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Conserved domains on  [gi|1539640456|emb|VED00141|]
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Transcriptional regulator, LysR family [Klebsiella variicola]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444118)

LysR family transcriptional regulator may function as a transcriptional activator or repressor 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, among others

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 4.87e-107

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: 309.16  E-value: 4.87e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGEL-ADSSLVARPLAPYRMVLCASPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08477    80 YLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08477   160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDF 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-57 3.73e-17

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.73e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQ 57
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 4.87e-107

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: 309.16  E-value: 4.87e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGEL-ADSSLVARPLAPYRMVLCASPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08477    80 YLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08477   160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 7.84e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 175.83  E-value: 7.84e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDM-ADEGLDVMIKIGELLHvNTLVARPIAPYR 157
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDAlLEGELDLAIRLGPPPD-PGLVARPLGEER 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 158 SVMCASPAyikragepitpeelchhrclgfaHPIAAnewtlqregkpvRAPVnitmtCNNGEALRRAALNGLGIIMQPEI 237
Cdd:COG0583   165 LVLVASPD-----------------------HPLAR------------RAPL-----VNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1539640456 238 LLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 2-288 4.07e-49

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 165.16  E-value: 4.07e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   2 AVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALH 81
Cdd:PRK14997    8 AWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  82 QKPRGKLRVGCPVS-FGVHaLSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKI-GELLHVNTLVARPIAPYRSV 159
Cdd:PRK14997   88 VEPRGIVKLTCPVTlLHVH-IGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrPRPFEDSDLVMRVLADRGHR 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 160 MCASPAYIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKpVRAPVNIT--MTCNNGEALRRAALNGLGIIMQPEI 237
Cdd:PRK14997  167 LFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQG-ARAEVHFTprMITTDMLALREAAMAGVGLVQLPVL 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1539640456 238 LLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:PRK14997  246 MVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYA 296
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-288 1.95e-29

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: 110.84  E-value: 1.95e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  85 RGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDMADEG-LDVMIkIGELLHVNTLVARPIAPYRSVMC 161
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAI-RRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 162 ASPAYIKRAGEPITPEELCHHRCLGFAHPiAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPG-SGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1539640456 242 DLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-287 3.66e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   3 VFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQ 82
Cdd:NF040786    8 AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  83 KPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDkSMDMADEGLDVMIKI---GELLHVNTLVARPIAPYRSV 159
Cdd:NF040786   88 ESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISD-SIKVIELLLEGEVDIgftGTKLEKKRLVYTPFYKDRLV 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 160 MCASPA--YIKRAGEPITPEELCHH----RCLGFAHPIAAnEWTLQREGKPVRApVNITMTCNNGEALRRAALNGLGIIM 233
Cdd:NF040786  167 LITPNGteKYRMLKEEISISELQKEpfimREEGSGTRKEA-EKALKSLGISLED-LNVVASLGSTEAIKQSVEAGLGISV 244

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1539640456 234 QPEILLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKF 287
Cdd:NF040786  245 ISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKERY 298
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-57 3.73e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.73e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQ 57
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-108 2.61e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 63.05  E-value: 2.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQK 83
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100
                  ....*....|....*....|....*
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQF 108
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAF 113
 
Name Accession Description Interval E-value
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 4.87e-107

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: 309.16  E-value: 4.87e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGEL-ADSSLVARPLAPYRMVLCASPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08477    80 YLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08477   160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDF 196
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 86-282 3.79e-73

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: 223.09  E-value: 3.79e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHvNTLVARPIAPYRSVMCASPA 165
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPD-SSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08422   160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 7.84e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 175.83  E-value: 7.84e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDM-ADEGLDVMIKIGELLHvNTLVARPIAPYR 157
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDAlLEGELDLAIRLGPPPD-PGLVARPLGEER 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 158 SVMCASPAyikragepitpeelchhrclgfaHPIAAnewtlqregkpvRAPVnitmtCNNGEALRRAALNGLGIIMQPEI 237
Cdd:COG0583   165 LVLVASPD-----------------------HPLAR------------RAPL-----VNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1539640456 238 LLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-287 6.09e-52

