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Conserved domains on  [gi|981601337|ref|WP_059801540|]
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LysR family transcriptional regulator [Burkholderia stagnalis]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444080)

LysR family transcriptional regulator MetR regulates the expression of methionine biosynthetic genes, metA, metE, metF, and metH

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 9.61e-102

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: 296.01  E-value: 9.61e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAE 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 173 THRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYADR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 981601337 253 IPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-63 8.77e-17

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.80  E-value: 8.77e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337    6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQ 63
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 9.61e-102

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: 296.01  E-value: 9.61e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAE 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 173 THRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYADR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 981601337 253 IPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-292 4.41e-69

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 217.19  E-value: 4.41e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAe 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  81 arMKQYADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDP 160
Cdd:PRK15421  80 --LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 161 VFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRhKVIETTDIMLQMVASGRGVAA 240
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSL-KSVDNTLLLIQMVAARMGIAA 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 981601337 241 LPRWLADEYADRIPVTPVKLGrDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:PRK15421 237 LPHWVVESFERQGLVVTKTLG-EGLWSRLYAAVRDGEQRQPVTEAFIRSARN 287
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-292 6.66e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.91  E-value: 6.66e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQ 85
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  86 YADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYE 165
Cdd:COG0583   85 LRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 166 QVLVVAETHRLAgvthvepaqltdeilitypvetdrldiynqfltpagvvpKRHKVIETTDIMLQMVASGRGVAALPRWL 245
Cdd:COG0583  165 LVLVASPDHPLA---------------------------------------RRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 981601337 246 ADEYADRIPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 1.05e-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: 117.00  E-value: 1.05e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   91 RGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVV 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  171 AETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYA 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 981601337  251 DRIPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-63 8.77e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.80  E-value: 8.77e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337    6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQ 63
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 1-96 5.60e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.82  E-value: 5.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAE 80
Cdd:PRK11074   1 MWSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETR 80

                         90
                 ....*....|....*.
gi 981601337  81 ARMKQYADGERGTLRI 96
Cdd:PRK11074  81 RQCQQVANGWRGQLSI 96
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
4-90 7.48e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 38.65  E-value: 7.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   4 RIHLviIREVERQGSLTAAAGAL---YltQSALSHtVKKIEQQLGTPIWDRE--GRS---LRLTQAGQyllalanRLLPQ 75
Cdd:COG2005   23 RIEL--LEAIDETGSISAAAKAMgmsY--KRAWDL-IDAMNNLLGEPLVERQtgGKGgggARLTPEGR-------RLLAL 90

                         90
                 ....*....|....*
gi 981601337  76 FEHAEARMKQYADGE 90
Cdd:COG2005   91 YRRLEAEAQRALAAL 105
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 9.61e-102

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: 296.01  E-value: 9.61e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAE 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 173 THRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYADR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 981601337 253 IPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-292 4.41e-69

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 217.19  E-value: 4.41e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAe 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  81 arMKQYADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDP 160
Cdd:PRK15421  80 --LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 161 VFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRhKVIETTDIMLQMVASGRGVAA 240
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSL-KSVDNTLLLIQMVAARMGIAA 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 981601337 241 LPRWLADEYADRIPVTPVKLGrDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:PRK15421 237 LPHWVVESFERQGLVVTKTLG-EGLWSRLYAAVRDGEQRQPVTEAFIRSARN 287
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-292 6.66e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.91  E-value: 6.66e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQ 85
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  86 YADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYE 165
Cdd:COG0583   85 LRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 166 QVLVVAETHRLAgvthvepaqltdeilitypvetdrldiynqfltpagvvpKRHKVIETTDIMLQMVASGRGVAALPRWL 245
Cdd:COG0583  165 LVLVASPDHPLA---------------------------------------RRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 981601337 246 ADEYADRIPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 1.05e-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: 117.00  E-value: 1.05e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   91 RGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVV 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  171 AETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYA 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 981601337  251 DRIPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALARE 292
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-290 5.03e-29

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: 109.61  E-value: 5.03e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAE 172
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 173 THRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLADEYADR 252
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 981601337 253 iPVTPVKLGRDGIAKQIFLGTREADGAIDYLAAFVALA 290
Cdd:cd05466  161 -GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
2-242 1.29e-21

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 92.09  E-value: 1.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   2 LERIHLVIIR---EVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEH 78
Cdd:PRK09986   4 LYRIDLKLLRyflAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  79 AEARMKQYADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDV----LVTPDPLnrP 154
Cdd:PRK09986  84 SLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAgiwrMADLEPN--P 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 155 GLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYP-VETD-RLDIYNQFLTpAGVVPK-RHKVIETTDImLQM 231
Cdd:PRK09986 162 GFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPfVHSDwGKFLQRVCQQ-AGFSPQiIRQVNEPQTV-LAM 239

                        250
                 ....*....|.
gi 981601337 232 VASGRGVAALP 242
Cdd:PRK09986 240 VSMGIGITLLP 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-292 3.01e-21

