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Conserved domains on  [gi|1995773780|gb|QSH06652|]
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transcriptional regulator TdcA [Enterobacter hormaechei]

Protein Classification

transcriptional regulator TdcA( domain architecture ID 11484667)

transcriptional regulator TdcA is a member of the LysR family and 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.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10341 PRK10341
transcriptional regulator TdcA;
1-306 0e+00

transcriptional regulator TdcA;


:

Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 577.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   1 MNTIILPKTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITRE 80
Cdd:PRK10341    1 MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  81 MKNMVSEINSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLL 160
Cdd:PRK10341   81 MKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 161 QDLHVEPLFESEFVLVASKSRTCTGPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNA 240
Cdd:PRK10341  161 QDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1995773780 241 DYLTVIPRDMIAPFGSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQYSSMNIEKRR 306
Cdd:PRK10341  241 DFLTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRR 306
 
Name Accession Description Interval E-value
PRK10341 PRK10341
transcriptional regulator TdcA;
1-306 0e+00

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 577.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   1 MNTIILPKTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITRE 80
Cdd:PRK10341    1 MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  81 MKNMVSEINSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLL 160
Cdd:PRK10341   81 MKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 161 QDLHVEPLFESEFVLVASKSRTCTGPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNA 240
Cdd:PRK10341  161 QDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1995773780 241 DYLTVIPRDMIAPFGSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQYSSMNIEKRR 306
Cdd:PRK10341  241 DFLTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRR 306
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 99-297 7.19e-92

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: 271.15  E-value: 7.19e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQDLHVEPLFESEFVLVAS 178
Cdd:cd08418     2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 179 KSRTCTGPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFG-SD 257
Cdd:cd08418    82 KDHPLQGARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLdSF 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1995773780 258 QFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQY 297
Cdd:cd08418   162 RLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-297 2.67e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.25  E-value: 2.67e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEIN 89
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  90 SLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTlsDGMLLQDLHVEPLF 169
Cdd:COG0583    84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 170 ESEFVLVASKSrtctgpTRLASLTHeqwvmpqtdmgyynellttlqdnhisienivQTDSVVTIYNLVLNADYLTVIPRD 249
Cdd:COG0583   162 EERLVLVASPD------HPLARRAP-------------------------------LVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1995773780 250 MIAPF-GSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQY 297
Cdd:COG0583   205 LAADElAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-296 3.28e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.85  E-value: 3.28e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESEFVLVAS 178
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP--DDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 179 KSRTCTG--PTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPF-G 255
Cdd:pfam03466  82 PDHPLARgePVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARElA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1995773780 256 SDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQ 296
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
 
Name Accession Description Interval E-value
PRK10341 PRK10341
transcriptional regulator TdcA;
1-306 0e+00

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 577.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   1 MNTIILPKTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITRE 80
Cdd:PRK10341    1 MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  81 MKNMVSEINSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLL 160
Cdd:PRK10341   81 MKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 161 QDLHVEPLFESEFVLVASKSRTCTGPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNA 240
Cdd:PRK10341  161 QDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1995773780 241 DYLTVIPRDMIAPFGSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQYSSMNIEKRR 306
Cdd:PRK10341  241 DFLTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRR 306
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 99-297 7.19e-92

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: 271.15  E-value: 7.19e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQDLHVEPLFESEFVLVAS 178
Cdd:cd08418     2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 179 KSRTCTGPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFG-SD 257
Cdd:cd08418    82 KDHPLQGARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLdSF 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1995773780 258 QFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQY 297
Cdd:cd08418   162 RLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-297 2.67e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.25  E-value: 2.67e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEIN 89
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  90 SLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTlsDGMLLQDLHVEPLF 169
Cdd:COG0583    84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 170 ESEFVLVASKSrtctgpTRLASLTHeqwvmpqtdmgyynellttlqdnhisienivQTDSVVTIYNLVLNADYLTVIPRD 249
Cdd:COG0583   162 EERLVLVASPD------HPLARRAP-------------------------------LVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1995773780 250 MIAPF-GSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQY 297
Cdd:COG0583   205 LAADElAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PRK09791 PRK09791
LysR family transcriptional regulator;
8-298 1.47e-40