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: 169.24  E-value: 6.09e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHL-PDSSLVATRVGSVRRVVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08471    80 YLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKF 287
Cdd:cd08471   160 GRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-285 1.09e-49

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: 163.45  E-value: 1.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGEL-ADSSLVARRLGELRMVTCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAAN--EWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDL 243
Cdd:cd08472    80 YLARHGTPRHPEDLERHRAVGYFSARTGRvlPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1539640456 244 QHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIE 285
Cdd:cd08472   160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 2-288 4.07e-49

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 165.16  E-value: 4.07e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   2 AVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALH 81
Cdd:PRK14997    8 AWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  82 QKPRGKLRVGCPVS-FGVHaLSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKI-GELLHVNTLVARPIAPYRSV 159
Cdd:PRK14997   88 VEPRGIVKLTCPVTlLHVH-IGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrPRPFEDSDLVMRVLADRGHR 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 160 MCASPAYIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKpVRAPVNIT--MTCNNGEALRRAALNGLGIIMQPEI 237
Cdd:PRK14997  167 LFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQG-ARAEVHFTprMITTDMLALREAAMAGVGLVQLPVL 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1539640456 238 LLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:PRK14997  246 MVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYA 296
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 3.65e-47

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 156.64  E-value: 3.65e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVhaLSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHvNTLVARPIAPYRSVMCASPA 165
Cdd:cd08476     1 GRLRVSLPLVGGL--LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPD-SRLMSRRLGSFRMVLVASPD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAA--NEWTLQREGK--PVRAPVniTMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:cd08476    78 YLARHGTPETPADLAEHACLRYRFPTTGklEPWPLRGDGGdpELRLPT--ALVCNNIEALIEFALQGLGIACLPDFSVRE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1539640456 242 DLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08476   156 ALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDF 196
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-286 5.31e-47

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 156.32  E-value: 5.31e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHvNTLVARPIAPYRSVMCASPA 165
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTD-SSLMARRLASRRHYVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLgfahPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08470    80 YLERHGTPHSLADLDRHNCL----LGTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1539640456 246 GRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEK 286
Cdd:cd08470   156 GRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-281 4.17e-45

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 151.55  E-value: 4.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQRE-GKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQ 244
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEqGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1539640456 245 HGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVD 281
Cdd:cd08475   161 RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVD 197
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 5.79e-45

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 150.95  E-value: 5.79e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELlHVNTLVARPIAPYRSVMCASPA 165
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPL-PDSSLVARKLGESRRVIVASPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDLQH 245
Cdd:cd08480    80 YLARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1539640456 246 GRLLPLMSEFQP-LAKPVHILtFANRQQLP-KIRLYVDF 282
Cdd:cd08480   160 GRLVPVLEEYNPgDREPIHAV-YVGGGRLPaRVRAFLDF 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-287 8.15e-45

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 154.15  E-value: 8.15e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:PRK10632    7 MSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGElLHVNTLVARPIAPYRSVM 160
Cdd:PRK10632   87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGA-LQDSSLFSRRLGAMPMVV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 161 CASPAYIKRAGEPITPEELCHHRCLGFA-HPiaANEWTL-QREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEIL 238
Cdd:PRK10632  166 CAAKSYLAQYGTPEKPADLSSHSWLEYSvRP--DNEFELiAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPLMW 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1539640456 239 LAEDLQHGRLLPLMSEFQPLAKPVHILtFANRQQLP-KIRLYVDFFIEKF 287
Cdd:PRK10632  244 VIDEINRGELEILFPRYQSDPRPVYAL-YTEKDKLPlKVQVCINYLTDYF 292
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-283 1.39e-42

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: 145.05  E-value: 1.39e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  86 GKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHVNtLVARPIAPYRSVMCASPA 165
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSS-LIARKLAPNRRILCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 166 YIKRAGEPITPEELCHHRCLGfahpIAANE-----WTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLA 240
Cdd:cd08479    80 YLERHGAPASPEDLARHDCLV----IRENDedfglWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1539640456 241 EDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFF 283
Cdd:cd08479   156 PYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 84-283 3.16e-40