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 91.17  E-value: 3.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERiHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAE 80
Cdd:PRK11242   1 MLLR-HIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  81 ARMKQYADGERGTLRIGMEchPCY-QWLL-KVVSPYLAQWPDVDVDVKQRFQfGGIGALFGYD-IDVLVTPDPLNRPGLR 157
Cdd:PRK11242  80 RAIHDVADLSRGSLRLAMT--PTFtAYLIgPLIDAFHARYPGITLTIREMSQ-ERIEALLADDeLDVGIAFAPVHSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 158 FDPVFDYEQVLVVAETHRLAGVTH-VEPAQLTDE--ILITYPVETdRLDIyNQFLTPAGVVPkrHKVIETTDI--MLQMV 232
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLAARRKaLTLDELADEplVLLSAEFAT-REQI-DRYFRRHGVTP--RVAIEANSIsaVLEIV 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 981601337 233 ASGRGVAALPRWLADEYAD--RIPVTPVKLGRdgiakQIFLGTREadGAIDYLA--AFVALARE 292
Cdd:PRK11242 233 RRGRLATLLPAAIAREHDGlcAIPLDPPLPQR-----TAALLRRK--GAYRSAAarAFIELALE 289
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-238 6.69e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 85.04  E-value: 6.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQG-SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREG-RSLRLTQAGQYLLALANRLLPQFEHAEARMK 84
Cdd:PRK12682   6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNIKRIGD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  85 QYADGERGTLRIGMeCHPCYQWLL-KVVSPYLAQWPDVDVDVKQRF--QFGGIGALFGYDIDVlVTPDPLNRPGLRFDPV 161
Cdd:PRK12682  86 DFSNQDSGTLTIAT-THTQARYVLpRVVAAFRKRYPKVNLSLHQGSpdEIARMVISGEADIGI-ATESLADDPDLATLPC 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 162 FDYEQVLVVAETHRLAGVTHVEPAQLTDEILITY-PVETDRLDIYNQFLTpAGVVPkrHKVIET--TDIMLQMVASGRGV 238
Cdd:PRK12682 164 YDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYhPGFTGRSRIDRAFAA-AGLQP--DIVLEAidSDVIKTYVRLGLGV 240
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-204 1.32e-18

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 83.92  E-value: 1.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQY 86
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  87 ADGERGTLRIGMEchpcyQWLLKVVSPYL-----AQWPDVDVDVK----QRFQFGGIGAlfgyDIDVLV----TPDPLnR 153
Cdd:CHL00180  90 KNLQRGTLIIGAS-----QTTGTYLMPRLiglfrQRYPQINVQLQvhstRRIAWNVANG----QIDIAIvggeVPTEL-K 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337 154 PGLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLT-----------------DEILITYPVETDRLDI 204
Cdd:CHL00180 160 KILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYrlnfitldsnstirkviDNILIQNGIDSKRFKI 227
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 2-258 1.46e-18

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 83.67  E-value: 1.46e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   2 LERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEA 81
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  82 RMKQYADGERgTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPV 161
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 162 FDYEQVLVVAETHRLAGVTHVEPAQLTDE-ILITYPVETDRL-DIYNQFLTPAGVVPkrhKVIETTDIML---QMVASGR 236
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVnFISTDPAYSGSLaPIIKAWFAQHNSQP---NIVQVATNILvtmNLVGMGL 236

                        250       260
                 ....*....|....*....|..
gi 981601337 237 GVAALPRWLADEYADRIPVTPV 258
Cdd:PRK09906 237 GCTIIPGYMNNFNTGQVVFRPL 258
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-63 8.77e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.80  E-value: 8.77e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337    6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQ 63
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 7-216 7.26e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 76.24  E-value: 7.26e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQG-SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREG-RSLRLTQAGQYLLALANRLLPQFEHAEARMK 84
Cdd:PRK12683   6 LRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENLRRLAE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  85 QYADGERGTLRIGMeCHPCYQWLL-KVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNR-PGLRFDPVF 162
Cdd:PRK12683  86 QFADRDSGHLTVAT-THTQARYALpKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVSFPYY 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 981601337 163 DYEQVLVVAETHRLAGVTHVEPAQLTDEILITY-PVETDRLDIyNQFLTPAGVVP 216
Cdd:PRK12683 165 SWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYdQGFTGRSRI-DQAFAEAGLVP 218
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 15-247 4.27e-15