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 142.98  E-value: 1.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   8 KTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSE 87
Cdd:PRK09791    6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  88 INSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQDLHVEP 167
Cdd:PRK09791   86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEK 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 168 LFESEFVLVASKSRTCTGPTRLASLTHEQWVMPQTDMGYYNEL--LTTLQDNHISIENIVQTDSVVTiyNLVLNADYLTV 245
Cdd:PRK09791  166 LLEKQFAVFCRPGHPAIGARSLKQLLDYSWTMPTPHGSYYKQLseLLDDQAQTPQVGVVCETFSACI--SLVAKSDFLSI 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1995773780 246 IPRDMI-APFGSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQYS 298
Cdd:PRK09791  244 LPEEMGcDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFRREC 297
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-296 3.28e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.85  E-value: 3.28e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESEFVLVAS 178
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP--DDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 179 KSRTCTG--PTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPF-G 255
Cdd:pfam03466  82 PDHPLARgePVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARElA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1995773780 256 SDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQ 296
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-294 3.37e-30

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: 113.08  E-value: 3.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESEFVLVAS 178
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPV--DDPGLESEPLFEEPLVLVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 179 KS-RTCTGPT-RLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFGS 256
Cdd:cd05466    80 PDhPLAKRKSvTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAD 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1995773780 257 DQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELA 294
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 116-293 8.01e-19

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: 82.71  E-value: 8.01e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 116 IKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQDLHVEPLFESEFVLVASKS--RTCTGPTRLASLT 193
Cdd:cd08435    19 IARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGhpLARRARLTLADLA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 194 HEQWVMPQTDMGYYNELLTTLQDNHISI-ENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFGSDQFIV-LPVEDELPVA 271
Cdd:cd08435    99 DYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDELRAGVLReLPLPLPTSRR 178

                         170       180
                  ....*....|....*....|..
gi 1995773780 272 RYAAVWSKNYSIKKSASVLVEL 293
Cdd:cd08435   179 PIGITTRRGGPLSPAARALLDA 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 3.50e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.50e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQ 68
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-180 4.85e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.20  E-value: 4.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   6 LPKT-QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNM 84
Cdd:CHL00180    3 LPFTlDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEET 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  85 VSEINSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAI--GTLSDGmLLQD 162
Cdd:CHL00180   83 CRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIvgGEVPTE-LKKI 161

                         170
                  ....*....|....*...
gi 1995773780 163 LHVEPLFESEFVLVASKS 180
Cdd:CHL00180  162 LEITPYVEDELALIIPKS 179
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 10-280 5.64e-14

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 70.95  E-value: 5.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEIN 89
Cdd:PRK09906    4 RHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRAR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  90 SLSFSTVMdvsfgypSLIGFTfLSGMIKKFKEVFPKARVSMYEA--QLSSF-----LPAIRDGRLDFAI---GTLSDGML 159
Cdd:PRK09906   84 KIVQEDRQ-------LTIGFV-PSAEVNLLPKVLPMFRLRHPDTliELVSLittqqEEKLRRGELDVGFmrhPVYSDEID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 160 LQDLHVEPLFeseFVLVASKSRTCTGPTRLASLTHEQWVMPQTDM-GYYNELLTTLQDNHISIENIVQT-DSVVTIYNLV 237
Cdd:PRK09906  156 YLELLDEPLV---VVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsGSLAPIIKAWFAQHNSQPNIVQVaTNILVTMNLV 232

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1995773780 238 LNADYLTVIPrDMIAPFGSDQFIVLPVEDELPVARYAAVWSKN 280
Cdd:PRK09906  233 GMGLGCTIIP-GYMNNFNTGQVVFRPLAGNVPSIALLMAWKKG 274
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
10-193 1.17e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 70.05  E-value: 1.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEIN 89
Cdd:PRK15421    5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  90 SLSfSTVMDVSFGYPSLIgfTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIgtLSDGMLLQDLHVEPLF 169
Cdd:PRK15421   85 EPQ-QTRLRIAIECHSCI--QWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM--TSDILPRSGLHYSPMF 159

                         170       180
                  ....*....|....*....|....*....
gi 1995773780 170 ESEFVLVAS-----KSRTCTGPTRLASLT 193
Cdd:PRK15421  160 DYEVRLVLApdhplAAKTRITPEDLASET 188
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 99-280 2.00e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 67.53  E-value: 2.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSdgMLLQDLHVEPLFESEFVLV-- 176
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPP--PDPPGLASRPLLREPLVVAlp 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 177 -----ASKSRtctgpTRLASLTHEQWVMPQTDM--GYYNELLTTLQDNHISIeNIVQT-DSVVTIYNLVLNADYLTVIPR 248
Cdd:cd08414    80 adhplAARES-----VSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTP-RIVQEaSDLQTLLALVAAGLGVALVPA 153