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 138.75  E-value: 3.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHVNtLVARPIAP-YRSVMCA 162
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKD-MVAVPLGPpLRMAVVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 163 SPAYIKRAGEPITPEELCHHRCLGFAHPI--AANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLA 240
Cdd:cd08474    80 SPAYLARHGTPEHPRDLLNHRCIRYRFPTsgALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1539640456 241 EDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFF 283
Cdd:cd08474   160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 84-282 5.35e-38

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: 133.23  E-value: 5.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHvNTLVARPIAPYRSVMCAS 163
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTD-STLHARPLGKSRLRILAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYIKRAGEPITPEELCHHRCLGFAHPIAANEWTLQR-EGKPVRapVNITMTCNNGEALRRAALNGLGIIMQPEILLAED 242
Cdd:cd08478    80 PDYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDaDGNLLK--IQPTITASSGETLRQLALSGCGIACLSDFMTDKD 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1539640456 243 LQHGRLLPLM-SEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08478   158 IAEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFIDF 198
PRK09801 PRK09801
LysR family transcriptional regulator;
1-255 1.01e-33

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 125.15  E-value: 1.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHvNTLVARPIAPYRSVM 160
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIP-DYYIAHLLTKNKRIL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 161 CASPAYIKRAGEPITPEELCHHRCL-----GFAHPIaaneWTL--QREGKPVRapVNITMTCNNGEALRRAALNGLGIIM 233
Cdd:PRK09801  170 CAAPEYLQKYPQPQSLQELSRHDCLvtkerDMTHGI----WELgnGQEKKSVK--VSGHLSSNSGEIVLQWALEGKGIML 243

                         250       260
                  ....*....|....*....|..
gi 1539640456 234 QPEILLAEDLQHGRLLPLMSEF 255
Cdd:PRK09801  244 RSEWDVLPFLESGKLVQVLPEY 265
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 84-283 8.09e-33

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 119.58  E-value: 8.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKI-GELLHVNTLVARPIAPYRSVMCA 162
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVrFPPLEDSSLVMRVLGQSRQRLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 163 SPAYIKRAGEPITPEELCHHRCLGFAHPIAANEWTL-QREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:cd08473    81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLeGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1539640456 242 DLQHGRLLPLMSEFQPlakPVHIL--TFANRQ-QLPKIRLYVDFF 283
Cdd:cd08473   161 ALRAGRLVRVLPDWTP---PRGIVhaVFPSRRgLLPAVRALIDFL 202
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-288 1.95e-29

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: 110.84  E-value: 1.95e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  85 RGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDMADEG-LDVMIkIGELLHVNTLVARPIAPYRSVMC 161
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAI-RRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 162 ASPAYIKRAGEPITPEELCHHRCLGFAHPiAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPG-SGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1539640456 242 DLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 12-288 8.14e-24

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 97.99  E-value: 8.14e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  12 SFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQafALHQKPRGKLRVG 91
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRK--LRARSAKGALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  92 CPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIG----ELLHVNTLVARPIAPyrsvMCaSPAYI 167
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGrgnwPGLRVEKLLDEYLLP----VC-SPALL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 168 kRAGEPI-TPEELCHHRCLgfaHPIAANEWtlqregKP-VRAPVNITMTCNNGE-------ALrRAALNGLGIIMQPEIL 238
Cdd:PRK11139  175 -NGGKPLkTPEDLARHTLL---HDDSREDW------RAwFRAAGLDDLNVQQGPifshssmAL-QAAIHGQGVALGNRVL 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1539640456 239 LAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQ 288
Cdd:PRK11139  244 AQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAA 293
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-287 3.66e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   3 VFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQ 82
Cdd:NF040786    8 AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  83 KPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDkSMDMADEGLDVMIKI---GELLHVNTLVARPIAPYRSV 159
Cdd:NF040786   88 ESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISD-SIKVIELLLEGEVDIgftGTKLEKKRLVYTPFYKDRLV 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 160 MCASPA--YIKRAGEPITPEELCHH----RCLGFAHPIAAnEWTLQREGKPVRApVNITMTCNNGEALRRAALNGLGIIM 233
Cdd:NF040786  167 LITPNGteKYRMLKEEISISELQKEpfimREEGSGTRKEA-EKALKSLGISLED-LNVVASLGSTEAIKQSVEAGLGISV 244

