NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|515630821|ref|WP_017063421|]
View 

MULTISPECIES: LysR family transcriptional regulator [Vibrio]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 86-284 6.13e-75

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: 228.09  E-value: 6.13e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSRERDYTsWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLR-WRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRASQLmPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08422  160 GRLVRVLPDWRPPPL-PIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-56 1.91e-17

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 1.91e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821    1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAG 56
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 86-284 6.13e-75

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: 228.09  E-value: 6.13e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSRERDYTsWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLR-WRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRASQLmPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08422  160 GRLVRVLPDWRPPPL-PIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-290 3.78e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.69  E-value: 3.78e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQ 80
Cdd:COG0583    6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  81 RDDISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLF--DYKVDMI-EERLDLWITNNEDLPEGYIAQRLADSQF 157
Cdd:COG0583   86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALlEGELDLAIRLGPPPDPGLVARPLGEERL 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 158 VVAASPDYLIKAGTPHVPSdlidhncliyrsrerdytswafdngqenlsvkvagdysvdlAEAVRDAAVSGWGVAYLATY 237
Cdd:COG0583  166 VLVASPDHPLARRAPLVNS-----------------------------------------LEALLAAVAAGLGIALLPRF 204

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 515630821 238 LVKEEFRTGKLIQV-LPEWRASqlMPFYAVYPSRKNMPKKLSAVIEFIKDHIGS 290
Cdd:COG0583  205 LAADELAAGRLVALpLPDPPPP--RPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
8-301 9.99e-54

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 177.53  E-value: 9.99e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   8 IKHEG-FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDDISG 86
Cdd:PRK09801  17 IVHSGsFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDYL 166
Cdd:PRK09801  97 MIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCAAPEYL 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 IKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRTG 246
Cdd:PRK09801 177 QKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVLPFLESG 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515630821 247 KLIQVLPEWraSQLMPFYAVYPSRKNMPKKLSAVIEFI----KDHIGSPtywDKNLKTC 301
Cdd:PRK09801 257 KLVQVLPEY--AQSANIWAVYREPLYRSMKLRVCVEFLaawcQQRLGKP---DEGYQVM 310
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-287 1.10e-39

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: 137.81  E-value: 1.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   85 SGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYK--VDMIEE-RLDLWITNNEDLPEGYIAQRLADSQFVVAA 161
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  162 SPDYLIKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAgdYSVDLAEAVRDAAVSGWGVAYLATYLVKE 241
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVV--LEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 515630821  242 EFRTGKLI-QVLPEWRASqlMPFYAVYPSRKNMPKKLSAVIEFIKDH 287
Cdd:pfam03466 159 ELADGRLVaLPLPEPPLP--RELYLVWRKGRPLSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-56 1.91e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 1.91e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821    1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAG 56
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-68 4.24e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.43  E-value: 4.24e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFN 68
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 86-284 6.13e-75

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: 228.09  E-value: 6.13e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSRERDYTsWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLR-WRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRASQLmPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08422  160 GRLVRVLPDWRPPPL-PIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-290 3.78e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.69  E-value: 3.78e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQ 80
Cdd:COG0583    6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  81 RDDISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLF--DYKVDMI-EERLDLWITNNEDLPEGYIAQRLADSQF 157
Cdd:COG0583   86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALlEGELDLAIRLGPPPDPGLVARPLGEERL 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 158 VVAASPDYLIKAGTPHVPSdlidhncliyrsrerdytswafdngqenlsvkvagdysvdlAEAVRDAAVSGWGVAYLATY 237
Cdd:COG0583  166 VLVASPDHPLARRAPLVNS-----------------------------------------LEALLAAVAAGLGIALLPRF 204

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 515630821 238 LVKEEFRTGKLIQV-LPEWRASqlMPFYAVYPSRKNMPKKLSAVIEFIKDHIGS 290
Cdd:COG0583  205 LAADELAAGRLVALpLPDPPPP--RPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
8-301 9.99e-54

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 177.53  E-value: 9.99e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   8 IKHEG-FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDDISG 86
Cdd:PRK09801  17 IVHSGsFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDYL 166
Cdd:PRK09801  97 MIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCAAPEYL 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 IKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRTG 246
Cdd:PRK09801 177 QKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVLPFLESG 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515630821 247 KLIQVLPEWraSQLMPFYAVYPSRKNMPKKLSAVIEFI----KDHIGSPtywDKNLKTC 301
Cdd:PRK09801 257 KLVQVLPEY--AQSANIWAVYREPLYRSMKLRVCVEFLaawcQQRLGKP---DEGYQVM 310
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-284 1.15e-53

