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Conserved domains on  [gi|2281791052|dbj|GBR15361|]
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LysR family transcriptional regulator [Komagataeibacter nataicola NRIC 0616]

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 ...
95-292 1.11e-105

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: 306.03  E-value: 1.11e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08441     1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPR 254
Cdd:cd08441    81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2281791052 255 FDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd08441   161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 5.18e-18

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.18e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGE 65
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
95-292 1.11e-105

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: 306.03  E-value: 1.11e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08441     1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPR 254
Cdd:cd08441    81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2281791052 255 FDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd08441   161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-292 6.85e-70

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 219.12  E-value: 6.85e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   3 VLERNHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFelae 82
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI---- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  83 SRLEQFANGGRGT-LRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFT 161
Cdd:PRK15421   77 SQALQACNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYS 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 162 PVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPrQQKQIETTDIMLVMVAHGRGVA 241
Cdd:PRK15421  157 PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIA 235
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2281791052 242 ALPRWLVEEYTpRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:PRK15421  236 ALPHWVVESFE-RQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSA 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-293 1.48e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.48e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDY 166
Cdd:COG0583    84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEE 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 167 ELVLAVGPEHPLRnekfvlpeqlagetlitypvlserldiytqflqpagigpRQQKQIETTDIMLVMVAHGRGVAALPRW 246
Cdd:COG0583   164 RLVLVASPDHPLA---------------------------------------RRAPLVNSLEALLAAVAAGLGIALLPRF 204
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2281791052 247 LVEEYTPRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFAA 293
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-293 8.97e-35

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: 125.09  E-value: 8.97e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  93 RGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAV 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 173 GPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYT 252
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2281791052 253 PRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFAA 293
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 5.18e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.18e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGE 65
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
9-98 8.98e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.05  E-value: 8.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQF 88
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86
                          90
                  ....*....|
gi 2281791052  89 ANGGRGTLRI 98
Cdd:PRK11074   87 ANGWRGQLSI 96
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
95-292 1.11e-105

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: 306.03  E-value: 1.11e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08441     1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPR 254
Cdd:cd08441    81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2281791052 255 FDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd08441   161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-292 6.85e-70

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 219.12  E-value: 6.85e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   3 VLERNHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFelae 82
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI---- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  83 SRLEQFANGGRGT-LRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFT 161
Cdd:PRK15421   77 SQALQACNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYS 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 162 PVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPrQQKQIETTDIMLVMVAHGRGVA 241
Cdd:PRK15421  157 PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIA 235
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2281791052 242 ALPRWLVEEYTpRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:PRK15421  236 ALPHWVVESFE-RQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSA 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-293 1.48e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.48e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDY 166
Cdd:COG0583    84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEE 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 167 ELVLAVGPEHPLRnekfvlpeqlagetlitypvlserldiytqflqpagigpRQQKQIETTDIMLVMVAHGRGVAALPRW 246
Cdd:COG0583   164 RLVLVASPDHPLA---------------------------------------RRAPLVNSLEALLAAVAAGLGIALLPRF 204
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2281791052 247 LVEEYTPRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFAA 293
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-293 8.97e-35

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: 125.09  E-value: 8.97e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  93 RGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAV 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 173 GPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYT 252
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2281791052 253 PRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFAA 293
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
95-292 4.83e-33

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: 120.01  E-value: 4.83e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPR 254
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2281791052 255 fDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd05466   161 -GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
1-244 5.43e-29

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 112.12  E-value: 5.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   1 MGVLERNHLTIIR---EVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQ 77
Cdd:PRK09986    1 MERLYRIDLKLLRyflAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  78 FELAESRLEQFANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVV--TPDPLYK 155
Cdd:PRK09986   81 AEQSLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPN 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 156 PGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFL-QPAGIGPRQQKQIETTDIMLVMV 234
Cdd:PRK09986  161 PGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVcQQAGFSPQIIRQVNEPQTVLAMV 240
                         250
                  ....*....|
gi 2281791052 235 AHGRGVAALP 244
Cdd:PRK09986  241 SMGIGITLLP 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
15-262 3.55e-24

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 99.26  E-value: 3.55e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  15 VAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGRG 94
Cdd:PRK11242   12 VAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLSRG 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMEchPCY-QWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAV 172
Cdd:PRK11242   92 SLRLAMT--PTFtAYLIgPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVV 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 173 GPEHPL-RNEKFVLPEQLAGETLItypVLS------ERLDIYtqfLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:PRK11242  170 GRHHPLaARRKALTLDELADEPLV---LLSaefatrEQIDRY---FRRHGVTPRVAIEANSISAVLEIVRRGRLATLLPA 243
                         250
                  ....*....|....*..
gi 2281791052 246 WLVEEYTprfDLYPVKL 262
Cdd:PRK11242  244 AIAREHD---GLCAIPL 257
rbcR CHL00180
LysR transcriptional regulator; Provisional
9-196 3.12e-20