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1539640456 234 QPEILLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKF 287
Cdd:NF040786  245 ISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKERY 298
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-57 3.73e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.73e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQ 57
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
1-289 2.16e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 77.73  E-value: 2.16e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   1 MAVFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIeDSESQAFAl 80
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTL-NQEILDIK- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGEL----LHVNTLVARPIAPy 156
Cdd:PRK10086   97 NQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDApsaqLTHHFLMDEEILP- 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 157 rsvMCaSPAYIKRAGEPITPEELCHHRCLgfaHPIAA-------NEWTL--QREGKPVRAP-VNITMTCNNGEALrrAAL 226
Cdd:PRK10086  176 ---VC-SPEYAERHALTGNPDNLRHCTLL---HDRQAwsndsgtDEWHSwaQHFGVNLLPPsSGIGFDRSDLAVI--AAM 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1539640456 227 NGLGIIMQPEILLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDFFIEKFQC 289
Cdd:PRK10086  247 NHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKT 309
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 88-281 8.30e-16

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: 74.15  E-value: 8.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  88 LRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGEL----LHVNTLVARPIAPyrsvMCaS 163
Cdd:cd08432     2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGdwpgLEAERLMDEELVP----VC-S 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYIKRaGEPITPEELCHHRCLGFAHPIAANEWTLQREGKPVRAPVNiTMTCNNGEALRRAALNGLGIIMQPEILLAEDL 243
Cdd:cd08432    77 PALLAG-LPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARR-GPRFDDSSLALQAAVAGLGVALAPRALVADDL 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1539640456 244 QHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVD 281
Cdd:cd08432   155 AAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-108 2.61e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 63.05  E-value: 2.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQK 83
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100
                  ....*....|....*....|....*
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQF 108
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAF 113
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 88-281 3.71e-11

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 60.82  E-value: 3.71e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  88 LRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGEL----LHVNTLVARPIapyrsVMCAS 163
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGdwpgLESEPLTAAPF-----VVVAA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYIK-RAGEpiTPEELCHHRCLgfaHPIAANE---WTLQREGKPVRAPVnitMTCNNGEALRRAALNGLGIIMQPEILL 239
Cdd:cd08483    77 PGLLGdRKVD--SLADLAGLPWL---QERGTNEqrvWLASMGVVPDLERG---VTFLPGQLVLEAARAGLGLSIQARALV 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1539640456 240 AEDLQHGRLLPLMsEFQPLAKPVHILTFANRQQlPKIRLYVD 281
Cdd:cd08483   149 EPDIAAGRLTVLF-EEEEEGLGYHIVTRPGVLR-PAAKAFVR 188
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-71 4.04e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.43  E-value: 4.04e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIE 71
Cdd:PRK10094   10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-248 4.74e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 59.26  E-value: 4.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   7 VVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQKPRG 86
Cdd:CHL00180   16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  87 KLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDL-VLSDKSM---------DMADEGLDVMIKIGELLHVNTLVARPIApy 156
Cdd:CHL00180   96 TLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIawnvangqiDIAIVGGEVPTELKKILEITPYVEDELA-- 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 157 rSVMCASPAYIKRagEPITPEELCHhrcLGFahpIAAN---------EWTLQREGKPVRApVNITMTCNNGEALRRAALN 227
Cdd:CHL00180  174 -LIIPKSHPFAKL--KKIQKEDLYR---LNF---ITLDsnstirkviDNILIQNGIDSKR-FKIEMELNSIEAIKNAVQS 243