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 74.11  E-value: 4.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  15 RQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFehAEARMKQYADGERGTL 94
Cdd:PRK11139  19 RHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL--AEATRKLRARSAKGAL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  95 RIGMECHPCYQWLLKVVSPYLAQWPDVDVdvkqRFQfgGIGALFGY---DIDVLVTPDPLNRPGLRFDPVFDyEQVLVVA 171
Cdd:PRK11139  97 TVSLLPSFAIQWLVPRLSSFNEAHPDIDV----RLK--AVDRLEDFlrdDVDVAIRYGRGNWPGLRVEKLLD-EYLLPVC 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 172 ETHRLAGVTHVE-PAQLTDEILItypvETDRLDIYNQFLTPAGV--VPKRHKVI-ETTDIMLQMVASGRGVAALPRWLAD 247
Cdd:PRK11139 170 SPALLNGGKPLKtPEDLARHTLL----HDDSREDWRAWFRAAGLddLNVQQGPIfSHSSMALQAAIHGQGVALGNRVLAQ 245
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 1-96 5.60e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.82  E-value: 5.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAE 80
Cdd:PRK11074   1 MWSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETR 80

                         90
                 ....*....|....*.
gi 981601337  81 ARMKQYADGERGTLRI 96
Cdd:PRK11074  81 RQCQQVANGWRGQLSI 96
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-246 2.42e-14

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: 70.23  E-value: 2.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAE 172
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 981601337 173 THRLAGVTHVEPAQLTDEILITYPvETDRLDIYNQFLTP---AGVVPKRHKVIETTDIMLQMVASGRGVAALPRWLA 246
Cdd:cd08414   81 DHPLAARESVSLADLADEPFVLFP-REPGPGLYDQILALcrrAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVA 156
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-127 1.74e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 69.62  E-value: 1.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQG-SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLR-LTQAGQYLLALANRLLPQFEHAEARMK 84
Cdd:PRK12684   6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGK 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 981601337  85 QYADGERGTLRIGMeCHPCYQWLL-KVVSPYLAQWPDVDVDVKQ 127
Cdd:PRK12684  86 EFAAQDQGNLTIAT-THTQARYALpAAIKEFKKRYPKVRLSILQ 128
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-251 1.98e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 69.45  E-value: 1.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  12 EVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADG-E 90
Cdd:PRK10094  12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGvE 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  91 RgtlrigmECHPCYQWLL---KVVSPYLA----QWPDVDVDVKQRFQFGGIGALF--GYDIDVLVT-PDPLNRpGLRFDP 160
Cdd:PRK10094  92 R-------QVNIVINNLLynpQAVAQLLAwlneRYPFTQFHISRQIYMGVWDSLLyeGFSLAIGVTgTEALAN-TFSLDP 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 161 VFDYEQVLVVAETHRLAGVthvePAQLTDEILITYPV----ETDRLdiynqfLTP--AGVVPKRHKVIeTTDIMLQMVA- 233
Cdd:PRK10094 164 LGSVQWRFVMAADHPLANV----EEPLTEAQLRRFPAvnieDSART------LTKrvAWRLPGQKEII-VPDMETKIAAh 232

                        250
                 ....*....|....*....
gi 981601337 234 -SGRGVAALPRWLADEYAD 251
Cdd:PRK10094 233 lAGVGIGFLPKSLCQSMID 251
cbl PRK12679
HTH-type transcriptional regulator Cbl;
7-241 2.79e-13

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 69.07  E-value: 2.79e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQG-SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREG-RSLRLTQAGQYLLALANRLLPQFEHAEARMK 84
Cdd:PRK12679   6 LKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNVRRLAD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  85 QYADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPL-NRPGLRFDPVFD 163
Cdd:PRK12679  86 LFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLsNDPQLVAFPWFR 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 981601337 164 YEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVE-TDRLDIYNQFlTPAGVVPKRHKVIETTDIMLQMVASGRGVAAL 241
Cdd:PRK12679 166 WHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGiTGRSRIDDAF-ARKGLLADIVLSAQDSDVIKTYVALGLGIGLV 243
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 6-257 1.04e-11

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 64.24  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRL---LPQFEHAEAR 82
Cdd:PRK11013   8 HIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAAES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  83 MKQYADGErgtLRIGmeCHPCY-QWLL-KVVSPYLAQWPDVDVDV-------------KQRFQFGgigalfgyDIDVLVT 147
Cdd:PRK11013  88 LREFRQGQ---LSIA--CLPVFsQSLLpGLCQPFLARYPDVSLNIvpqesplleewlsAQRHDLG--------LTETLHT 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 148 PdplnrPGLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYpvetDRLDIYNQFL----TPAGVvpKRHKVIE 223
Cdd:PRK11013 155 P-----AGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISL----SRTDSYRQLLdqlfAEHGV--KRRMVVE 223

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 981601337 224 TTDI--MLQMVASGRGVAALPRWLADEYADR-IPVTP 257
Cdd:PRK11013 224 THSAasVCAMVRAGVGVSIVNPLTALDYAGSgLVVRR 260
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 105-242 1.30e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 62.39  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 105 QWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHVEP 184
Cdd:cd08450   13 QWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPP 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 185 AQLTDEILITyPVETDRL--DIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALP 242
Cdd:cd08450   93 QDLAGENFIS-PAPTAPVlqQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLP 151
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
2-248 6.06e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 62.09  E-value: 6.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   2 LERI-HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAE 80
Cdd:PRK10632   1 MERLkRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  81 ARMKQYADGERGTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVkqrfqFGGIGA--LFGYDIDVLVTPDPLNRPGLRF 158
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL-----VTGIPApdLIADGLDVVIRVGALQDSSLFS 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 159 DPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDrldiyNQF--LTPAGVV----PKRHKVIETTDIMLQMV 232
Cdd:PRK10632 156 RRLGAMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPD-----NEFelIAPEGIStrliPQGRFVTNDPQTLVRWL 230