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1995773780 249 DMiAPFGSDQFIVLPVEDELPVARYAAVWSKN 280
Cdd:cd08414   154 SV-ARLQRPGVVYRPLADPPPRSELALAWRRD 184
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 12-199 4.57e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 65.09  E-value: 4.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  12 LVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREmknmVSEINSL 91
Cdd:PRK10837    8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEIEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  92 SFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDfaIGTLSDGMLLQDLHVEPLFES 171
Cdd:PRK10837   84 FREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVD--IGLIEGPCHSPELISEPWLED 161

                         170       180
                  ....*....|....*....|....*....
gi 1995773780 172 EFVLVAS-KSRTCTGPTRLASLTHEQWVM 199
Cdd:PRK10837  162 ELVVFAApDSPLARGPVTLEQLAAAPWIL 190
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-300 7.33e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 58.81  E-value: 7.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  11 HLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEINS 90
Cdd:PRK11242    5 HIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  91 lsfstVMDVSFGypSL-IGFT-----FLSG-MIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTlsDGMLLQDL 163
Cdd:PRK11242   85 -----VADLSRG--SLrLAMTptftaYLIGpLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF--APVHSPEI 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 164 HVEPLFESEFVLVASKSRtctgptrlaSLTHEQWVMPQTDMGyyNELLTTLQDNHISIENI--------------VQTDS 229
Cdd:PRK11242  156 EAQPLFTETLALVVGRHH---------PLAARRKALTLDELA--DEPLVLLSAEFATREQIdryfrrhgvtprvaIEANS 224

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1995773780 230 VVTIYNLVLNADYLTVIPrDMIApFGSDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELAKQYSSM 300
Cdd:PRK11242  225 ISAVLEIVRRGRLATLLP-AAIA-REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAE 293
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-180 1.33e-09

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 56.76  E-value: 1.33e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1995773780 104 PSLIgFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMllQDLHVEPLFESEFVLVASKS 180
Cdd:cd08440     8 PSLA-ATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEAD--PDLEFEPLLRDPFVLVCPKD 81
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-77 2.07e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 57.33  E-value: 2.07e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1995773780   9 TQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESI 77
Cdd:PRK03601    3 TELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETL 71
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 10-195 2.66e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 57.31  E-value: 2.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSG-SIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVK-LTAAGQVLLSYAESITREMKNM--V 85
Cdd:PRK12682    4 QQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIkrI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  86 SEINS------LSFSTVmdvsfgypSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTlSDGML 159
Cdd:PRK12682   84 GDDFSnqdsgtLTIATT--------HTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT-ESLAD 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1995773780 160 LQDLHVEPLFESEFVLVASKSR--TCTGPTRLASLTHE 195
Cdd:PRK12682  155 DPDLATLPCYDWQHAVIVPPDHplAQEERITLEDLAEY 192
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 110-281 3.07e-09

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: 55.68  E-value: 3.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 110 TFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESEFVLVASKSRtctgPTRL 189
Cdd:cd08417    13 LLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPE--LPPGLRSQPLFEDRFVCVARKDH----PLAG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 190 ASLTHEQW-----VMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFG-SDQFIVLP 263
Cdd:cd08417    87 GPLTLEDYlaaphVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAeRLGLRVLP 166