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: 173.94  E-value: 1.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRAsQLMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08479  161 GRLVRVLPDWQL-PDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-284 7.47e-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 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: 161.24  E-value: 7.47e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYrSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08477   81 LARHGTPTTPEDLARHECLGF-SYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRASQlMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08477  160 GRLVELLPDYLPPP-RPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 85-284 9.06e-48

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 158.78  E-value: 9.06e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  85 SGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQ-FVVAASP 163
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLrMAVVASP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 164 DYLIKAGTPHVPSDLIDHNCLIYR-SRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEE 242
Cdd:cd08474   82 AYLARHGTPEHPRDLLNHRCIRYRfPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAEH 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515630821 243 FRTGKLIQVLPEWrASQLMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08474  162 LASGRLVRVLEDW-SPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 1.05e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 148.09  E-value: 1.05e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNE-DLPEGYIAQRLADSQFVVAASPD 164
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGElADSTGLVARRLGTQRMVLCASPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YLIKAGTPHVPSDLIDHNCLIYRSRERDYtSWAFDNGQENL-SVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEF 243
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGQPL-PWRLADEQGRLvRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHL 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 244 RTGKLIQVLPEwRASQLMPFYAVYPSRKNMPKKLSAVIE 282
Cdd:cd08475  160 QRGELVEVLPE-LAPEGLPIHAVWPRTRHLPPKVRAAVD 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-282 1.47e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 148.04  E-value: 1.47e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRS-RERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFR 244
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFSaRTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLA 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 515630821 245 TGKLIQVLPEWRASQlMPFYAVYPSRKNMPKKLSAVIE 282
Cdd:cd08472  161 SGRLVEVLPDWRPPP-LPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-288 8.31e-40

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: 138.21  E-value: 8.31e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSRerdytSWAF-DNGQENlSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFR 244
Cdd:cd08470   81 LERHGTPHSLADLDRHNCLLGTSD-----HWRFqENGRER-SVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 515630821 245 TGKLIQVLPEWRASQlMPFYAVYPSRKNMPKKLSAVIEFIKDHI 288
Cdd:cd08470  155 AGRLVPVLEDYRPPD-EGIWALYPHNRHLSPKVRLLVDYLADAL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-287 1.10e-39

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: 137.81  E-value: 1.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   85 SGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYK--VDMIEE-RLDLWITNNEDLPEGYIAQRLADSQFVVAA 161
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  162 SPDYLIKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAgdYSVDLAEAVRDAAVSGWGVAYLATYLVKE 241
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVV--LEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 515630821  242 EFRTGKLI-QVLPEWRASqlMPFYAVYPSRKNMPKKLSAVIEFIKDH 287
Cdd:pfam03466 159 ELADGRLVaLPLPEPPLP--RELYLVWRKGRPLSPAVRAFIEFLREA 203
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 4-286 2.22e-39

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 140.13  E-value: 2.22e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 ISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWIT------NNEDLpegyIAQRLADSQF 157
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRvrprpfEDSDL----VMRVLADRGH 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 158 VVAASPDYLIKAGTPHVPSDLIDHNCLIYRSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATY 237
Cdd:PRK14997 166 RLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVL 245

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 515630821 238 LVKEEFRTGKLIQVLPEWRASQLMpFYAVYPSRKNMPKKLSAVIEFIKD 286
Cdd:PRK14997 246 MVKEQLAAGELVAVLEEWEPRREV-IHAVFPSRRGLLPSVRALVDFLTE 293
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-283 1.50e-37

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 132.26  E-value: 1.50e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEdLPE-GYIAQRLADSQFVVAASPD 164
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGH-LPDsSLVATRVGSVRRVVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YLIKAGTPHVPSDLIDHNCLIYRSRERdYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFR 244
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFTGLSP-APEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 245 TGKLIQVLPEWrASQLMPFYAVYPSRKNMPKKLSAVIEF 283
Cdd:cd08471  159 AGRLQRVLEDF-EPPPLPVHLVHPEGRLAPAKVRAFVDF 196
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-284 9.09e-37