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 88.54  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQF 88
Cdd:CHL00180   10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  89 ANGGRGTLRIGMEchpcyQWLLKVVSPYL-----ERWP----KVDVDVRQKFQFGGIgalfSNEIDIVV----TPDPLYK 155
Cdd:CHL00180   90 KNLQRGTLIIGAS-----QTTGTYLMPRLiglfrQRYPqinvQLQVHSTRRIAWNVA----NGQIDIAIvggeVPTELKK 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2281791052 156 pGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLIT 196
Cdd:CHL00180  161 -ILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFIT 200
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
9-197 4.76e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 88.12  E-value: 4.76e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREG-SLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLV-LNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:PRK12682    6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGD 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMeCHPCYQWLL-KVVSPYLERWPKVDVDVRQKF--QFGGIgaLFSNEIDI-VVTPDPLYKPGLKFTP 162
Cdd:PRK12682   86 DFSNQDSGTLTIAT-THTQARYVLpRVVAAFRKRYPKVNLSLHQGSpdEIARM--VISGEADIgIATESLADDPDLATLP 162
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2281791052 163 VFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITY 197
Cdd:PRK12682  163 CYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITY 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
9-197 4.92e-19

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 85.41  E-value: 4.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREG-SLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLV-LNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:PRK12684    6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGK 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMeCHPCYQWLL-KVVSPYLERWPKVDVDVRQkfqfggiGA-------LFSNEIDIVVTPDPLYK-PG 157
Cdd:PRK12684   86 EFAAQDQGNLTIAT-THTQARYALpAAIKEFKKRYPKVRLSILQ-------GSptqiaemVLHGQADLAIATEAIADyKE 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2281791052 158 LKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITY 197
Cdd:PRK12684  158 LVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITY 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
4-290 1.21e-18

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 84.05  E-value: 1.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   4 LERNHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAES 83
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  84 RLEQFANGGRgTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPV 163
Cdd:PRK09906   81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 164 FDYELVLAVGPEHPLRNEKFVLPEQLAGETLI-TYPVLSERL-DIYTQFLQPAGIGPrqqKQIETTDIMLV---MVAHGR 238
Cdd:PRK09906  160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFIsTDPAYSGSLaPIIKAWFAQHNSQP---NIVQVATNILVtmnLVGMGL 236
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2281791052 239 GVAALPRWLVEEYTPRFDLYPVKLGKKGIAkqIFLGYREtDEEVRYLQDFIE 290
Cdd:PRK09906  237 GCTIIPGYMNNFNTGQVVFRPLAGNVPSIA--LLMAWKK-GEMKPALRDFIA 285
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 5.18e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.18e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGE 65
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
9-197 3.63e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 80.09  E-value: 3.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREG-SLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLV-LNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:PRK12683    6 LRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAE 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMeCHPCYQWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYK-PGLKFTPVF 164
Cdd:PRK12683   86 QFADRDSGHLTVAT-THTQARYALpKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVSFPYY 164
                         170       180       190
                  ....*....|....*....|....*....|...
gi 2281791052 165 DYELVLAVGPEHPLRNEKFVLPEQLAGETLITY 197
Cdd:PRK12683  165 SWHHVVVVPKGHPLTGRENLTLEAIAEYPIITY 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
95-292 4.93e-17

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: 77.55  E-value: 4.93e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYP--VLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYT 252
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPrePGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2281791052 253 PRFDLYPVKLGKKGIakQIFLGYReTDEEVRYLQDFIEFA 292
Cdd:cd08414   161 PGVVYRPLADPPPRS--ELALAWR-RDNASPALRAFLELA 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
9-250 2.89e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 74.34  E-value: 2.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQfelaESRLEQF 88
Cdd:PRK10837    8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEIEQL 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  89 ANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYEL 168
Cdd:PRK10837   84 FREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLEDEL 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 169 VLAVGPEHPLRNEKFVLpEQLAGETLItypvlserldiytqfLQPAGIGPRqqkqiETTDIML---------VM------ 233
Cdd:PRK10837  164 VVFAAPDSPLARGPVTL-EQLAAAPWI---------------LRERGSGTR-----EIVDYLLlshlprfelAMelgnse 222
                         250       260
                  ....*....|....*....|..
gi 2281791052 234 -----VAHGRGVAALPRWLVEE 250
Cdd:PRK10837  223 aikhaVRHGLGISCLSRRVIAD 244
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
9-98 8.98e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.05  E-value: 8.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQF 88
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86
                          90
                  ....*....|
gi 2281791052  89 ANGGRGTLRI 98
Cdd:PRK11074   87 ANGWRGQLSI 96
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-243 4.04e-14

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 71.38  E-value: 4.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAR-EGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLV-LNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:PRK12679    6 LKIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLAD 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYK-PGLKFTPVFD 165
Cdd:PRK12679   86 LFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNdPQLVAFPWFR 165
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052 166 YELVLAVGPEHPLRNEKFVLPEQLAGETLITYPV-LSERLDIYTQFlQPAGIGPRQQKQIETTDIMLVMVAHGRGVAAL 243
Cdd:PRK12679  166 WHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQgITGRSRIDDAF-ARKGLLADIVLSAQDSDVIKTYVALGLGIGLV 243
PRK09791 PRK09791
LysR family transcriptional regulator;
14-180 3.62e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 68.64  E-value: 3.62e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  14 EVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGR 93
Cdd:PRK09791   15 EVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLA 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVV---TPDPlYKPGLKFTPVFDYELVL 170
Cdd:PRK09791   95 GQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyYQGP-YDHEFTFEKLLEKQFAV 173
                         170
                  ....*....|
gi 2281791052 171 AVGPEHPLRN 180
Cdd:PRK09791  174 FCRPGHPAIG 183
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
107-257 3.66e-13