                        250
                 ....*....|....*..
gi 981601337 233 ASGRGVAALP-RWLADE 248
Cdd:PRK10632 231 TAGAGIAYVPlMWVIDE 247
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-290 1.93e-10

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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 59.15  E-value: 1.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGME--CHPCYqwLLKVVSPYLAQWPDVDVDVKQrfqfGGIGALF------GYDIDVLVTPDPLNrPGLRFDPVFDY 164
Cdd:cd08436    1 RLAIGTItsLAAVD--LPELLARFHRRHPGVDIRLRQ----AGSDDLLaavregRLDLAFVGLPERRP-PGLASRELARE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 165 EQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVvpKRHKVIETTD--IMLQMVASGRGVAALP 242
Cdd:cd08436   74 PLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGV--RRRVAFEVSDvdLLLDLVARGLGVALLP 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 981601337 243 RwLADEYADRIPVTPVklgRDGIAKQIFLGTReADGAIDYLAAFVALA 290
Cdd:cd08436  152 A-SVAARLPGLAALPL---EPAPRRRLYLAWS-APPPSPAARAFLELL 194
cysB PRK12681
HTH-type transcriptional regulator CysB;
10-127 8.07e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 58.76  E-value: 8.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  10 IREVERQG-SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSL-RLTQAGQYLLALANRLLPQFEHAEARMKQYA 87
Cdd:PRK12681   9 IVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESIKSVAGEHT 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 981601337  88 DGERGTLRIGMEcHPCYQWLL-KVVSPYLAQWPDVDVDVKQ 127
Cdd:PRK12681  89 WPDKGSLYIATT-HTQARYALpPVIKGFIERYPRVSLHMHQ 128
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 105-260 9.01e-10

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: 57.16  E-value: 9.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 105 QWLL-KVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHVE 183
Cdd:cd08434   12 TSLVpDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVD 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 981601337 184 PAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKrhKVIETTDI--MLQMVASGRGVAALPRwladeyADRIPVTPVKL 260
Cdd:cd08434   92 LAELADEPFVLLSPGFGLRPIVDELCAAAGFTPK--IAFEGEEDstIAGLVAAGLGVAILPE------MTLLNPPGVKK 162
PRK10341 PRK10341
transcriptional regulator TdcA;
6-67 1.06e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 58.34  E-value: 1.06e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 981601337   6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLA 67
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 93-249 2.35e-09

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 56.03  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVdvkQRFQFGGIG---ALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLV 169
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIEL---ELVEYGGKKveqAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 170 VAETHRLAGVTHVEPAQLTDEILITYPVE---TDR-LDIYNQfltpAGVVPkrHKVIETT--DIMLQMVASGRGVAALPR 243
Cdd:cd08438   78 LPRGHPLAGRKTVSLADLADEPFILFNEDfalHDRiIDACQQ----AGFTP--NIAARSSqwDFIAELVAAGLGVALLPR 151


                 ....*.
gi 981601337 244 WLADEY 249
Cdd:cd08438  152 SIAQRL 157
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-258 3.39e-09

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 55.65  E-value: 3.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGmeCHPCYQW--LLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVV 170
Cdd:cd08415    1 TLRIA--ALPALALslLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 171 AETHRLAGVTHVEPAQLTDEILITYPVET---DRLDiynQFLTPAGVVPKRhkVIETT--DIMLQMVASGRGVAALPRWL 245
Cdd:cd08415   79 PPGHPLARKDVVTPADLAGEPLISLGRGDplrQRVD---AAFERAGVEPRI--VIETQlsHTACALVAAGLGVAIVDPLT 153

                        170
                 ....*....|....*..
gi 981601337 246 ADEYADR----IPVTPV 258
Cdd:cd08415  154 AAGYAGAglvvRPFRPA 170
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
12-73 8.89e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 55.41  E-value: 8.89e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 981601337  12 EVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLL 73
Cdd:PRK03601  11 EVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLM 72
PRK09791 PRK09791
LysR family transcriptional regulator;
12-259 1.15e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 1.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  12 EVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADGER 91
Cdd:PRK09791  15 EVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  92 GTLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLV---TPDPLNRPgLRFDPVFDYEQVL 168
Cdd:PRK09791  95 GQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyYQGPYDHE-FTFEKLLEKQFAV 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 169 VVAETHRLAGVTHVEpaQLTDeilITYPVETDRLDIYNQF---LTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPRWL 245
Cdd:PRK09791 174 FCRPGHPAIGARSLK--QLLD---YSWTMPTPHGSYYKQLselLDDQAQTPQVGVVCETFSACISLVAKSDFLSILPEEM 248