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 130.15  E-value: 9.09e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDY 165
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 166 LIKAGTPHVPSDLIDHNCLIYRSReRDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGFNFR-RALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630821 246 GKLIQVLPEWRASQLMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08480  160 GRLVPVLEEYNPGDREPIHAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-284 4.25e-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 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: 120.43  E-value: 4.25e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  86 GILRVGLSQSFGTLhiIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEdLPEG-YIAQRLADSQFVVAASPD 164
Cdd:cd08476    1 GRLRVSLPLVGGLL--LPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGE-LPDSrLMSRRLGSFRMVLVASPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YLIKAGTPHVPSDLIDHNCLIYRSRErdyT----SWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVK 240
Cdd:cd08476   78 YLARHGTPETPADLAEHACLRYRFPT---TgklePWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVR 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 515630821 241 EEFRTGKLIQVLPEWRASQLMpFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08476  155 EALADGRLVTVLDDYVEERGQ-FRLLWPSSRHLSPKLRVFVDFM 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-287 5.39e-33

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 123.33  E-value: 5.39e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQ 80
Cdd:PRK10632   7 MSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  81 RDDISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVA 160
Cdd:PRK10632  87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVC 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 161 ASPDYLIKAGTPHVPSDLIDHNCLIYRSR-ERDYTSWAfdngQENLSVKV--AGDYSVDLAEAVRDAAVSGWGVAYLATY 237
Cdd:PRK10632 167 AAKSYLAQYGTPEKPADLSSHSWLEYSVRpDNEFELIA----PEGISTRLipQGRFVTNDPQTLVRWLTAGAGIAYVPLM 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 515630821 238 LVKEEFRTGKLIQVLPEWRaSQLMPFYAVYPSRKNMPKKLSAVIEFIKDH 287
Cdd:PRK10632 243 WVIDEINRGELEILFPRYQ-SDPRPVYALYTEKDKLPLKVQVCINYLTDY 291
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 85-284 3.17e-32

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: 118.21  E-value: 3.17e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  85 SGILRVGLSQSFgTLHII-PAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASP 163
Cdd:cd08478    2 SGLLRVDAATPF-VLHLLaPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 164 DYLIKAGTPHVPSDLIDHNCLIYRSRERdYTSWAFDNGQENLsVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEF 243
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQLLGFTEPAS-LNTWPIKDADGNL-LKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 515630821 244 RTGKLIQVLPEWRASQLMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08478  159 AEGRLIPLFAEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 85-283 7.07e-29

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 109.57  E-value: 7.07e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  85 SGILRV----GLSQSfgtlHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWI------TNNEDLpegyIAQRLAD 154
Cdd:cd08473    2 RGTVRVscppALAQE----LLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvrfppLEDSSL----VMRVLGQ 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 155 SQFVVAASPDYLIKAGTPHVPSDLIDHNCLIYRSRERDYtSWAFDnGQENLSVKVAGD--YSVDLAEAVRDAAVSGWGVA 232
Cdd:cd08473   74 SRQRLVASPALLARLGRPRSPEDLAGLPTLSLGDVDGRH-SWRLE-GPDGESITVRHRprLVTDDLLTLRQAALAGVGIA 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 515630821 233 YLATYLVKEEFRTGKLIQVLPEWRASQLMpFYAVYPSRKNMPKKLSAVIEF 283
Cdd:cd08473  152 LLPDHLCREALRAGRLVRVLPDWTPPRGI-VHAVFPSRRGLLPAVRALIDF 201
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-275 3.03e-27

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 107.62  E-value: 3.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK11139  14 FEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 isGILRVGLSQSFGTLHIIPAIDQLRQLYPQlrIEVHLFdyKVDMIEERLdlwiTNNEDLP--------EGYIAQRLADS 155
Cdd:PRK11139  94 --GALTVSLLPSFAIQWLVPRLSSFNEAHPD--IDVRLK--AVDRLEDFL----RDDVDVAirygrgnwPGLRVEKLLDE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 156 QFVVAASPDYLIKAGTPHVPSDLIDHNcLIYRSRERDYTSWAFDNGQENLSVKVAGDYSvdLAEAVRDAAVSGWGVAYLA 235
Cdd:PRK11139 164 YLLPVCSPALLNGGKPLKTPEDLARHT-LLHDDSREDWRAWFRAAGLDDLNVQQGPIFS--HSSMALQAAIHGQGVALGN 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 515630821 236 TYLVKEEFRTGKLIQVLPEWRASqlmP--FYAVYP-SRKNMPK 275
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPS---PnaFYLVCPdSQAELPK 280
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 87-284 5.89e-21