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: 66.63  E-value: 3.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 107 QWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLP 186
Cdd:cd08450    13 QWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPP 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 187 EQLAGETLI----TYPVLSerlDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWL------------VEE 250
Cdd:cd08450    93 QDLAGENFIspapTAPVLQ---QVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYAnnllppsvvarpLSG 169

                  ....*..
gi 2281791052 251 YTPRFDL 257
Cdd:cd08450   170 ETPTIDL 176
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
108-292 8.51e-13

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: 65.98  E-value: 8.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 108 WLLKVVSPYLERWPKVDVDVRqkfqfggIG-------ALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRN 180
Cdd:cd08420    14 LLPRLLARFRKRYPEVRVSLT-------IGnteeiaeRVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAG 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 181 EKFVLPEQLAGETLItypvLSE-----RlDIYTQFLQPAGIGPRQQK---QIETTDIMLVMVAHGRGVAALPRWLVEEYT 252
Cdd:cd08420    87 RKEVTAEELAAEPWI----LREpgsgtR-EVFERALAEAGLDGLDLNivmELGSTEAIKEAVEAGLGISILSRLAVRKEL 161
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2281791052 253 PRFDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd08420   162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
14-251 1.12e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.14  E-value: 1.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  14 EVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGR 93
Cdd:PRK10094   12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVE 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRI---GMECHPcyQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALF--SNEIDIVVTPDPLYKPGLKFTPVFDYEL 168
Cdd:PRK10094   92 RQVNIvinNLLYNP--QAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLyeGFSLAIGVTGTEALANTFSLDPLGSVQW 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 169 VLAVGPEHPLRNekfvLPEQLAGETLITYPVL-----SERLDIYTQFLQPAgigprqQKQIETTDIMLVMVAH--GRGVA 241
Cdd:PRK10094  170 RFVMAADHPLAN----VEEPLTEAQLRRFPAVniedsARTLTKRVAWRLPG------QKEIIVPDMETKIAAHlaGVGIG 239
                         250
                  ....*....|
gi 2281791052 242 ALPRWLVEEY 251
Cdd:PRK10094  240 FLPKSLCQSM 249
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
107-292 1.61e-12

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: 64.86  E-value: 1.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 107 QWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVL 185
Cdd:cd08434    12 TSLVpDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVD 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 186 PEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRwlveeyTPRFDLYPVK---L 262
Cdd:cd08434    92 LAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE------MTLLNPPGVKkipI 165
                         170       180       190
                  ....*....|....*....|....*....|
gi 2281791052 263 GKKGIAKQIFLGYRETDEEVRYLQDFIEFA 292
Cdd:cd08434   166 KDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
16-249 2.14e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 66.02  E-value: 2.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  16 AREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEqfANGGRGT 95
Cdd:PRK11139   18 ARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLR--ARSAKGA 95
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  96 LRIGMEchPCY--QWLLKVVSPYLERWPkvDVDVRQKFQFGGIGALfSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVG 173
Cdd:PRK11139   96 LTVSLL--PSFaiQWLVPRLSSFNEAHP--DIDVRLKAVDRLEDFL-RDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCS 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 174 PEHPLRNEKFVLPEQLAGETLITypvlSERLDIYTQFLQPAGIG--PRQQKQIeTTDIMLVMVA--HGRGVAALPRWLVE 249
Cdd:PRK11139  171 PALLNGGKPLKTPEDLARHTLLH----DDSREDWRAWFRAAGLDdlNVQQGPI-FSHSSMALQAaiHGQGVALGNRVLAQ 245
leuO PRK09508
leucine transcriptional activator; Reviewed
7-257 7.50e-12

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 64.66  E-value: 7.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   7 NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLL-----ALAnrlLPQFELA 81
Cdd:PRK09508   25 NLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFgpvrqALQ---LVQNELP 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  82 ESRLEQFANGGRGTLRIgmeCHPCYQWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKF 160
Cdd:PRK09508  102 GSGFEPESSERVFNLCI---CSPLDIRLTsQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTS 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 161 TPVFDYELVLAVGPEHPlRNEKFVLPEQLAGEtliTYPVLSerLDIYTQFLQPAGIGPRQQKQI--ETTDIM--LVMVAH 236
Cdd:PRK09508  179 VPLFKDELVLVASKNHP-RIKGPITEEQLYNE---QHAVVS--LDRFASFSQPWYDTVDKQASIayQGTALSsvLNVVSQ 252
                         250       260
                  ....*....|....*....|.
gi 2281791052 237 GRGVAALPRWLVEEYTPRFDL 257
Cdd:PRK09508  253 THLVAIAPRWLAEEFAESLEL 273
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
95-254 1.39e-11

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: 62.19  E-value: 1.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVrqkFQFGGIG---ALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLA 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELEL---VEYGGKKveqAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 172 VGPEHPLRNEKFVLPEQLAGETLITYP---VLSERLDiytQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLV 248
Cdd:cd08438    78 LPRGHPLAGRKTVSLADLADEPFILFNedfALHDRII---DACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIA 154

                  ....*.
gi 2281791052 249 EEYTPR 254
Cdd:cd08438   155 QRLDNA 160
PRK10341 PRK10341
transcriptional regulator TdcA;
8-187 2.92e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 62.96  E-value: 2.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   8 HLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQ 87
Cdd:PRK10341   11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEING 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  88 FANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEID--IVVTPDPLYKPGLKFTPVFD 165
Cdd:PRK10341   91 MSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDfaIGTLSNEMKLQDLHVEPLFE 170
                         170       180       190
                  ....*....|....*....|....*....|.
gi 2281791052 166 YELVLAVGPEHP---------LRNEKFVLPE 187
Cdd:PRK10341  171 SEFVLVASKSRTctgtttlesLKNEQWVLPQ 201
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-245 5.88e-11