                         170
                  ....*....|....*...
gi 1995773780 264 VEDELPVARYAAVWSKNY 281
Cdd:cd08417   167 LPFELPPFTVSLYWHPRR 184
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-77 5.99e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 56.13  E-value: 5.99e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTgVKLTAAGQVLLSYAESI 77
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQV 71
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-153 1.18e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 55.37  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   8 KTQHLVVFQEVIKSG-SIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVK-LTAAGQVLLSYAESITREMKNM- 84
Cdd:PRK12684    2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLk 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1995773780  85 -VSEinslSFSTVMDVSFgypsLIGFTF------LSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGT 153
Cdd:PRK12684   82 rVGK----EFAAQDQGNL----TIATTHtqaryaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAT 149
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 10-153 4.63e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 53.51  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  10 QHLVVFQEVIKSG-SIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKN---TGvkLTAAGQVLLSYAESITREMKNmv 85
Cdd:PRK12683    4 QQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkrlTG--LTEPGKELLQIVERMLLDAEN-- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1995773780  86 seINSLSfSTVMDVSFGYpSLIGFTF------LSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGT 153
Cdd:PRK12683   80 --LRRLA-EQFADRDSGH-LTVATTHtqaryaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAT 149
PRK09986 PRK09986
LysR family transcriptional regulator;
15-207 1.19e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 52.03  E-value: 1.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  15 FQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSyaesitrEMKNMVSEINSlSFS 94
Cdd:PRK09986   15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILME-------ESRRLLDNAEQ-SLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  95 TVMDVSFGYPS-----LIGFTFLSGMI---KKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQDLHVE 166
Cdd:PRK09986   87 RVEQIGRGEAGrieigIVGTALWGRLRpamRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSR 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1995773780 167 PLFESEFVLVASKSRTCTGPTR--LASLTHEQWV-MP--QTDMGYY 207
Cdd:PRK09986  167 RLHESAFAVAVPEEHPLASRSSvpLKALRNEYFItLPfvHSDWGKF 212
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-75 1.30e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.08  E-value: 1.30e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1995773780  11 HLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRkNTGVKLTAAGQVLLSYAE 75
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHAR 69
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 103-294 1.47e-07

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.01  E-value: 1.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 103 YPSLIGFtFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESE-FVLVASKSR 181
Cdd:cd08412     7 FSTLAPY-YLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLD--LPEDIAFEPLARLPpYVWLPADHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 182 TCTGPT-RLASLTHEQWVM---PQTDmgyyNELLTTLQDNHISiENIVQ-TDSVVTIYNLVLNA---DYLTVIPRDMIAP 253
Cdd:cd08412    84 LAGKDEvSLADLAAEPLILldlPHSR----EYFLSLFAAAGLT-PRIAYrTSSFEAVRSLVANGlgySLLNDRPYRPWSY 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1995773780 254 FGSDqFIVLPVEDELPVARYAAVWSKNYSIKKSASVLVELA 294
Cdd:cd08412   159 DGKR-LVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 15-185 1.63e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.61  E-value: 1.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  15 FQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEINSLSFS 94
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  95 TVMDVSFGY-PSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIgtLSDGMLLQDLHVEPLFESEF 173
Cdd:PRK11233   89 LSGQVSIGLaPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAV--IYEHSPVAGLSSQPLLKEDL 166

                         170
                  ....*....|..
gi 1995773780 174 VLVAskSRTCTG 185
Cdd:PRK11233  167 FLVG--TQDCPG 176
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 27-151 1.40e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.87  E-value: 1.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  27 AARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKnMVSEINSL---SFSTVMDVSFgY 103
Cdd:PRK11151   21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVK-VLKEMASQqgeTMSGPLHIGL-I 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1995773780 104 PSlIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAI 151
Cdd:PRK11151   99 PT-VGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI 145
PRK09801 PRK09801
LysR family transcriptional regulator;
7-128 1.68e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.88  E-value: 1.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   7 PKTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVS 86
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1995773780  87 EINSLSFS----TVMDVSFGYpsliGFTFLSGMIKKFKEVFPKARV 128
Cdd:PRK09801   86 DVTQIKTRpegmIRIGCSFGF----GRSHIAPAITELMRNYPELQV 127
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 111-179 3.10e-06

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 47.13  E-value: 3.10e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1995773780 111 FLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMllQDLHVEPLFESEFVLVASK 179
Cdd:cd08411    15 LLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDE--PGLEEEPLFDEPFLLAVPK 81
leuO PRK09508
leucine transcriptional activator; Reviewed
 12-268 4.74e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 47.32  E-value: 4.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  12 LVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSyaeSITREMKNMVSEINSL 91
Cdd:PRK09508   27 LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFG---PVRQALQLVQNELPGS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  92 SFST-----VMDVSFGYPSLIGFTflSGMIKKFKEVFPKARV---SMYEAQLSSFLpaiRDGRLDFAIGTLS-DGmllQD 162
Cdd:PRK09508  104 GFEPesserVFNLCICSPLDIRLT--SQIYNRIEQIAPNIHVvfkSSLNQNIEHQL---RYQETEFVISYEEfDR---PE 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 163 LHVEPLFESEFVLVASKSR-TCTGPTRLASLTHEQWVMPQTD------MGYYnellttlqDNHISIENIV-QTDSVVTIY 234
Cdd:PRK09508  176 FTSVPLFKDELVLVASKNHpRIKGPITEEQLYNEQHAVVSLDrfasfsQPWY--------DTVDKQASIAyQGTALSSVL 247