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: 88.41  E-value: 5.89e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQlrIEVHLF--DYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPD 164
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPD--IDLRLStsDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YLiKAGTPHVPSDLIDHnCLIyRSRERDYTSWAFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFR 244
Cdd:cd08432   79 LL-AGLPLLSPADLARH-TLL-HDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 515630821 245 TGKLIQVLPEWRASQLmPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08432  156 AGRLVRPFDLPLPSGG-AYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-291 1.64e-20

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 89.68  E-value: 1.64e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRdd 83
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQE-- 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 ISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASP 163
Cdd:PRK10086 100 LSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSP 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 164 DYLIK---AGTPHVPSD---LIDHNCLIYRSRERDYTSWA--FDNGQENLSVKVAGDYSvDLAEAvrdAAVSGWGVAYLA 235
Cdd:PRK10086 180 EYAERhalTGNPDNLRHctlLHDRQAWSNDSGTDEWHSWAqhFGVNLLPPSSGIGFDRS-DLAVI---AAMNHIGVAMGR 255

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821 236 TYLVKEEFRTGKLIQVLPEWRASQLMPFYAVYPSRKnMPKKLSAVIEFIKDHIGSP 291
Cdd:PRK10086 256 KRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGR-QWPKIEAFIDWLKEQVKTT 310
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 88-284 3.11e-20

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: 86.50  E-value: 3.11e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYK--VDMIEE-RLDLWITNNEDLPEGYIAQRLADSQFVVAASPD 164
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSelLEALLEgELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YLIKAGTPHVPSDLIDHNCLIYRSRE--RDYTSWAFDngQENLSVKVAgdYSVDLAEAVRDAAVSGWGVAYLATYLVkEE 242
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSglRRLLDRAFA--EAGFTPNIA--LEVDSLEAIKALVAAGLGIALLPESAV-EE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515630821 243 FRTGKLIQVLPEWRASQlMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd05466  157 LADGGLVVLPLEDPPLS-RTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-56 1.91e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 1.91e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821    1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAG 56
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
4-249 1.42e-16

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 78.56  E-value: 1.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 ISGILRVGLSQSFgTLHIIPAIdqLRQLYPQLR--IEVHLFDYKVDMIEERLDLWI--TNNEDLPEGYIAQ-RLADSQ-F 157
Cdd:PRK10082  99 AQRKIKIAAAHSL-SLGLLPSI--ISQMPPLFTwaIEAIDVDEAVDKLREGQSDCIfsFHDEDLLEAPFDHiRLFESQlF 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 158 VVAASPDY---LIKAGTPHVPSDLIDHNCLIYRSRERDYTSWAfdngqenlSVKVAGDYSVDLAEAVRDAAVSGWGVAYL 234
Cdd:PRK10082 176 PVCASDEHgeaLFNLAQPHFPLLNYSRNSYMGRLINRTLTRHS--------ELSFSTFFVSSMSELLKQVALDGCGIAWL 247

                        250
                 ....*....|....*
gi 515630821 235 ATYLVKEEFRTGKLI 249
Cdd:PRK10082 248 PEYAIQQEIRSGQLV 262
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-137 5.41e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 76.53  E-value: 5.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515630821  84 ISGILRVGLSQSFGTLHIIPAIDQLRQLYP----------QLRIEVHLfdykvdmIEERLDLWI 137
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPgitltiremsQERIEALL-------ADDELDVGI 145
PRK10341 PRK10341
transcriptional regulator TdcA;
1-162 3.81e-14

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 71.43  E-value: 3.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQ 80
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  81 RDDISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRI---EVHLFDYKVDMIEERLDLWI--TNNEDLPEGYIAQRLADS 155
Cdd:PRK10341  92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVsmyEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEPLFES 171


                 ....*..
gi 515630821 156 QFVVAAS 162
Cdd:PRK10341 172 EFVLVAS 178
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-141 9.29e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.43  E-value: 9.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHAlIKHEG-FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDS 79
Cdd:CHL00180  10 LRILKA-IATEGsFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALED 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821  80 QRDDISGILRVGLSQSFGTlHIIPAIDQL-RQLYPQLRIEVHLFDYKV---DMIEERLDLWITNNE 141
Cdd:CHL00180  89 LKNLQRGTLIIGASQTTGT-YLMPRLIGLfRQRYPQINVQLQVHSTRRiawNVANGQIDIAIVGGE 153
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-165 1.32e-12