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: 60.69  E-value: 5.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGME--CHPCYqwLLKVVSPYLERWPKVDVDVRQkfqfGGIGALF----SNEIDIVVTPDPLYKP-GLKFTPVFDYE 167
Cdd:cd08436     1 RLAIGTItsLAAVD--LPELLARFHRRHPGVDIRLRQ----AGSDDLLaavrEGRLDLAFVGLPERRPpGLASRELAREP 74
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2281791052 168 LVLAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08436    75 LVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPA 152
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
95-254 6.30e-11

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: 60.65  E-value: 6.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGmeCHPCYQW--LLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAV 172
Cdd:cd08415     1 TLRIA--ALPALALslLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 173 GPEHPLRNEKFVLPEQLAGETLITYPV---LSERLDiytQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAalprwLVE 249
Cdd:cd08415    79 PPGHPLARKDVVTPADLAGEPLISLGRgdpLRQRVD---AAFERAGVEPRIVIETQLSHTACALVAAGLGVA-----IVD 150

                  ....*
gi 2281791052 250 EYTPR 254
Cdd:cd08415   151 PLTAA 155
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
94-245 1.74e-10

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: 59.46  E-value: 1.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIGMechpcyqwlLKVVSPYL---------ERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVF 164
Cdd:cd08411     1 GPLRLGV---------IPTIAPYLlprllpalrQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLF 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 165 DYELVLAVGPEHPLRNEKFVLPEQLAGETLITypvLSE----RldiyTQFLQPAGI-GPRQQKQIETTDI-MLV-MVAHG 237
Cdd:cd08411    72 DEPFLLAVPKDHPLAKRKSVTPEDLAGERLLL---LEEghclR----DQALELCRLaGAREQTDFEATSLeTLRqMVAAG 144

                  ....*...
gi 2281791052 238 RGVAALPR 245
Cdd:cd08411   145 LGITLLPE 152
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-250 2.25e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.16  E-value: 2.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   4 LER-NHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAE 82
Cdd:PRK10632    1 MERlKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  83 SRLEQFANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVrqkfqFGGIGA--LFSNEIDIVVTPDPLYKPGLKF 160
Cdd:PRK10632   81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL-----VTGIPApdLIADGLDVVIRVGALQDSSLFS 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 161 TPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITYPVlseRLDIYTQFLQPAGIGPR--QQKQIETTDIMLVM--VAH 236
Cdd:PRK10632  156 RRLGAMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSV---RPDNEFELIAPEGISTRliPQGRFVTNDPQTLVrwLTA 232
                         250
                  ....*....|....*
gi 2281791052 237 GRGVAALP-RWLVEE 250
Cdd:PRK10632  233 GAGIAYVPlMWVIDE 247
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-245 5.63e-10

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: 57.66  E-value: 5.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08447     1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPA 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYPVLSERL--DIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08447    81 GHPLAGAERLTLEDLDGQPFIMYSPTEARYfhDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPA 153
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
95-262 6.79e-10

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: 57.67  E-value: 6.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQkfqfgGIG-----ALFSNEIDIVV--TPDPLYKPGLKFTPVFDYE 167
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVE-----GTSdelleGLRAGELDLAIgrLADDEQPPDLASEELADEP 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 168 LVLAVGPEHPLRNEKFVLPEQLAGETLITYP---VLSERLDiytQFLQPAGIGPRqQKQIETTDIMLV--MVAHGRGVAA 242
Cdd:cd08435    76 LVVVARPGHPLARRARLTLADLADYPWVLPPpgtPLRQRLE---QLFAAAGLPLP-RNVVETASISALlaLLARSDMLAV 151
                         170       180
                  ....*....|....*....|
gi 2281791052 243 LPRWLVEEYTPRFDLYPVKL 262
Cdd:cd08435   152 LPRSVAEDELRAGVLRELPL 171
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
95-249 1.98e-09

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: 56.08  E-value: 1.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIG-MECHPCYqWLLKVVSPYLERWPKVDVDVrqkfQFGGIGALFSN----EIDIVVTPDPLYKPGLKFTPVFDYELV 169
Cdd:cd08442     1 PLRLGsMETTAAV-RLPPLLAAYHARYPKVDLSL----STGTTGALIQAvlegRLDGAFVAGPVEHPRLEQEPVFQEELV 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 170 LAVGPEHPlrneKFVLPEQLAGETLITYPV-LSERlDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLV 248
Cdd:cd08442    76 LVSPKGHP----PVSRAEDLAGSTLLAFRAgCSYR-RRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVL 150

                  .
gi 2281791052 249 E 249
Cdd:cd08442   151 D 151
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
95-244 3.76e-09