                        250
                 ....*....|....*.
gi 981601337 246 ADE--YADRIPVTPVK 259
Cdd:PRK09791 249 GCDplHGQGLVMLPVS 264
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-72 1.36e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.98  E-value: 1.36e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDReGRSLRLTQAGQYLLALANRL 72
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV 71
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 116-288 1.45e-08

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: 53.76  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 116 AQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRP-----GLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDE 190
Cdd:cd08423   24 ARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPppddpGLTRVPLLDDPLDLVLPADHPLAGREEVALADLADE 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 191 ILITYPVETDRLDIYNQFLTPAGVVPK-RHKVIETTdIMLQMVASGRGVAALPRWLADEYADRIPVTPVklgRDGIAKQI 269
Cdd:cd08423  104 PWIAGCPGSPCHRWLVRACRAAGFTPRiAHEADDYA-TVLALVAAGLGVALVPRLALGARPPGVVVRPL---RPPPTRRI 179

                        170
                 ....*....|....*....
gi 981601337 270 FLGTREADGAIDYLAAFVA 288
Cdd:cd08423  180 YAAVRAGAARRPAVAAALE 198
PRK12680 PRK12680
LysR family transcriptional regulator;
6-241 2.33e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.24  E-value: 2.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   6 HLVIIREVERqgSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLR-LTQAGQYLLALANRLLpqfehAEA-RM 83
Cdd:PRK12680   8 YLVAIADAEL--NITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVL-----SEAnNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  84 KQYADGERGTLRIGMECHPCYQWLLKVVSPYLAQ----WPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFD 159
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQikqaYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 160 -PVFDYEQVLVVAETHRLAGVTHV-EPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRG 237
Cdd:PRK12680 161 vPLYRWRRLVVVPRGHALDTPRRApDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLG 240


                 ....
gi 981601337 238 VAAL 241
Cdd:PRK12680 241 VGLL 244
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-96 3.50e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 53.62  E-value: 3.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   1 MLERIHLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDReGRSLRLTQAGQYLLALAN--RLLpqfEH 78
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARqvRLL---EA 76

                         90
                 ....*....|....*...
gi 981601337  79 AEARMKQYADGERGTLRI 96
Cdd:PRK03635  77 ELLGELPALDGTPLTLSI 94
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-97 5.16e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 53.15  E-value: 5.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQfehaEARMKQY 86
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEIEQL 83

                         90
                 ....*....|.
gi 981601337  87 ADGERGTLRIG 97
Cdd:PRK10837  84 FREDNGALRIY 94
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-242 6.64e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 51.89  E-value: 6.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDV------KQrfqfggIGALFGYDIDV--LVTPDPLNRPGLRFDPVFDY 164
Cdd:cd08449    1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFhelspeAQ------KAALLSKRIDLgfVRFADTLNDPPLASELLWRE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 165 EQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRL--DIYNQFLTpAGVVPK-RHKVIETTDIMlQMVASGRGVAAL 241
Cdd:cd08449   75 PMVVALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRFadFLINCCLQ-AGFTPQiTQEVVEPQTLM-ALVAAGFGVALV 152


                 .
gi 981601337 242 P 242
Cdd:cd08449  153 P 153
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-96 8.67e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 52.13  E-value: 8.67e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 981601337  31 SALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADGERGTLRI 96
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL 71
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 141-285 1.48e-07

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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 (PBP2). The PBP2 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: 176108  Cd Length: 199  Bit Score: 50.81  E-value: 1.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 141 DIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYpveTDRLDIYNQFLTP---AGVVPK 217
Cdd:cd08416   51 DAILVATPEGLNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVTL---SEGFATYRGFDEAfeiAGFEPN 127

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 981601337 218 rhKVIETTDI--MLQMVASGRGVAALPRWLADEYADRIPVTPVKlGRDGIAKQI---FLGTREADGAIDYLAA 285
Cdd:cd08416  128 --VVMRVNDIfsLMSMVSGGVGYALLPGRIADVYEDKVQLIPLA-EPYQIRQTIglvFLRSRERDPNLLALAA 197
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-243 1.54e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 50.72  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDV-LVTPdPLNRPGLRFDPVFDYEQVLVVA 171
Cdd:cd08447    1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLgLLRP-PFARPGLETRPLVREPLVAAVP 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 981601337 172 ETHRLAGVTHVEPAQLTDEILITY-PVETDRL-DIYNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALPR 243
Cdd:cd08447   80 AGHPLAGAERLTLEDLDGQPFIMYsPTEARYFhDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPA 153
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-274 1.93e-07

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: 50.60  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 103 CYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHV 182
Cdd:cd08440   11 AATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 183 EPAQLTDEILITYPVETD-RLDIYNQFLTpAGVVPKRHKVIETTDIMLQMVASGRGVAALPRwLADEYADRIPVTPVKLG 261
Cdd:cd08440   91 TWAELAGYPLIALGRGSGvRALIDRALAA-AGLTLRPAYEVSHMSTALGMVAAGLGVAVLPA-LALPLADHPGLVARPLT 168