                         250       260
                  ....*....|....*....|.
gi 1539640456 228 GLGIIMQPEILLAEDLQHGRL 248
Cdd:CHL00180  244 GLGAAFVSVSAIEKELELGLL 264
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 87-283 2.02e-09

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: 56.07  E-value: 2.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  87 KLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLV--LSDKSMDMADEG-LDVMIkIGELLHVNTLVARPIAPYRSVMCAS 163
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVegGSSELLEALLEGeLDLAI-VALPVDDPGLESEPLFEEPLVLVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYIKRAGEPITPEELCHHRCLGFAHPIAANEWtLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAEDL 243
Cdd:cd05466    80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRL-LDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1539640456 244 QHG-RLLPLmsEFQPLAKPVHILTFANRQQLPKIRLYVDFF 283
Cdd:cd05466   159 DGGlVVLPL--EDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-255 5.15e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.94  E-value: 5.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   7 VVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTT--RrqsLTDFGQ---GYYQSCRRILADIEdseSQAFALH 81
Cdd:PRK03635   13 VVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQpcR---PTEAGQrllRHARQVRLLEAELL---GELPALD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  82 QKPRgklrvgcPVSFGVHALS------PVTAQFLiEWTDMAVDLVLSDKsmdmaDEGLDVMiKIGELLHVNTLVARPIAP 155
Cdd:PRK03635   87 GTPL-------TLSIAVNADSlatwflPALAPVL-ARSGVLLDLVVEDQ-----DHTAELL-RRGEVVGAVTTEPQPVQG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 156 YRS--------VMCASPAYIKR---AGepITPEELCHHRCLGFAHPIA-ANEWTLQREGKPVRAPvnITMTCNNGEALRR 223
Cdd:PRK03635  153 CRVdplgamryLAVASPAFAARyfpDG--VTAEALAKAPAVVFNRKDDlQDRFLRQAFGLPPGSV--PCHYVPSSEAFVR 228

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1539640456 224 AALNGLGIIMQPEILLAEDLQHGRLLPLMSEF 255
Cdd:PRK03635  229 AALAGLGWGMIPELQIEPELASGELVDLTPGR 260
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-258 6.44e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 6.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   3 VFVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRIL---ADIEDsesqafa 79
Cdd:PRK10837   10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLeqaVEIEQ------- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  80 LHQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDkSMDMADEGLDVMIKIGEL---LHVNTLVARPIAPY 156
Cdd:PRK10837   83 LFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGN-SQDVINAVLDFRVDIGLIegpCHSPELISEPWLED 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 157 RSVMCASPAYiKRAGEPITPEELchhrclgfahpiAANEWTLQREGKPVRAPVN-----------ITMTCNNGEALRRAA 225
Cdd:PRK10837  162 ELVVFAAPDS-PLARGPVTLEQL------------AAAPWILRERGSGTREIVDylllshlprfeLAMELGNSEAIKHAV 228

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1539640456 226 LNGLGIIMQPEILLAEDLQHGRLLPLMSEFQPL 258
Cdd:PRK10837  229 RHGLGISCLSRRVIADQLQAGTLVEVAVPLPRL 261
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-120 8.46e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.55  E-value: 8.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  13 FSAVAEEMRISGTMVGLH---------IKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQK 83
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHtaqpslsqqIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE 88

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1539640456  84 PRgKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLV 120
Cdd:PRK09906   89 DR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELV 124
PRK09986 PRK09986
LysR family transcriptional regulator;
13-182 8.99e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 52.42  E-value: 8.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  13 FSAVAEEMR---------ISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQK 83
Cdd:PRK09986   15 FLAVAEELHfgraaarlnISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRG 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  84 PRGKLRVGCPVSFGVHALSPVTAQFLIEWTDmaVDLVLSDKS--MDMA---DEGLDVMIKIGELLHVNT-LVARPIAPyR 157
Cdd:PRK09986   95 EAGRIEIGIVGTALWGRLRPAMRHFLKENPN--VEWLLRELSpsMQMAaleRRELDAGIWRMADLEPNPgFTSRRLHE-S 171