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: 55.24  E-value: 3.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGmechpCYQWLLKVVSPYL-----ERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELV 169
Cdd:cd08412     1 TLRIG-----CFSTLAPYYLPGLlrrfrEAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPY 75
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2281791052 170 LAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERlDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALP 244
Cdd:cd08412    76 VWLPADHPLAGKDEVSLADLAAEPLILLDLPHSR-EYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLN 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
29-195 5.54e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 56.19  E-value: 5.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  29 NLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELaesrLEQFANG-GR---GTLRIGmechp 104
Cdd:PRK11151   26 HVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKV----LKEMASQqGEtmsGPLHIG----- 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 105 cyqwLLKVVSPYL---------ERWPKVDVDVR--QKFQFggIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVG 173
Cdd:PRK11151   97 ----LIPTVGPYLlphiipmlhQTFPKLEMYLHeaQTHQL--LAQLDSGKLDCAILALVKESEAFIEVPLFDEPMLLAVY 170
                         170       180
                  ....*....|....*....|..
gi 2281791052 174 PEHPLRNEKFVLPEQLAGETLI 195
Cdd:PRK11151  171 EDHPWANRDRVPMSDLAGEKLL 192
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
95-244 8.61e-09

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: 54.20  E-value: 8.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDI--VVTPDPLYKPGLKFTPVFDYELVLAV 172
Cdd:cd08449     1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLgfVRFADTLNDPPLASELLWREPMVVAL 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2281791052 173 GPEHPLRNEKFVLPEQLAGETLITYPVLSERldiYTQFL----QPAGIGPRQQKQ-IETTDIMlVMVAHGRGVAALP 244
Cdd:cd08449    81 PEEHPLAGRKSLTLADLRDEPFVFLRLANSR---FADFLinccLQAGFTPQITQEvVEPQTLM-ALVAAGFGVALVP 153
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
118-245 1.21e-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: 54.14  E-value: 1.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 118 ERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPD-----PLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGE 192
Cdd:cd08423    24 ARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtpPPDDPGLTRVPLLDDPLDLVLPADHPLAGREEVALADLADE 103
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2281791052 193 TLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08423   104 PWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
cysB PRK12681
HTH-type transcriptional regulator CysB;
9-197 1.33e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 54.90  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREG-SLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLV-LNQAGEWLLALANRLLPQFELAESRLE 86
Cdd:PRK12681    6 LRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIKSVAG 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  87 QFANGGRGTLRIGMEcHPCYQWLL-KVVSPYLERWPKVDVDVRQkfqfggiG-------ALFSNEIDIVVTPDPLYK-PG 157
Cdd:PRK12681   86 EHTWPDKGSLYIATT-HTQARYALpPVIKGFIERYPRVSLHMHQ-------GsptqiaeAAAKGNADFAIATEALHLyDD 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2281791052 158 LKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITY 197
Cdd:PRK12681  158 LIMLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTY 197
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
96-245 1.37e-08

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: 53.66  E-value: 1.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  96 LRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPE 175
Cdd:cd08452     2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQ 81
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2281791052 176 HPLRNEKFVLPEQLAGETLITYP--VLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08452    82 HPLASKEEITIEDLRDEPIITVAreAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPS 153
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
8-241 3.68e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 53.84  E-value: 3.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   8 HLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRL---LPQFELAESR 84
Cdd:PRK11013    8 HIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAAES 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  85 LEQFANGgrgtlRIGMECHPCY-QWLL-KVVSPYLERWPKVDVDV-------------RQKFQFGgigaLFSNEidivVT 149
Cdd:PRK11013   88 LREFRQG-----QLSIACLPVFsQSLLpGLCQPFLARYPDVSLNIvpqesplleewlsAQRHDLG----LTETL----HT 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 150 PdplykPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITypvLSeRLDIYTQFL----QPAGIGPRQqkQIE 225
Cdd:PRK11013  155 P-----AGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFIS---LS-RTDSYRQLLdqlfAEHGVKRRM--VVE 223
                         250
                  ....*....|....*...
gi 2281791052 226 TTDIMLV--MVAHGRGVA 241
Cdd:PRK11013  224 THSAASVcaMVRAGVGVS 241
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
107-262 5.87e-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: 176113  Cd Length: 198  Bit Score: 51.75  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 107 QWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLP 186
Cdd:cd08421    13 EFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAF 92
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052 187 EQLAGETLITypvLSERLDIYTQFLQPA---GIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPRFDLYPVKL 262
Cdd:cd08421    93 ADTLDHDFVG---LPAGSALHTFLREAAarlGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRVVPL 168
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
94-262 7.93e-08

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (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.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 51.56  E-value: 7.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIGMEchPCY-QWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLA 171
Cdd:cd08425     1 GSLRLAMT--PTFtAYLIgPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 172 VGPEHPLRNEKFVL-PEQLAGETL-ITYPVLSERLDIyTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVE 249
Cdd:cd08425    79 VGATHPLAQRRTALtLDDLAAEPLaLLSPDFATRQHI-DRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAR 157
                         170
                  ....*....|...
gi 2281791052 250 EYTprfDLYPVKL 262
Cdd:cd08425   158 EQP---GLCAVAL 167
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
105-257 1.53e-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: 1.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 105 CYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFV 184
Cdd:cd08440    11 AATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSV 90
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2281791052 185 LPEQLAGETLITYPVLSE-RLDIYTQFLQpAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRwLVEEYTPRFDL 257
Cdd:cd08440    91 TWAELAGYPLIALGRGSGvRALIDRALAA-AGLTLRPAYEVSHMSTALGMVAAGLGVAVLPA-LALPLADHPGL 162
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
112-244 2.88e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 50.00  E-value: 2.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 112 VVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAG 191
Cdd:cd08426    18 LIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLAG 97
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2281791052 192 ETLI-TYPVLSERLDIYTQFLQpAGIGPRQQKQIETTDIMLVMVAHGRGVAALP 244
Cdd:cd08426    98 YPLAlPPPSFSLRQILDAAFAR-AGVQLEPVLISNSIETLKQLVAAGGGISLLT 150
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
95-245 6.12e-07