                        170
                 ....*....|...
gi 981601337 262 RDGIAKQIFLGTR 274
Cdd:cd08440  169 EPVVTRTVGLIRR 181
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-243 3.41e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 49.53  E-value: 3.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIG-MECHPCYqWLLKVVSPYLAQWPDVDVDVkqrfQFGGIGALF----GYDID-VLVTpDPLNRPGLRFDPVFDYEQ 166
Cdd:cd08442    1 PLRLGsMETTAAV-RLPPLLAAYHARYPKVDLSL----STGTTGALIqavlEGRLDgAFVA-GPVEHPRLEQEPVFQEEL 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 981601337 167 VLVVAETHRlagvTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVVPkrHKVIE--TTDIMLQMVASGRGVAALPR 243
Cdd:cd08442   75 VLVSPKGHP----PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSP--GKIMEfgSYHAILGCVAAGMGIALLPR 147
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-260 4.91e-07

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: 176113  Cd Length: 198  Bit Score: 49.44  E-value: 4.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 105 QWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHVEP 184
Cdd:cd08421   13 EFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAF 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 981601337 185 AQLTDEILITYPVETDrldIYNQFLTPAGVVPKRHKV---IETTDIMLQMVASGRGVAALPRWLADEYADRIPVTPVKL 260
Cdd:cd08421   93 ADTLDHDFVGLPAGSA---LHTFLREAAARLGRRLRLrvqVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRVVPL 168
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-260 5.38e-07

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: 49.19  E-value: 5.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQrfqfgGIG-----ALFGYDIDVLV--TPDPLNRPGLRFDPVFDYE 165
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVE-----GTSdelleGLRAGELDLAIgrLADDEQPPDLASEELADEP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 166 QVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGvVPKRHKVIETTDIM--LQMVASGRGVAALPR 243
Cdd:cd08435   76 LVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAG-LPLPRNVVETASISalLALLARSDMLAVLPR 154

                        170
                 ....*....|....*..
gi 981601337 244 WLADEYADRIPVTPVKL 260
Cdd:cd08435  155 SVAEDELRAGVLRELPL 171
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-263 9.13e-07

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: 48.64  E-value: 9.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 106 WLLKVVSPYLAQWPDVDVDVKqrfqfggIG-------ALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAG 178
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLT-------IGnteeiaeRVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 179 VTHVEPAQLTDEILITYpvETD---RlDIYNQFLTPAGVVPKR-HKVIE--TTDIMLQMVASGRGVAALPRW-LADEYAD 251
Cdd:cd08420   87 RKEVTAEELAAEPWILR--EPGsgtR-EVFERALAEAGLDGLDlNIVMElgSTEAIKEAVEAGLGISILSRLaVRKELEL 163

                        170
                 ....*....|....*.
gi 981601337 252 R----IPVTPVKLGRD 263
Cdd:cd08420  164 GrlvaLPVEGLRLTRP 179
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
15-178 1.53e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 48.84  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  15 RQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALanrLLPQFEHAEARMKQYADGE-RGT 93
Cdd:PRK10086  27 RHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA---LKSSLDTLNQEILDIKNQElSGT 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  94 LRIgmECHP----CyqWLLKVVSPYLAQWPDVDVDVKQR-----FQfggigalfGYDIDVLVTPDPLNRPGLRFDPVFDy 164
Cdd:PRK10086 104 LTV--YSRPsiaqC--WLVPRLADFTRRYPSISLTILTGnenvnFQ--------RAGIDLAIYFDDAPSAQLTHHFLMD- 170

                        170
                 ....*....|....*....
gi 981601337 165 EQVLVV-----AETHRLAG 178
Cdd:PRK10086 171 EEILPVcspeyAERHALTG 189
PRK09801 PRK09801
LysR family transcriptional regulator;
7-97 2.45e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.11  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   7 LVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQY 86
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90
                 ....*....|.
gi 981601337  87 ADGERGTLRIG 97
Cdd:PRK09801  91 KTRPEGMIRIG 101
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 18-97 4.15e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 47.33  E-value: 4.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  18 SLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLpQFeHAEARMK-QYADGErGTLRI 96
Cdd:PRK15092  27 TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL-RF-NDEACSSlMYSNLQ-GVLTI 103


                 .
gi 981601337  97 G 97
Cdd:PRK15092 104 G 104
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-72 5.07e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 47.31  E-value: 5.07e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 981601337   6 HLVIIREVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRL 72
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 141-243 9.89e-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: 45.59  E-value: 9.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 141 DIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITypvetdrLD----IYNQFLTPAGVVP 216
Cdd:cd08411   50 ELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAGERLLL-------LEeghcLRDQALELCRLAG 122