                         170       180
                  ....*....|....*....|....*.
gi 1539640456 158 SVMCASPAYIKRAGEPITP-EELCHH 182
Cdd:PRK09986  172 AFAVAVPEEHPLASRSSVPlKALRNE 197
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
12-292 9.61e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 9.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  12 SFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQKPRGKLRVG 91
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIA 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  92 CPVSFGVHALSPVTAQF--LIEWTDMAVDLvlsDKSMDMADEGLDVMIKIgelLHVNTLVARPIAPYRSV------MCAS 163
Cdd:PRK10082  107 AAHSLSLGLLPSIISQMppLFTWAIEAIDV---DEAVDKLREGQSDCIFS---FHDEDLLEAPFDHIRLFesqlfpVCAS 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYikraGEPITPEELCHHRCLGFAHpiaaNEW-------TLQREGKpvrAPVNITMTCNNGEALRRAALNGLGIIMQPE 236
Cdd:PRK10082  181 DEH----GEALFNLAQPHFPLLNYSR----NSYmgrlinrTLTRHSE---LSFSTFFVSSMSELLKQVALDGCGIAWLPE 249

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1539640456 237 ILLAEDLQHGRLLPLMSEfqPLAKPVHILTFANRQQLPKIrlyVDFFIEKFQCITL 292
Cdd:PRK10082  250 YAIQQEIRSGQLVVLNRD--ELVIPIQAYAYRMNTRMNPV---AERFWRELRELEI 300
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-251 1.10e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.20  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRtTRRQSLTDFGQGYYQSCRRIlaDIEDSESQAfalHQK 83
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV--ALLEADLLS---TLP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  84 PRGKLRVGcpVSFGVHALS------PVTAQFLIEwTDMAVDLVLSDksmdmADEGLDVmIKIGELLHVNTLVARPI---- 153
Cdd:PRK13348   84 AERGSPPT--LAIAVNADSlatwflPALAAVLAG-ERILLELIVDD-----QDHTFAL-LERGEVVGCVSTQPKPMrgcl 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 154 APYRSVM----CASPAYIKR-AGEPITPEELCHHRCLGFAHPIAANE-WTLQREGKPVRA------PVNitmtcnngEAL 221
Cdd:PRK13348  155 AEPLGTMryrcVASPAFAARyFAQGLTRHSALKAPAVAFNRKDTLQDsFLEQLFGLPVGAyprhyvPST--------HAH 226

                         250       260       270
                  ....*....|....*....|....*....|
gi 1539640456 222 RRAALNGLGIIMQPEILLAEDLQHGRLLPL 251
Cdd:PRK13348  227 LAAIRHGLGYGMVPELLIGPLLAAGRLVDL 256
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 87-282 3.18e-05

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: 44.02  E-value: 3.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  87 KLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDM-ADEGLDVMIkIGELLHVNTLVARPIAPYRSVMCAS 163
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIgnTEEIAERvLDGEIDLGL-VEGPVDHPDLIVEPFAEDELVLVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYIKRAGEPITPEELCHHRclgfahpiaaneW---------------TLQREGKPVRAPvNITMTCNNGEALRRAALNG 228
Cdd:cd08420    80 PDHPLAGRKEVTAEELAAEP------------WilrepgsgtrevferALAEAGLDGLDL-NIVMELGSTEAIKEAVEAG 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1539640456 229 LGIIMQPEILLAEDLQHGRLLPLMSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08420   147 LGISILSRLAVRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEF 200
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 4-182 9.93e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 43.11  E-value: 9.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSF--SAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRR-QSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:PRK12683    8 IIREAVRQNFnlTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRlTGLTEPGKELLQIVERMLLDAENLRRLAEQF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDmaVDLVLSDKS------MDMADEGlDVMIKIGELLHVNTLVARPIA 154
Cdd:PRK12683   88 ADRDSGHLTVATTHTQARYALPKVVRQFKEVFPK--VHLALRQGSpqeiaeMLLNGEA-DIGIATEALDREPDLVSFPYY 164