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: 49.10  E-value: 6.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGME----CHPcyqWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIV-VTPDPLYKPGLKFTPVFDYELV 169
Cdd:cd08451     1 RLRVGFTssaaFHP---LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAfVRPPVARSDGLVLELLLEEPML 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 170 LAVGPEHPLRNEKFVLPEQLAGETLITYPVLSERLdIYTQFLQP---AGIGPR---QQKQIETTdimLVMVAHGRGVAAL 243
Cdd:cd08451    78 VALPAGHPLARERSIPLAALADEPFILFPRPVGPG-LYDAIIAAcrrAGFTPRigqEAPQMASA---INLVAAGLGVSIV 153

                  ..
gi 2281791052 244 PR 245
Cdd:cd08451   154 PA 155
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
138-279 8.41e-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: 48.50  E-value: 8.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 138 ALFSNEIDIVV--TPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLITypvLSERLDIYTQFL---Q 212
Cdd:cd08416    44 KLKDGELDAILvaTPEGLNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVT---LSEGFATYRGFDeafE 120
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2281791052 213 PAGIGPrqQKQIETTDI--MLVMVAHGRGVAALPRWLVEEYTPRFDLYPVKlGKKGIAKQI---FLGYRETD 279
Cdd:cd08416   121 IAGFEP--NVVMRVNDIfsLMSMVSGGVGYALLPGRIADVYEDKVQLIPLA-EPYQIRQTIglvFLRSRERD 189
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
106-245 1.02e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 48.51  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 106 YQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEID--IVVTPDP-LYKPGLKFTPVFDYELVLAVGPEHPLRNEK 182
Cdd:cd08453    12 YSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDagIVIPPPGaSAPPALAYRPLLSEPLVLAVPAAWAAEGGA 91
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2281791052 183 FVLPEQLAGETLITYP--VLSERLDIYTQFLQPAGIGPR-QQKQIETTDImLVMVAHGRGVAALPR 245
Cdd:cd08453    92 PLALAAVAAEPLVIFPrrIAPAFHDAVTGYYRAAGQTPRiAQEAIQMQTI-ISLVSAGMGVALVPA 156
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
34-244 1.19e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 48.66  E-value: 1.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  34 ALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGRGTLRIGmechpC-----YQW 108
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLF-----CsvtaaYSH 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 109 LLKVVSPYLERWPKVDVDVR--------QKFQfggigalfSNEIDIVVT--PDPLyKPGLKFTPVFDYELVLaVGPEHP- 177
Cdd:PRK11716   82 LPPILDRFRAEHPLVEIKLTtgdaadavEKVQ--------SGEADLAIAakPETL-PASVAFSPIDEIPLVL-IAPALPc 151
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052 178 -----LRNEK-------FVLPEQLAGEtlitypvlsERLDiytQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALP 244
Cdd:PRK11716  152 pvrqqLSQEKpdwsripFILPEHGPAR---------RRID---LWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLLP 218
PRK12680 PRK12680
LysR family transcriptional regulator;
18-260 1.19e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 49.24  E-value: 1.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  18 EGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSL-VLNQAGEWLLALANRLLPQFE-----LAESRLEqfaNG 91
Cdd:PRK12680   16 ELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANnirtyAANQRRE---SQ 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  92 GRGTLrigMECHPCYQWLL-KVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKF-TPVFDYELV 169
Cdd:PRK12680   93 GQLTL---TTTHTQARFVLpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIaVPLYRWRRL 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 170 LAVGPEHPLRNEKfVLPE--QLAGETLITYPVLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWL 247
Cdd:PRK12680  170 VVVPRGHALDTPR-RAPDmaALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGLLAEMA 248
                         250
                  ....*....|...
gi 2281791052 248 VEEYTPRFDLYPV 260
Cdd:PRK12680  249 VNANDEDLRAWPA 261
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-119 1.79e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 48.43  E-value: 1.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   4 LERNHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRReGRSLVLNQAGEWLLalanRLLPQFELAES 83
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLL----RHLRQVALLEA 76
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2281791052  84 RLEQF---ANGGRGTLRIGMECHPCYQWLLKVVSPYLER 119
Cdd:PRK13348   77 DLLSTlpaERGSPPTLAIAVNADSLATWFLPALAAVLAG 115
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
15-195 2.16e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 48.46  E-value: 2.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  15 VAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPqfELAESRLEQFANGGRG 94
Cdd:PRK10086   25 AARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD--TLNQEILDIKNQELSG 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIgmECHP----CyqWLLKVVSPYLERWPKVDVDVRQ-----KFQFGGigalfsneIDIVVTPDPLYKPGLKFTPVFD 165
Cdd:PRK10086  103 TLTV--YSRPsiaqC--WLVPRLADFTRRYPSISLTILTgnenvNFQRAG--------IDLAIYFDDAPSAQLTHHFLMD 170
                         170       180       190
                  ....*....|....*....|....*....|
gi 2281791052 166 YELVLAVGPEHPLRNEKFVLPEQLAGETLI 195
Cdd:PRK10086  171 EEILPVCSPEYAERHALTGNPDNLRHCTLL 200
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
121-257 3.35e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 46.82  E-value: 3.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 121 PKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKfVLPEQLAGETLITYPVL 200
Cdd:cd08417    27 PGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGP-LTLEDYLAAPHVLVSPR 105
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052 201 SERLDIYTQFLQPAGIGPRQqkQIETTDIMLV--MVAHGRGVAALPRWLVEEYTPRFDL 257
Cdd:cd08417   106 GRGHGLVDDALAELGLSRRV--ALTVPHFLAApaLVAGTDLIATVPRRLAEALAERLGL 162
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
14-289 7.27e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 46.52  E-value: 7.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  14 EVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGR 93
Cdd:PRK14997   12 HVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPR 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIgmechPCYQWLLKV-----VSPYLERWPKVDVDVR---QKFQFGGIGAlfsnEIDIVVTPDPLYKPGLKFTPVFD 165
Cdd:PRK14997   92 GIVKL-----TCPVTLLHVhigpmLAKFMARYPDVSLQLEatnRRVDVVGEGV----DVAIRVRPRPFEDSDLVMRVLAD 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 166 YELVLAVGPEHPLRNEKFVLPEQLAGetlitYPVLS--ERLDIYT-QFLQPAG------IGPRqqkqIETTDIMLVMVA- 235
Cdd:PRK14997  163 RGHRLFASPDLIARMGIPSAPAELSH-----WPGLSlaSGKHIHRwELYGPQGaraevhFTPR----MITTDMLALREAa 233
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2281791052 236 -HGRGVAALPRWLVEEYTPRFDLYPVKLG---KKGIAKQIFLGYRETDEEVRYLQDFI 289
Cdd:PRK14997  234 mAGVGLVQLPVLMVKEQLAAGELVAVLEEwepRREVIHAVFPSRRGLLPSVRALVDFL 291
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
95-280 8.11e-06