                         90       100       110
                 ....*....|....*....|....*....|...
gi 981601337 217 KRHKV------IETtdiMLQMVASGRGVAALPR 243
Cdd:cd08411  123 AREQTdfeatsLET---LRQMVAAGLGITLLPE 152
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-242 1.06e-05

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: 45.23  E-value: 1.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGmechpCYQWLLKVVSPYLAQW-----PDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQV 167
Cdd:cd08412    1 TLRIG-----CFSTLAPYYLPGLLRRfreayPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPY 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 981601337 168 LVVAETHRLAGVTHVEPAQLTDE--ILITYPVETDRLdiyNQFLTPAGVVPKRHKVIETTDIMLQMVASGRGVAALP 242
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEplILLDLPHSREYF---LSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLN 149
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-249 1.25e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 44.95  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDV-LVTPDPLnRPGLRFDPVFDYEQVLVVA 171
Cdd:cd08448    1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLgFVHSRRL-PAGLSARLLHREPFVCCLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 172 ETHRLAGVTHVEPAQLTDEILITYPvETDRLDIYNQFLT---PAGVVPK-RHKVIETTDIMlQMVASGRGVAALPRWLAD 247
Cdd:cd08448   80 AGHPLAARRRIDLRELAGEPFVLFS-REVSPDYYDQIIAlcmDAGFHPKiRHEVRHWLTVV-ALVAAGMGVALVPRSLAR 157


                 ..
gi 981601337 248 EY 249
Cdd:cd08448  158 AG 159
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 94-258 3.77e-05

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 43.64  E-value: 3.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  94 LRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAET 173
Cdd:cd08452    2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 174 HRLAGVTHVEPAQLTDEILITYPVETDRlDIYNQFLT---PAGVVPKrhKVIETTD--IMLQMVASGRGVAALPRWLADE 248
Cdd:cd08452   82 HPLASKEEITIEDLRDEPIITVAREAWP-TLYDEIIQlceQAGFRPK--IVQEATEyqTVIGLVSAGIGVTFVPSSAKKL 158

                        170
                 ....*....|
gi 981601337 249 YADRIPVTPV 258
Cdd:cd08452  159 FNLEVAYRKI 168
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-258 9.98e-05

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 42.41  E-value: 9.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQR----------FQFGGIGAlfgydIDVLVTPdplnrPGLRFDPVF 162
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRdsptveqwlsAQQCDLGL-----VSTLHEP-----PGIERERLL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 163 DYEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLDIYNQFLTPAGVvpKRHKVIETTD--IMLQMVASGRGVAA 240
Cdd:cd08456   71 RIDGVCVLPPGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGV--KRRIVVETSYaaTICALVAAGVGVSV 148

                        170       180
                 ....*....|....*....|..
gi 981601337 241 LPRWLADEYADR----IPVTPV 258
Cdd:cd08456  149 VNPLTALDYAAAglvvRRFSPA 170
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 17-98 1.59e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 42.75  E-value: 1.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  17 GSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADGERGTLRI 96
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSI 95


                 ..
gi 981601337  97 GM 98
Cdd:PRK11233  96 GL 97
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 12-151 1.74e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 42.67  E-value: 1.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  12 EVERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADGER 91
Cdd:PRK14997  12 HVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPR 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337  92 GTLRIgmechPCYQWLLKV-----VSPYLAQWPDVDVDVK---QRFQFGGIGAlfgyDIDVLVTPDPL 151
Cdd:PRK14997  92 GIVKL-----TCPVTLLHVhigpmLAKFMARYPDVSLQLEatnRRVDVVGEGV----DVAIRVRPRPF 150
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 150-260 2.55e-04

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 41.39  E-value: 2.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 150 PLNRP-GLRFDPVFDYEQVLVVAETHRLAGVTHVEPAQLTDEILITYPVETDRLdIYNQFLTP---AGVVPKRhkVIETT 225
Cdd:cd08451   59 PVARSdGLVLELLLEEPMLVALPAGHPLARERSIPLAALADEPFILFPRPVGPG-LYDAIIAAcrrAGFTPRI--GQEAP 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 981601337 226 DIM--LQMVASGRGVAALPRWLAD---------EYADRIPVTPVKL 260
Cdd:cd08451  136 QMAsaINLVAAGLGVSIVPASMRQlqapgvvyrPLAGAPLTAPLAL 181
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
13-263 4.97e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.19  E-value: 4.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  13 VERQGSLTAAAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLPQFEHAEARMKQYADGERG 92
Cdd:PRK10082  22 LEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQR 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVS--PYLAQWPDVDVDVKQ---RFQFGGIGALFGY-DIDVLVTPdplnrpglrFDPVFDYEQ 166
Cdd:PRK10082 102 KIKIAAAHSLSLGLLPSIISqmPPLFTWAIEAIDVDEavdKLREGQSDCIFSFhDEDLLEAP---------FDHIRLFES 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 167 VL--VVAETHRLAGVTHVEPAQLTdeiLITYPVETDRLDIYNQFLTpagvvpkRHK--------VIETTDIMLQMVASGR 236
Cdd:PRK10082 173 QLfpVCASDEHGEALFNLAQPHFP---LLNYSRNSYMGRLINRTLT-------RHSelsfstffVSSMSELLKQVALDGC 242

