSHS 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2546352544 223 DHWVMKTlcLDGLGIALMPDYFVQPELRHQGLVPVLPEWKPAPRR 267
Cdd:PRK11139  224 SMALQAA--IHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNA 266
PRK09986 PRK09986
LysR family transcriptional regulator;
17-94 1.57e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 42.79  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  17 TRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQRLDD----ARTEVQDLSAGRT 92
Cdd:PRK09986   25 GRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARveqiGRGEAGRIEIGIV 104


                  ..
gi 2546352544  93 GT 94
Cdd:PRK09986  105 GT 106
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-257 1.88e-04

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 41.53  E-value: 1.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  94 TLRVLADPQFGTAFVCQVVRLYMASYPGVHCRMDIAG---MPGSLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASP 170
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVAStadVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 171 SY-LARAGAPdTPDALAEHDAIVLHDALG-RGDLTLLRGRAHalIRPRAAFSTNDHWVMKTLCLDGLGIALMPDYFVQPE 248
Cdd:cd08426    81 GHpLARQPSV-TLAQLAGYPLALPPPSFSlRQILDAAFARAG--VQLEPVLISNSIETLKQLVAAGGGISLLTELAVRRE 157


                  ....*....
gi 2546352544 249 LRHQGLVPV 257
Cdd:cd08426   158 IRRGQLVAV 166
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 168-287 2.37e-04

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: 41.41  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 168 ASPSYLARaGAPDTPDALAEHDaiVLHDA---LGRGDLTLLRGRAHALIRPRAAFSTNDHwvMKTLCLDGLGIALMPDYF 244
Cdd:cd08432    75 CSPALLAG-LPLLSPADLARHT--LLHDAtrpEAWQWWLWAAGVADVDARRGPRFDDSSL--ALQAAVAGLGVALAPRAL 149

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2546352544 245 VQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVD 287
Cdd:cd08432   150 VADDLAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
8-77 2.59e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 40.34  E-value: 2.59e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2546352544   8 VHIMKSGSLTRAE--QSSGMSKASLSRHLAQLEAslgAELIQRG-------SRHLRPTEAGRAFFARCEPMLVELTQRL 77
Cdd:COG1846    45 AALAEAGGLTQSElaERLGLTKSTVSRLLDRLEE---KGLVEREpdpedrrAVLVRLTEKGRALLEEARPALEALLAEL 120
cbl PRK12679
HTH-type transcriptional regulator Cbl;
26-82 5.74e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.95  E-value: 5.74e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  26 SKASLSRHLAQLEASLGAEL-IQRGSRHLRPTEAGRAFFARCEPMLVELT--QRLDDART 82
Cdd:PRK12679   29 SQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASnvRRLADLFT 88
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 103-286 1.64e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 38.67  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 103 FGTAFVCQVVRLYMASYPGV------HCRMDIAGMpgsLSPEEADCYVCAAPPDSQQLVLKSIGQLGFGLYASPSY-LAR 175
Cdd:cd08434    10 LGTSLVPDLIRAFRKEYPNVtfelhqGSTDELLDD---LKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHpLAG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 176 AGAPDTPDaLAEHDAIVLHDALGRGDLT--LLrgrAHALIRPRAAFSTNDHWVMKTLCLDGLGIALMPDyfvQPELRHQG 253
Cdd:cd08434    87 RDSVDLAE-LADEPFVLLSPGFGLRPIVdeLC---AAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE---MTLLNPPG 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2546352544 254 LVpVLP-EWKPAPRRIHCAFRRQRY---AGSKLRDFV 286
Cdd:cd08434   160 VK-KIPiKDPDAERTIGLAWLKDRYlspAARRFKDFV 195
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 168-288 2.81e-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: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 168 ASPSY-LARAGAPdTPDALAEHDAI----------VLHDALGRGDLTLLRgrahalIRPRAAFSTNDhwVMKTLCLDGLG 236
Cdd:cd08420    78 VPPDHpLAGRKEV-TAEELAAEPWIlrepgsgtreVFERALAEAGLDGLD------LNIVMELGSTE--AIKEAVEAGLG 148

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2546352544 237 IALMPDYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRYAGSKLRDFVDL 288
Cdd:cd08420   149 ISILSRLAVRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEF 200
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 134-287 2.89e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 38.02  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544 134 SLSPEEADCYVCAAP-PDSQQLVLKSIGQLGFGLYASPS-YLARAGAPDTPDALAEHDAIVLHDAlgrgdLTLLRGRAHA 211
Cdd:cd08431    44 ALASGRADLVIGATGeLPPGGVKTRPLGEVEFVFAVAPNhPLAKLDGPLDASAIKQYPAIVVADT-----SRNLPPRSSG 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2546352544 212 LI--RPRAAFSTNDHWVmKTLCLdGLGIALMPDYFVQPELRHQGLVPVLPEWKPAPRRIHCAFRRQRyAGSKLRDFVD 287
Cdd:cd08431   119 LLegQDRIRVPTMQAKI-DAQVL-GLGVGYLPRHLAKPELASGELVEKALEDPRPPQELFLAWRKDQ-RGKALAWFVQ 193
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
13-79 4.82e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.03  E-value: 4.82e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2546352544   13 SGSLTRAE--QSSGMSKASLSRHLAQLEaslGAELIQRG-------SRHLRPTEAGRAFFARCEPMLVELTQRLDD 79
Cdd:smart00347  22 EGPLSVSElaKRLGVSPSTVTRVLDRLE---KKGLVRREpspedrrSVLVSLTEEGRELIEQLLEARSETLAELLA 94
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-97 5.87e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 37.49  E-value: 5.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2546352544  25 MSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVE---LTQRLDDARTEVQdlsagrtGTLRV 97
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQwqqLRHTLDQQGPSLS-------GELSL 71
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
15-103 6.31e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 37.67  E-value: 6.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546352544  15 SLTRAEQSSGMSKASLSRHLAQLEASLGAELIQRGSRHLRPTEAGRAFFARCEPMLVELTQRLDDARTevQDLSagrtGT 94
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKN--QELS----GT 103


                  ....*....
gi 2546352544  95 LRVLADPQF 103
Cdd:PRK10086  104 LTVYSRPSI 112
 
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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