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: 45.68  E-value: 8.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDI----VVTPDPlykpGLKFTPVFDYELVL 170
Cdd:cd08445     2 TFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVgfgrLRIEDP----AIRRIVLREEPLVV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 171 AVGPEHPLRNEKFVLP-EQLAGETLITYPVlSER---LDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRW 246
Cdd:cd08445    78 ALPAGHPLAQEKAPLTlAQLADEPLILYPA-SPRpsfADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPAS 156
                         170       180       190
                  ....*....|....*....|....*....|....
gi 2281791052 247 LveEYTPRFDLYPVKLGKKGIAKQIFLGYRETDE 280
Cdd:cd08445   157 V--QRLRRDDVVYRPLLDPDATSPIIMSVRAGDE 188
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
138-257 1.02e-05

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: 45.32  E-value: 1.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 138 ALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKfVLPEQLAGETLITYPVLSERL---DIYTQFLQPA 214
Cdd:cd08466    44 DLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDHPRIQGS-LSLEQYLAEKHVVLSLRRGNLsalDLLTEEVLPQ 122
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2281791052 215 gigpRQQKQiETTDI--MLVMVAHGRGVAALPRWLVEEYTPRFDL 257
Cdd:cd08466   123 ----RNIAY-EVSSLlsMLAVVSQTDLIAIAPRWLADQYAEQLNL 162
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
143-290 1.23e-05

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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 45.26  E-value: 1.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 143 EID--IVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNekfvLPEQLAGETLITY--PVLSERLdiYTQFLQPAGIGP 218
Cdd:cd08427    49 ELDaaIVVEPPFPLPKDLVWTPLVREPLVLIAPAELAGDD----PRELLATQPFIRYdrSAWGGRL--VDRFLRRQGIRV 122
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2281791052 219 RQQKQIETTDIMLVMVAHGRGVAALPRWLVEEYTPRfDLYPVKLGKKGIAKQIFLGYRETDEEVRYLQDFIE 290
Cdd:cd08427   123 REVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGP-RVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLE 193
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-245 1.92e-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: 44.57  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDI-VVTPDPLyKPGLKFTPVFDYELVLAVG 173
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLgFVHSRRL-PAGLSARLLHREPFVCCLP 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2281791052 174 PEHPLRNEKFVLPEQLAGETLITYP--VLSERLDIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08448    80 AGHPLAARRRIDLRELAGEPFVLFSreVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPR 153
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
15-149 2.25e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.02  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  15 VAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLpQFE------LAESRLEqf 88
Cdd:PRK15092   22 VADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL-RFNdeacssLMYSNLQ-- 98
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2281791052  89 anggrGTLRIGME---CHPCYQWLL-KVVSPYlerwPKVDVDVRQKFQFGGIGALFSNEIDIVVT 149
Cdd:PRK15092   99 -----GVLTIGASddtADTILPFLLnRVSSVY----PKLALDVRVKRNAFMMEMLESQEVDLAVT 154
nhaR PRK11062
transcriptional activator NhaR; Provisional
1-74 2.52e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 45.00  E-value: 2.52e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2281791052   1 MGVLERNHLTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRL 74
Cdd:PRK11062    1 MSHINYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
114-245 2.89e-05