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1995773780 235 NLVLNADYLTVIPRDMIAPFG-SDQFIVLPVEDEL 268
Cdd:PRK09508  248 NVVSQTHLVAIAPRWLAEEFAeSLELQILPLPLKN 282
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-159 4.82e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 47.45  E-value: 4.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   8 KTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSE 87
Cdd:PRK10632    3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQ 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1995773780  88 INSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSmyeaqLSSFLPA---IRDGrLDFAI--GTLSDGML 159
Cdd:PRK10632   83 LYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVN-----LVTGIPApdlIADG-LDVVIrvGALQDSSL 153
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 99-237 5.42e-06

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 46.17  E-value: 5.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFA-IGTLSDgMLLQDLHVEPLFESEFVLVA 177
Cdd:cd08437     2 LRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAlLGSLTP-LENSALHSKIIKTQHFMIIV 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1995773780 178 SKSRTCTGPT--RLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLV 237
Cdd:cd08437    81 SKDHPLAKAKkvNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMV 142
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-200 6.54e-06

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 46.05  E-value: 6.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 110 TFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDGMLLQD---LHVEPLFESEFVLVASKSRTCTG- 185
Cdd:cd08423    13 ALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDdpgLTRVPLLDDPLDLVLPADHPLAGr 92

                          90
                  ....*....|....*.
gi 1995773780 186 -PTRLASLTHEQWVMP 200
Cdd:cd08423    93 eEVALADLADEPWIAG 108
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 99-278 7.39e-06

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 45.66  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  99 VSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAqLSSFL-PAIRDGRLDFAIgtLSDGMLLQDLHVEPLFESEFVLVA 177
Cdd:cd08433     2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEG-LSGHLlEWLLNGRLDLAL--LYGPPPIPGLSTEPLLEEDLFLVG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 178 SKSRTCT--GPTRLASLTHEQWVMPQTDMGYYNELLTTLQDNHISIENIVQTDSVVTIYNLVlnADYL--TVIPRDMIAP 253
Cdd:cd08433    79 PADAPLPrgAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALV--AAGLgyTILPASAVAA 156

                         170       180
                  ....*....|....*....|....*.
gi 1995773780 254 -FGSDQFIVLPVEDELPVARYAAVWS 278
Cdd:cd08433   157 eVAAGRLVAAPIVDPALTRTLSLATP 182
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 107-199 3.52e-05

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 44.02  E-value: 3.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 107 IGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAI--GTLSDGmllqDLHVEPLFESEFVLVASKSRTCT 184
Cdd:cd08420    10 IGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLveGPVDHP----DLIVEPFAEDELVLVVPPDHPLA 85

                          90
                  ....*....|....*..
gi 1995773780 185 GPTR--LASLTHEQWVM 199
Cdd:cd08420    86 GRKEvtAEELAAEPWIL 102
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-88 4.30e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 44.41  E-value: 4.30e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1995773780  12 LVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEI 88
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSEL 83
cbl PRK12679
HTH-type transcriptional regulator Cbl;
28-153 7.89e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 43.64  E-value: 7.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  28 ARQLGLTQPAVSKIISDIESYFGVEVMVRKntGVKL---TAAGQVLLSYAESITREMKNM--VSEINSLSFSTVMDVSFG 102
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFIRR--GKRLlgmTEPGKALLVIAERILNEASNVrrLADLFTNDTSGVLTIATT 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1995773780 103 YPSliGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGT 153
Cdd:PRK12679  101 HTQ--ARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS 149
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 98-199 8.85e-05

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 42.52  E-value: 8.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  98 DVSFGYPSLIGFTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIgtLSDGMLLQDLHVEPLFESEFVLV- 176
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLAL--CSPVPDEPDIEWIPLFTEELVLVv 78

                          90       100
                  ....*....|....*....|....*....
gi 1995773780 177 ------ASKSRtctgpTRLASLTHEQWVM 199
Cdd:cd08434    79 pkdhplAGRDS-----VDLAELADEPFVL 102
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
8-181 2.39e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.96  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   8 KTQHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSE 87
Cdd:PRK10082   12 ETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  88 INSLSFSTVMDVSFGYPSLIGFTFLSGMIKKFKEVFPKArvsmYEA-QLSSFLPAIRDGRLDFaIGTLSDGMLLQDL--H 164
Cdd:PRK10082   92 LRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWA----IEAiDVDEAVDKLREGQSDC-IFSFHDEDLLEAPfdH 166