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 66.98  E-value: 1.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   6 ALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQmDMDSQR-DDI 84
Cdd:PRK11151  11 ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLK-EMASQQgETM 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  85 SGILRVGLSQSFGTL---HIIPaidQLRQLYPQLriEVHLFDYK----VDMIEE-RLDLWITNNEDLPEGYIAQRLADSQ 156
Cdd:PRK11151  90 SGPLHIGLIPTVGPYllpHIIP---MLHQTFPKL--EMYLHEAQthqlLAQLDSgKLDCAILALVKESEAFIEVPLFDEP 164


                 ....*....
gi 515630821 157 FVVAASPDY 165
Cdd:PRK11151 165 MLLAVYEDH 173
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 88-284 1.94e-12

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: 64.82  E-value: 1.94e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTlHIIPA-IDQLRQLYPQLRIEVHLFDYK--VDMIEE-RLDLWITNNEDLPEGYIAQRLADSQFVVAASP 163
Cdd:cd08420    2 LRIGASTTIGE-YLLPRlLARFRKRYPEVRVSLTIGNTEeiAERVLDgEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 164 DYLIKAGTPHVPSDLIDHNcLIyrSRE-----RDYTSWAF-DNGQENLSVKVAgdysVDLA--EAVRDAAVSGWGVAYLA 235
Cdd:cd08420   81 DHPLAGRKEVTAEELAAEP-WI--LREpgsgtREVFERALaEAGLDGLDLNIV----MELGstEAIKEAVEAGLGISILS 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 515630821 236 TYLVKEEFRTGKLIQV-LPEWRASqlMPFYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08420  154 RLAVRKELELGRLVALpVEGLRLT--RPFSLIYHKDKYLSPAAEAFLEFL 201
PRK09791 PRK09791
LysR family transcriptional regulator;
4-182 3.27e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 65.94  E-value: 3.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK09791  13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQ 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 ISGILRVGLSQSFGTlHIIPA-IDQLRQLYPQ--LRI-EVHLfdykVDMIEE--RLDLWITNNEDLPEGYIA----QRLA 153
Cdd:PRK09791  93 LAGQINIGMGASIAR-SLMPAvISRFHQQHPQvkVRImEGQL----VSMINElrQGELDFTINTYYQGPYDHeftfEKLL 167

                        170       180
                 ....*....|....*....|....*....
gi 515630821 154 DSQFVVAASPDYLIKAGTPhvPSDLIDHN 182
Cdd:PRK09791 168 EKQFAVFCRPGHPAIGARS--LKQLLDYS 194
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 88-249 1.82e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 59.34  E-value: 1.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNE-DLPEGYIAQRLADSQFVVAASPDYL 166
Cdd:cd08482    2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDaPWPAGMQVIELFPERVGPVCSPSLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 IKAGTPHVP-SDLIDHNCLIYRSRERDYTSWAFDNGQ--ENLSVKVAGDYSVDLAEAvrdaAVSGWGVAYLATYLVKEEF 243
Cdd:cd08482   82 PTVPLRQAPaAALLGAPLLHTRSRPQAWPDWAAAQGLapEKLGTGQSFEHFYYLLEA----AVAGLGVAIAPWPLVRDDL 157


                 ....*.
gi 515630821 244 RTGKLI 249
Cdd:cd08482  158 ASGRLV 163
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 87-284 2.36e-10

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: 58.85  E-value: 2.36e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDYL 166
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 IKAGtPHVPSDLIDHNCLIYRSRERDYTSWAFDNGqenlsVKVAGDYS---VDLAEAVRDAAVSGWGVAYLATYLVKEEF 243
Cdd:cd08481   81 AGRA-LAAPADLAHLPLLQQTTRPEAWRDWFEEVG-----LEVPTAYRgmrFEQFSMLAQAAVAGLGVALLPRFLIEEEL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 515630821 244 RTGKLIQVlpeWRASQLMP--FYAVYPSRKNMPKKLSAVIEFI 284
Cdd:cd08481  155 ARGRLVVP---FNLPLTSDkaYYLVYPEDKAESPPVQAFRDWL 194
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-68 4.24e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.43  E-value: 4.24e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFN 68
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-120 4.88e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 59.40  E-value: 4.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  13 FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCE-QLFNTVKAAQMDMDSQRDDIsgILRVG 91
Cdd:PRK09906  18 FTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARaILEQAEKAKLRARKIVQEDR--QLTIG 95