                        250       260       270
                 ....*....|....*....|....*....|
gi 981601337 237 GVAALPrwladEYADRIPVTP---VKLGRD 263
Cdd:PRK10082 243 GIAWLP-----EYAIQQEIRSgqlVVLNRD 267
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-292 6.88e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 39.90  E-value: 6.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  93 TLRIGMECHPCYQWLLKVVSPYLAQWPDVDVDVKQRFQFGGIGALFGYDIDV----LVTPDP-LNRPGLRFDPVfdyeqV 167
Cdd:cd08445    2 TFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVgfgrLRIEDPaIRRIVLREEPL-----V 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 168 LVVAETHRLAGV-THVEPAQLTDEILITYPVET--DRLDIYNQFLTPAGVVPkrHKVIETTDIM--LQMVASGRGVAALP 242
Cdd:cd08445   77 VALPAGHPLAQEkAPLTLAQLADEPLILYPASPrpSFADQVLSLFRDHGLRP--RVIQEVRELQtaLGLVAAGEGVTLVP 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 981601337 243 ----RWLADEyadripVTPVKLGRDGIAKQIFLGTREADGAiDYLAAFVALARE 292
Cdd:cd08445  155 asvqRLRRDD------VVYRPLLDPDATSPIIMSVRAGDES-PYIALILQLIRE 201
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
4-90 7.48e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 38.65  E-value: 7.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337   4 RIHLviIREVERQGSLTAAAGAL---YltQSALSHtVKKIEQQLGTPIWDRE--GRS---LRLTQAGQyllalanRLLPQ 75
Cdd:COG2005   23 RIEL--LEAIDETGSISAAAKAMgmsY--KRAWDL-IDAMNNLLGEPLVERQtgGKGgggARLTPEGR-------RLLAL 90

                         90
                 ....*....|....*
gi 981601337  76 FEHAEARMKQYADGE 90
Cdd:COG2005   91 YRRLEAEAQRALAAL 105
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 22-115 1.11e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.01  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337  22 AAGALYLTQSALSHTVKKIEQQLGTPIWDREGRSLRLTQAGQYLLALANRLLpqfehAEAR-MKQYADGE----RGTLRI 96
Cdd:PRK11151  21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL-----REVKvLKEMASQQgetmSGPLHI 95

                         90
                 ....*....|....*....
gi 981601337  97 GmechpcyqwLLKVVSPYL 115
Cdd:PRK11151  96 G---------LIPTVGPYL 105
leuO PRK09508
leucine transcriptional activator; Reviewed
 141-252 1.78e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 39.24  E-value: 1.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 141 DIDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETH-RLAGvtHVEPAQLTDEiliTYPVETdrLDIYNQFLTPAGVVPKRH 219
Cdd:PRK09508 161 ETEFVISYEEFDRPEFTSVPLFKDELVLVASKNHpRIKG--PITEEQLYNE---QHAVVS--LDRFASFSQPWYDTVDKQ 233

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 981601337 220 KVI--ETTDIM--LQMVASGRGVAALPRWLADEYADR 252
Cdd:PRK09508 234 ASIayQGTALSsvLNVVSQTHLVAIAPRWLAEEFAES 270
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 105-249 1.80e-03

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: 38.72  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 105 QWLLkvvsPYL----AQWPDVDVDVK---QRFQFGGIGalfgydIDVLV---TPDPlnrPGLRFDPVFDyEQVLVVAETH 174
Cdd:cd08432   13 RWLI----PRLarfqARHPDIDLRLStsdRLVDFAREG------IDLAIrygDGDW---PGLEAERLMD-EELVPVCSPA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 981601337 175 RLAGVTHVEPAQLTDEILITypvETDRLDIYNQFLTPAGVV---PKRHKVIETTDIMLQMVASGRGVAALPRWLADEY 249
Cdd:cd08432   79 LLAGLPLLSPADLARHTLLH---DATRPEAWQWWLWAAGVAdvdARRGPRFDDSSLALQAAVAGLGVALAPRALVADD 153
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 142-251 2.31e-03

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: 38.39  E-value: 2.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 981601337 142 IDVLVTPDPLNRPGLRFDPVFDYEQVLVVAETH-RLAGvtHVEPAQLTDEILITYPVETDRLDIYNQFLTPagVVPKRHK 220
Cdd:cd08466   50 VDLVIDYVPFRDPSFKSELLFEDELVCVARKDHpRIQG--SLSLEQYLAEKHVVLSLRRGNLSALDLLTEE--VLPQRNI 125

                         90       100       110
                 ....*....|....*....|....*....|...
gi 981601337 221 VIETTDI--MLQMVASGRGVAALPRWLADEYAD 251
Cdd:cd08466  126 AYEVSSLlsMLAVVSQTDLIAIAPRWLADQYAE 158
 
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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