                         170
                  ....*....|....*...
gi 1995773780 165 VEpLFESE-FVLVASKSR 181
Cdd:PRK10082  167 IR-LFESQlFPVCASDEH 183
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-84 2.87e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.85  E-value: 2.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1995773780  10 QHLVVFQEVIKSGSIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNM 84
Cdd:PRK11074    5 YSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQET 79
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 27-77 6.44e-04

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 40.60  E-value: 6.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1995773780  27 AARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVKLTAAGQvllSYAESI 77
Cdd:PRK11139   26 AAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQ---RYFLDI 73
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
37-177 6.50e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 6.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780  37 AVSKIISDIESYFGVEVMVRKNTGVKLTAAGQVLLSYAESITREMKNMVSEINSLSfstvmdvsfgyPSLIG-------- 108
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQG-----------PSLSGelslfcsv 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1995773780 109 ---FTFLSGMIKKFKEVFPKArvsmyEAQLSSFLPA-----IRDGRLDFAIGTLSDgMLLQDLHVEPLFESEFVLVA 177
Cdd:PRK11716   76 taaYSHLPPILDRFRAEHPLV-----EIKLTTGDAAdavekVQSGEADLAIAAKPE-TLPASVAFSPIDEIPLVLIA 146
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 141-297 9.77e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 39.54  E-value: 9.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 141 AIRDGRLDFAIGTlsdgMLLQD--LHVEPLFESEFVLVASKsrtctGPTRLA-SLTHEQW-----VMPQTDMGYYNELLT 212
Cdd:cd08466    44 DLRLQEVDLVIDY----VPFRDpsFKSELLFEDELVCVARK-----DHPRIQgSLSLEQYlaekhVVLSLRRGNLSALDL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 213 TLQDNHISIENIVQTDSVVTIYNLVLNADYLTVIPRDMIAPFG-SDQFIVLPVEDELPVARYAAVWSKNYSIKKSASVLV 291
Cdd:cd08466   115 LTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAeQLNLQILPLPFKTKPIPLYMVWHKSRERDPAHQWLR 194


                  ....*.
gi 1995773780 292 ELAKQY 297
Cdd:cd08466   195 EQIKQL 200
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 109-248 1.00e-03

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. 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. 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: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 39.73  E-value: 1.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780 109 FTFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIG-TLSDGMLLQDLHVEPLFESEFVLVASKsrtctGPT 187
Cdd:cd08468    12 LAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGySHDDGAEPRLIEERDWWEDTYVVIASR-----DHP 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1995773780 188 RLASLTHEQ-------WVMP-QTDMGYYNELLTTLqdnHISIENIVQTDSVVTIYNLVLNADYLTVIPR 248
Cdd:cd08468    87 RLSRLTLDAflaerhlVVTPwNEDRGVVDQVLEKQ---GLEREIALQLPNVLNAPFIVASSDLLMTLPR 152
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 110-180 1.42e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 39.10  E-value: 1.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1995773780 110 TFLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGTLSDgmLLQDLHVEPLFESEFVLVASKS 180
Cdd:cd08459    13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPD--LGAGFFQQRLFRERYVCLVRKD 81
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 139-201 1.42e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 39.09  E-value: 1.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1995773780 139 LPAIRDGRLDFAIgtLSDGMLLQDLHVEPLFESEFVLVASKSrtctgpTRLASLTheqWVMPQ 201
Cdd:cd08441    42 LPALLRGELDLVI--TSDPLPLPGIAYEPLFDYEVVLVVAPD------HPLAAKE---FITPE 93
cysB PRK12681
HTH-type transcriptional regulator CysB;
8-153 1.54e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 39.50  E-value: 1.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1995773780   8 KTQHLVVFQEVIKSG-SIGSAARQLGLTQPAVSKIISDIESYFGVEVMVRKNTGVK-LTAAGQVLLSYAESITREMKNMV 85
Cdd:PRK12681    2 KLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1995773780  86 S--------EINSLSFSTVmDVSFGYPsligftfLSGMIKKFKEVFPKARVSMYEAQLSSFLPAIRDGRLDFAIGT 153
Cdd:PRK12681   82 SvagehtwpDKGSLYIATT-HTQARYA-------LPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIAT 149
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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