                         90       100       110
                 ....*....|....*....|....*....|
gi 515630821  92 LSQSfGTLHIIP-AIDQLRQLYPQLRIEVH 120
Cdd:PRK09906  96 FVPS-AEVNLLPkVLPMFRLRHPDTLIELV 124
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-74 6.41e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.83  E-value: 6.41e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRtTRSLTLTEAGDVFYQHCEQ-------LFNTVKAAQ 74
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQvalleadLLSTLPAER 86
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-189 7.33e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 58.88  E-value: 7.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDD 83
Cdd:PRK15421  10 LQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  84 IsgiLRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVH---LFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVA 160
Cdd:PRK15421  90 R---LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKsgvTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLV 166

                        170       180       190
                 ....*....|....*....|....*....|..
gi 515630821 161 ASPDYLIKAGTPHVPSDLIDHNCLIY---RSR 189
Cdd:PRK15421 167 LAPDHPLAAKTRITPEDLASETLLIYpvqRSR 198
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
21-120 3.43e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.37  E-value: 3.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  21 NVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDDISGILR----VGLSQSf 96
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSlfcsVTAAYS- 80

                         90       100
                 ....*....|....*....|....
gi 515630821  97 gtlHIIPAIDQLRQLYPQLRIEVH 120
Cdd:PRK11716  81 ---HLPPILDRFRAEHPLVEIKLT 101
PRK09986 PRK09986
LysR family transcriptional regulator;
4-197 5.92e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 55.88  E-value: 5.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTV------------- 70
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAeqslarveqigrg 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  71 KAAQMDMDSQRDDISGILRVGLSQsFGTLHiiPAID-QLRQLYPQLRIEvhlfdykvdMIEER-LDLWITNNEDL--PEG 146
Cdd:PRK09986  95 EAGRIEIGIVGTALWGRLRPAMRH-FLKEN--PNVEwLLRELSPSMQMA---------ALERReLDAGIWRMADLepNPG 162

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 515630821 147 YIAQRLADSQFVVAASPDYLIkAGTPHVPSDLIDHNCLIYRSreRDYTSWA 197
Cdd:PRK09986 163 FTSRRLHESAFAVAVPEEHPL-ASRSSVPLKALRNEYFITLP--FVHSDWG 210
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 87-250 7.02e-09

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: 54.47  E-value: 7.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDyl 166
Cdd:cd08487    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPE-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 iKAGTPHVPSDLIdhNCLIYRS-RERDYTSWaFDngQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08487   79 -IAKRLSHPADLI--NETLLRSyRTDEWLQW-FE--AANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIEN 152


                 ....*
gi 515630821 246 GKLIQ 250
Cdd:cd08487  153 GQLVQ 157
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 14-93 1.11e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.46  E-value: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDDISGILRVGLS 93
Cdd:PRK11233  19 TQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSIGLA 98
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 88-249 2.09e-08

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: 53.12  E-value: 2.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWIT-NNEDLPeGYIAQRLADSQFVVAASPDYL 166
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRyGNGDWP-GLESEPLTAAPFVVVAAPGLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 iKAGTPHVPSDLIDHNCLIYRSReRDYTSWAFDNGQENLSVKVagdYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRTG 246
Cdd:cd08483   81 -GDRKVDSLADLAGLPWLQERGT-NEQRVWLASMGVVPDLERG---VTFLPGQLVLEAARAGLGLSIQARALVEPDIAAG 155


                 ...
gi 515630821 247 KLI 249
Cdd:cd08483  156 RLT 158
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 14-120 3.24e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 53.84  E-value: 3.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLT-LTEAGDVFYQHCEQLFNtvkaaqmdmdsqrdDISGILRVGL 92
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILR--------------EVGNIKRIGD 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 515630821  93 ---SQSFGTLHII-----------PAIDQLRQLYPQLRIEVH 120
Cdd:PRK12682  86 dfsNQDSGTLTIAtthtqaryvlpRVVAAFRKRYPKVNLSLH 127
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 87-250 4.18e-08

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: 52.37  E-value: 4.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQ--LRIEVHlfDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPD 164
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFidLRLSTN--NNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 165 YlikAGTPHVPSDLIDHNclIYRS-RERDYTSWaFDNGQENlSVKVAG---DYSVDLAEavrdAAVSGWGVAYLATYLVK 240
Cdd:cd08484   79 L---ARRLSEPADLANET--LLRSyRADEWPQW-FEAAGVP-PPPINGpvfDSSLLMVE----AALQGAGVALAPPSMFS 147