                         170       180
                  ....*....|....*....|....*...
gi 1539640456 155 PYRSVMCASPAYIKRAGEPITPEELCHH 182
Cdd:PRK12683  165 SWHHVVVVPKGHPLTGRENLTLEAIAEY 192
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-282 1.50e-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: 41.91  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  87 KLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDL-------VLSDKSMDMADEGLDVMIKIGELLHVntlVARPIAPYRSV 159
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVdvastadVLEAVLSGEADIGLAFSPPPEPGIRV---HSRQPAPIGAV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 160 McaSPAYIKRAGEPITPEELCHHRcLGFAHP-------IAANEWTLQREGKPVrapvnitMTCNNGEALRRAALNGLGII 232
Cdd:cd08426    78 V--PPGHPLARQPSVTLAQLAGYP-LALPPPsfslrqiLDAAFARAGVQLEPV-------LISNSIETLKQLVAAGGGIS 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1539640456 233 MQPEILLAEDLQHGRL--LPLmSEFQPLAKPVHILTFANRQQLPKIRLYVDF 282
Cdd:cd08426   148 LLTELAVRREIRRGQLvaVPL-ADPHMNHRQLELQTRAGRQLPAAASAFLQL 198
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 7-76 2.24e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 42.24  E-value: 2.24e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1539640456   7 VVD----RGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQ 76
Cdd:PRK11074    9 VVDavarTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQ 82
PRK09791 PRK09791
LysR family transcriptional regulator;
4-70 3.57e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 41.29  E-value: 3.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADI 70
Cdd:PRK09791   13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEEL 79
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 88-263 4.72e-04

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 40.43  E-value: 4.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  88 LRVGCPVSFGVHALSPVTAQFliEWTDMAVDLVLS--DKSMDMADEGLDVMIKIGE----LLHVNTLVARPIAPyrsvMC 161
Cdd:cd08484     2 LTVGAVGTFAVGWLLPRLAEF--RQLHPFIDLRLStnNNRVDIAAEGLDFAIRFGEgawpGTDATRLFEAPLSP----LC 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 162 aSPAYIKRAGEpitPEELCHHRCLgfaHPIAANEWTLQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:cd08484    76 -TPELARRLSE---PADLANETLL---RSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSR 148

                         170       180
                  ....*....|....*....|..
gi 1539640456 242 DLQHGRLLplmsefQPLAKPVH 263
Cdd:cd08484   149 ELASGALV------QPFKITVS 164
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 88-259 6.85e-04

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 39.82  E-value: 6.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  88 LRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGE----LLHVNTLVARPIAPyrsvMCaS 163
Cdd:cd08488     2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSgawhGIDATRLFEAPLSP----LC-T 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 164 PAYikrAGEPITPEELCHHRCLgfaHPIAANEWT--LQREGKPVRAPVNITMTCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:cd08488    77 PEL---ARQLREPADLARHTLL---RSYRADEWPqwFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSR 150

                         170
                  ....*....|....*...
gi 1539640456 242 DLQHGRLLplmsefQPLA 259
Cdd:cd08488   151 QLASGALV------QPFA 162
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-179 8.26e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 40.39  E-value: 8.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  11 GSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIedseSQAFALHQKP-RGKLR 89
Cdd:PRK15421   17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI----SQALQACNEPqQTRLR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  90 VGCPVSFGVHALSPVTAQFLIEWTDMAVDL---VLSDKSMDMADEGLDvMIKIGELLHVNTLVARPIAPYRSVMCASPAY 166
Cdd:PRK15421   93 IAIECHSCIQWLTPALENFHKNWPQVEMDFksgVTFDPQPALQQGELD-LVMTSDILPRSGLHYSPMFDYEVRLVLAPDH 171

                         170
                  ....*....|...
gi 1539640456 167 IKRAGEPITPEEL 179
Cdd:PRK15421  172 PLAAKTRITPEDL 184
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 4-106 1.34e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.67  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFGQGYYQSCRRILADIEDSESQAFALHQK 83
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQA 88

                          90       100
                  ....*....|....*....|...
gi 1539640456  84 PRGKLRVGcpvsfgvhaLSPVTA 106
Cdd:PRK11233   89 LSGQVSIG---------LAPGTA 102
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 88-263 1.39e-03

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 39.07  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  88 LRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHVNTLVARPIAPYRSVMCASpayi 167
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSP---- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 168 kRAGEPIT-PEELCHHRCLgfaHPIAANEWTL-----QREGKPVRAPVnitmtCNNGEALRRAALNGLGIIMQPEILLAE 241
Cdd:cd08487    78 -EIAKRLShPADLINETLL---RSYRTDEWLQwfeaaNMPPIKIRGPV-----FDSSRLMVEAAMQGAGVALAPAKMFSR 148

                         170       180
                  ....*....|....*....|..
gi 1539640456 242 DLQHGRLLplmsefQPLAKPVH 263
Cdd:cd08487   149 EIENGQLV------QPFKIEVE 164
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 95-281 1.42e-03

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 38.82  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  95 SFGVHALSPVTAQFLIEWTDMAVDLVLSDKSMDMADEGLDVMIKIGELLHVNT----LVARPIAPyrsvmCASPAYIKRA 170
Cdd:cd08481     9 TFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAeseyLMDEEVVP-----VCSPALLAGR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 171 GePITPEELCHHRCLGFAH-PIAANEWtLQREGKPVRAPVN------ITMTCNngealrrAALNGLGIIMQPEILLAEDL 243
Cdd:cd08481    84 A-LAAPADLAHLPLLQQTTrPEAWRDW-FEEVGLEVPTAYRgmrfeqFSMLAQ-------AAVAGLGVALLPRFLIEEEL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1539640456 244 QHGRL-----LPLMSEFqplakpVHILTFAN-RQQLPKIRLYVD 281
Cdd:cd08481   155 ARGRLvvpfnLPLTSDK------AYYLVYPEdKAESPPVQAFRD 192
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 4-182 1.95e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.20  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSF--SAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRR-QSLTDFGQGYYQSCRRILADIEDSESQAFAL 80
Cdd:PRK12682    8 FVREAVRRNLnlTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRlKGLTEPGKAVLDVIERILREVGNIKRIGDDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDmaVDLVLSDKSMD-----MADEGLDVMIKIGELLHVNTLVARPIAP 155
Cdd:PRK12682   88 SNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPK--VNLSLHQGSPDeiarmVISGEADIGIATESLADDPDLATLPCYD 165

                         170       180
                  ....*....|....*....|....*..
gi 1539640456 156 YRSVMCASPAYIKRAGEPITPEELCHH 182
Cdd:PRK12682  166 WQHAVIVPPDHPLAQEERITLEDLAEY 192
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-243 2.30e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456   4 FVRVVDRGSFSAVAEEMRISGTMVGLHIKALEEHLGVRLLNRTTRRQSLTDFG-Q--GYyqsCRRILaDIEDsESQAFAL 80
Cdd:PRK15092   19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGiQllGY---ARKIL-RFND-EACSSLM 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456  81 HQKPRGKLRVGCPVSFGVHALSPVTAQFLIEWTDMAVDLVL--SDKSMDMADEG-LDVMIKIGELLHVNTLVAR--PIAP 155
Cdd:PRK15092   94 YSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVkrNAFMMEMLESQeVDLAVTTHRPSSFPALNLRtsPTLW 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539640456 156 YrsvmCAsPAYIKRAGEPItP----EELCHHRCLGFAHpiaanewtLQREGKPVR-APVNITMTcnngeALRRAALNGLG 230
Cdd:PRK15092  174 Y----CA-AEYVLQKGEPI-PlvllDEPSPFRDMALAT--------LNAAGIPWRiAYVASTLS-----AVRAAVKAGLG 234

                         250
                  ....*....|...
gi 1539640456 231 IIMQPEILLAEDL 243
Cdd:PRK15092  235 VTARPVEMMSPDL 247
 
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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