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 44.03  E-value: 2.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 114 SPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGET 193
Cdd:cd08419    19 GAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREP 98
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2281791052 194 LITYPVLSE-RLDIyTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08419    99 FLLREPGSGtRLAM-ERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSL 150
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
20-84 4.24e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.27  E-value: 4.24e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2281791052  20 SLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFE--LAESR 84
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLEsnLAELR 93
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
97-260 4.39e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 43.50  E-value: 4.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  97 RIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVT--PDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08418     3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGtlPDEMYLKELISEPLFESDFVVVARK 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHP---------LRNEKFVLPEQLAGetliTYPVLSErldiytqFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08418    83 DHPlqgarsleeLLDASWVLPGTRMG----YYNNLLE-------ALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSR 151
                         170
                  ....*....|....*
gi 2281791052 246 WLVEEYTPRFDLYPV 260
Cdd:cd08418   152 DMGRGPLDSFRLITI 166
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
15-74 4.51e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.99  E-value: 4.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  15 VAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRReGRSLVLNQAGEWLLALANRL 74
Cdd:PRK03635   13 VVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV 71
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
109-290 5.79e-05

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176134  Cd Length: 198  Bit Score: 43.32  E-value: 5.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 109 LLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLY-KPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPE 187
Cdd:cd08443    15 LPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHdYDDLITLPCYHWNRCVVVKRDHPLADKQSISIE 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 188 QLAGETLITYPV-LSERLDIYTQFlQPAGIGPRQQKQIETTDIMLVMVAHGRGV---AALPrwlveeYTPRFD------- 256
Cdd:cd08443    95 ELATYPIVTYTFgFTGRSELDTAF-NRAGLTPNIVLTATDADVIKTYVRLGLGVgviASMA------YDPVDDpdlvird 167
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2281791052 257 ---LYPVKLGKKGIAKQIFLGyretdeevRYLQDFIE 290
Cdd:cd08443   168 ardLFPWSVTKIAFRRGTFLR--------SYMYDFIQ 196
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
14-81 1.23e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.70  E-value: 1.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2281791052  14 EVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELA 81
Cdd:PRK03601   11 EVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAA 78
PRK09801 PRK09801
LysR family transcriptional regulator;
9-147 1.79e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.33  E-value: 1.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052   9 LTIIREVAREGSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQF 88
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2281791052  89 ANGGRGTLRIGMECHPCYQWLLKVVSPYLERWPKVDVdvrqKFQfggigaLFSNEIDIV 147
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV----HFE------LFDRQIDLV 139
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
95-254 2.45e-04

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: 41.25  E-value: 2.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  95 TLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGP 174
Cdd:cd08456     1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 175 EHPLRNEKFVLPEQLAGETLITYP---VLSERLDiytQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPRWLVEEY 251
Cdd:cd08456    81 GHRLAVKKVLTPSDLEGEPFISLArtdGTRQRVD---ALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDY 157

                  ...
gi 2281791052 252 TPR 254
Cdd:cd08456   158 AAA 160
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
118-245 1.30e-03

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 39.12  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 118 ERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVGPEHPLRNEKFVLPEQLAGETLI-- 195
Cdd:cd08433    24 RRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLPRGAPVPLAELARLPLIlp 103
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2281791052 196 -TYPVLSERLDiytQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08433   104 sRGHGLRRLVD---EAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPA 151
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
19-244 1.33e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.67  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  19 GSLTAAGMRLNLTQPALSHAIRKIEQQLGVKIWRREGRSLVLNQAGEWLLALANRLLPQFELAESRLEQFANGGRGTLRI 98
Cdd:PRK11233   16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSI 95
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  99 GMECHPCYQW----LLKVVSpylERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLaVGP 174
Cdd:PRK11233   96 GLAPGTAASSltmpLLQAVR---AEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPLLKEDLFL-VGT 171
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2281791052 175 EHPLRNEkfVLPEQLAGETLI---TYPVLSERLDiyTQFLQpAGIGPRQQKQIETTDIMLVMVAHGRGVAALP 244
Cdd:PRK11233  172 QDCPGQS--VDLAAVAQMNLFlprDYSAVRLRVD--EAFSL-RRLTAKVIGEIESIATLTAAIASGMGVTVLP 239
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
94-245 1.51e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 38.80  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRQKFQFGGIGALFSNEIDIVVTPDPLYKPGLKFTPVFDYELVLAVG 173
Cdd:cd08446     1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVP 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2281791052 174 PEHPLRNEKFVLPEQLAGETLITYPVLSERL--DIYTQFLQPAGIGPRQQKQIETTDIMLVMVAHGRGVAALPR 245
Cdd:cd08446    81 KSHPLAARPAVSLADLRNEPLILFPRGGRPSfaDEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPE 154
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
94-251 4.82e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 37.42  E-value: 4.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052  94 GTLRIGMECHPCYQWLLKVVSPYLERWPKVDVDVRqkfqfggigalFSNE--------IDIVVTPDPLYKPGLKFTPVFD 165
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV-----------LSDRlvdlveegFDLAIRIGELPDSSLVARRLGP 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2281791052 166 YELVLAVGPE------HPLRnekfvlPEQLAGETLITYPVLSERLDIytQFLQPAG---IGPRQQKQIETTDIMLVMVAH 236
Cdd:cd08422    70 VRRVLVASPAylarhgTPQT------PEDLARHRCLGYRLPGRPLRW--RFRRGGGeveVRVRGRLVVNDGEALRAAALA 141
                         170
                  ....*....|....*
gi 2281791052 237 GRGVAALPRWLVEEY 251
Cdd:cd08422   142 GLGIALLPDFLVAED 156
 
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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