                        170
                 ....*....|
gi 515630821 241 EEFRTGKLIQ 250
Cdd:cd08484  148 RELASGALVQ 157
cbl PRK12679
HTH-type transcriptional regulator Cbl;
2-120 1.13e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 52.50  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   2 VIFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKL-VQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMDSQ 80
Cdd:PRK12679   8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLF 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 515630821  81 RDDISGILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVH 120
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELI 127
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 13-180 2.12e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 51.57  E-value: 2.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  13 FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFYQHCEQLFNTVKAAQMDMdsQRDDISGILRVGL 92
Cdd:PRK15092  28 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL--MYSNLQGVLTIGA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  93 S-QSFGTlhIIPAI-DQLRQLYPQLRIE--VHLFDYKVDMIEE-RLDLWITNNEdlPEGYIAQRLADSQFVVAASPDYLI 167
Cdd:PRK15092 106 SdDTADT--ILPFLlNRVSSVYPKLALDvrVKRNAFMMEMLESqEVDLAVTTHR--PSSFPALNLRTSPTLWYCAAEYVL 181

                        170
                 ....*....|...
gi 515630821 168 KAGTPhVPSDLID 180
Cdd:PRK15092 182 QKGEP-IPLVLLD 193
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-283 6.09e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 50.07  E-value: 6.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   3 IFHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVFY----------QHCEQLFntvka 72
Cdd:PRK10837  10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYpralalleqaVEIEQLF----- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  73 aqmdmdsQRDdiSGILRVGLSQSFGTlHIIPA-IDQLRQLYPQLRIEVHLFDYKvDMIEE----RLDLwitnneDLPEG- 146
Cdd:PRK10837  85 -------RED--NGALRIYASSTIGN-YILPAmIARYRRDYPQLPLELSVGNSQ-DVINAvldfRVDI------GLIEGp 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 147 -----YIAQRLADSQFVVAASPDYLIkAGTPHVPSDLIDHNCLIyrsRER--------DYTSWA----FDNGQEnlsvkv 209
Cdd:PRK10837 148 chspeLISEPWLEDELVVFAAPDSPL-ARGPVTLEQLAAAPWIL---RERgsgtreivDYLLLShlprFELAME------ 217

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515630821 210 AGDysvdlAEAVRDAAVSGWGVAYLATYLVKEEFRTGKLIQV-LPEWRASQLMpfYAVYPSRKNMPKKLSAVIEF 283
Cdd:PRK10837 218 LGN-----SEAIKHAVRHGLGISCLSRRVIADQLQAGTLVEVaVPLPRLMRTL--YRIHHRQKHLSNALQRFLSY 285
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-66 1.11e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 49.00  E-value: 1.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515630821   4 FHALIKHEGFTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRtTRSLTLTEAGDVFYQHCEQL 66
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV 71
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-120 1.16e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.19  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLT-LTEAGDVFYQHCEQLF----NTVKAAqmDMDSQRDdiSGIL 88
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaeNLRRLA--EQFADRD--SGHL 95

                         90       100       110
                 ....*....|....*....|....*....|..
gi 515630821  89 RVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVH 120
Cdd:PRK12683  96 TVATTHTQARYALPKVVRQFKEVFPKVHLALR 127
PRK12680 PRK12680
LysR family transcriptional regulator;
14-121 1.63e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.77  E-value: 1.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSL-TLTEAGDVFYQHCEQLFNTVKAAQMDMDSQRDDISGILRVGL 92
Cdd:PRK12680  20 TLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTT 99

                         90       100
                 ....*....|....*....|....*....
gi 515630821  93 SQSFGTLHIIPAIDQLRQLYPQlrIEVHL 121
Cdd:PRK12680 100 THTQARFVLPPAVAQIKQAYPQ--VSVHL 126
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 88-276 6.16e-05

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


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 43.03  E-value: 6.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTLHIIPAIDQLRQLYPQLRIevhLFDYKV------DMIEERLDLWITNNEDLPEGYIAQR-LADSQFVVA 160
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRI---RLSEEVlggtwdALASGRADLVIGATGELPPGGVKTRpLGEVEFVFA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 161 ASPD-YLIKAGTPHVPSDLidhncliyrsreRDYTSWAFDNGQENLSVKVAGDYS------VDLAEAVRDAAVSGWGVAY 233
Cdd:cd08431   79 VAPNhPLAKLDGPLDASAI------------KQYPAIVVADTSRNLPPRSSGLLEgqdrirVPTMQAKIDAQVLGLGVGY 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 515630821 234 LATYLVKEEFRTGKLIQVLPEWRASQLMPFYAvypSRKNMPKK 276
Cdd:cd08431  147 LPRHLAKPELASGELVEKALEDPRPPQELFLA---WRKDQRGK 186
cysB PRK12681
HTH-type transcriptional regulator CysB;
14-56 1.34e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.96  E-value: 1.34e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLT-LTEAG 56
Cdd:PRK12681  20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAG 63
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
14-120 1.48e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.66  E-value: 1.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  14 TSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLT-LTEAGdvfyqhcEQLFNTVKAAQMDMDSqrddisgILRVGL 92
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPG-------RIILASVERILQEVEN-------LKRVGK 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 515630821  93 ---SQSFGTLHII-----------PAIDQLRQLYPQLRIEVH 120
Cdd:PRK12684  86 efaAQDQGNLTIAtthtqaryalpAAIKEFKKRYPKVRLSIL 127
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 89-164 1.99e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 41.43  E-value: 1.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  89 RVGLSqSFGTLHIIPAI-DQLRQLYPQLRIEVHLFDYKV---DMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPD 164
Cdd:cd08417    3 RIAAS-DYLEALLLPPLlARLRQEAPGVRLRFVPLDRDDleeALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKD 81
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 87-253 3.68e-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: 40.59  E-value: 3.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  87 ILRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVHLFDYKVDMIEERLDLWITNNEDLPEGYIAQRLADSQFVVAASPDYl 166
Cdd:cd08488    1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPEL- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821 167 ikAGTPHVPSDLIDHNCLiyRS-RERDYTSWaFDNGQENLSVKVAGDYSVDLAEAVRDAAVSGWGVAYLATYLVKEEFRT 245
Cdd:cd08488   80 --ARQLREPADLARHTLL--RSyRADEWPQW-FEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLAS 154


                 ....*...
gi 515630821 246 GKLIQVLP 253
Cdd:cd08488  155 GALVQPFA 162
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-59 4.16e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.47  E-value: 4.16e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 515630821  13 FTSAAKSLNVSVSHISKQVALLEDSIGIKLVQRTTRSLTLTEAGDVF 59
Cdd:PRK11074  19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWF 65
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 89-164 1.34e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 39.26  E-value: 1.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  89 RVGLSQSFGTLHIIPAIDQLRQLYPQLRI---EVHLFDYKVDMIEERLDLWITN--NEDLPEGYIAQRLADSQFVVAASP 163
Cdd:cd08418    3 SIGVSSLIAHTLMPAVINRFKEQFPDVQIsiyEGQLSSLLPELRDGRLDFAIGTlpDEMYLKELISEPLFESDFVVVARK 82


                 .
gi 515630821 164 D 164
Cdd:cd08418   83 D 83
PRK11482 PRK11482
DNA-binding transcriptional regulator;
1-129 6.10e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 37.78  E-value: 6.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821   1 MVIFHALIKHEGFTSAAKSLNVSVSHISKQV----ALLEDSIGIklvqRTTRSLTLTEAGDVFYQHCEQLFNTVKAAqMD 76
Cdd:PRK11482  34 LTIFEAVYVHKGIVNAAKILNLTPSAISQSIqklrVIFPDPLFI----RKGQGVTPTAYATHLHEYISQGLESILGA-LD 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515630821  77 M----DSQRddisgILRVGLSQSFGTLhIIPAIDQ-LRQLYPQLRI--------EVHLFDYKVDMI 129
Cdd:PRK11482 109 ItgsyDKQR-----TITIATTPSVGAL-VMPVIYQaIKTHYPQLLLrnipisdaENQLSQFQTDLI 168
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 88-181 6.69e-03

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 37.25  E-value: 6.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630821  88 LRVGLSQSFGTLHIIPAIDQLRQLYPQLRIEVH--LFDYKVDMIEE-RLDLWI--TNNEDLPEGYIAQRLADSQFVVAAS 162
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVegTSDELLEGLRAgELDLAIgrLADDEQPPDLASEELADEPLVVVAR 81

                         90       100
                 ....*....|....*....|
gi 515630821 163 PDYLIkAGTPHVP-SDLIDH 181
Cdd:cd08435   82 PGHPL-ARRARLTlADLADY 100
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH