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Conserved domains on  [gi|519083138|ref|WP_020239013|]
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HTH-type transcriptional regulator MetR [Escherichia coli]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11487786)

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
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-317 0e+00

HTH-type transcriptional regulator MetR;


:

Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 679.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
Cdd:PRK15421  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 161 YEVRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 519083138 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPITEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
Cdd:PRK15421 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
 
Name Accession Description Interval E-value
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-317 0e+00

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 679.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
Cdd:PRK15421  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 161 YEVRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 519083138 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPITEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
Cdd:PRK15421 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
90-285 5.91e-114

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: 327.60  E-value: 5.91e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 170 DHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIAALPHWVVESFERQ 248
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPkRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 519083138 249 GLVVTKTLGE-GLWSRLYAAVRDGEQRQPITEAFIRSA 285
Cdd:cd08441  161 GLVVARPLGEeGLWRTLYAAVRTEDADQPYLQDFLELA 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-291 3.43e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.06  E-value: 3.43e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  82 ACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158
Cdd:COG0583   81 ELRALRGGprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 159 FDYEVRLVLAPDHPLAAKTRItpeelasetlliypvqrsrldvwrhflqpagvspslksVDNTLLLIQMVAARMGIAALP 238
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL--------------------------------------VNSLEALLAAVAAGLGIALLP 202
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 519083138 239 HWVVESFERQGLVVTKTLGEGLWSR-LYAAVRDGEQRQPITEAFIRSARNHACD 291
Cdd:COG0583  203 RFLAADELAAGRLVALPLPDPPPPRpLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-289 1.42e-42

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: 145.89  E-value: 1.42e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  170 DHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESFERQ 248
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 519083138  249 GLVVTKTLGE-GLWSRLYAAVRDGEQRQPITEAFIRSARNHA 289
Cdd:pfam03466 163 GRLVALPLPEpPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
 
Name Accession Description Interval E-value
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-317 0e+00

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 679.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
Cdd:PRK15421  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 161 YEVRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHW 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 519083138 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPITEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
Cdd:PRK15421 241 VVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL 317
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
90-285 5.91e-114

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: 327.60  E-value: 5.91e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 170 DHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIAALPHWVVESFERQ 248
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPkRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 519083138 249 GLVVTKTLGE-GLWSRLYAAVRDGEQRQPITEAFIRSA 285
Cdd:cd08441  161 GLVVARPLGEeGLWRTLYAAVRTEDADQPYLQDFLELA 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-291 3.43e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.06  E-value: 3.43e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  82 ACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158
Cdd:COG0583   81 ELRALRGGprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 159 FDYEVRLVLAPDHPLAAKTRItpeelasetlliypvqrsrldvwrhflqpagvspslksVDNTLLLIQMVAARMGIAALP 238
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL--------------------------------------VNSLEALLAAVAAGLGIALLP 202
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 519083138 239 HWVVESFERQGLVVTKTLGEGLWSR-LYAAVRDGEQRQPITEAFIRSARNHACD 291
Cdd:COG0583  203 RFLAADELAAGRLVALPLPDPPPPRpLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-289 1.42e-42

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: 145.89  E-value: 1.42e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  170 DHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESFERQ 248
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 519083138  249 GLVVTKTLGE-GLWSRLYAAVRDGEQRQPITEAFIRSARNHA 289
Cdd:pfam03466 163 GRLVALPLPEpPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
90-283 7.27e-41

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: 141.20  E-value: 7.27e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 170 DHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESFERQ 248
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIAlEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 519083138 249 GLVVTKTLGEGLWSRLYAAVRDGEQRQPITEAFIR 283
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
PRK09986 PRK09986
LysR family transcriptional regulator;
2-283 2.30e-21

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 91.71  E-value: 2.30e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL- 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLa 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 --QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM--TSDILPRSGLHYS 156
Cdd:PRK09986  87 rvEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSR 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 157 PMFDYEVRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFL-QPAGVSPSL-KSVDNTLLLIQMVAARMGI 234
Cdd:PRK09986 167 RLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVcQQAGFSPQIiRQVNEPQTVLAMVSMGIGI 246
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 519083138 235 AALPhwvvESFERQGL--VVTKTLGEGLWSRLYaAVRDGEQRQPITEAFIR 283
Cdd:PRK09986 247 TLLP----DSYAQIPWpgVVFRPLKERIPADLY-AVYHPDQVTPALNKLLA 292
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
2-278 1.70e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 89.44  E-value: 1.70e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL- 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKl 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 ---QACNEPQQtrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157
Cdd:PRK09906  81 rarKIVQEDRQ--LTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 158 MFDYEVRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRL--DVWRHFLQPAGVSPSL-KSVDNTLLLIQMVAARMGI 234
Cdd:PRK09906 159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSlaPIIKAWFAQHNSQPNIvQVATNILVTMNLVGMGLGC 238
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 519083138 235 AALPHWvVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPIT 278
Cdd:PRK09906 239 TIIPGY-MNNFNTGQVVFRPLAGNVPSIALLMAWKKGEMKPALR 281
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
90-285 3.74e-20

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: 86.41  E-value: 3.74e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 170 DHPLAAKTRITPEELASETLLIYP-VQRSRL-DVWRHFLQPAGVSPSLKS-VDNTLLLIQMVAARMGIAALPHWVVeSFE 246
Cdd:cd08414   81 DHPLAARESVSLADLADEPFVLFPrEPGPGLyDQILALCRRAGFTPRIVQeASDLQTLLALVAAGLGVALVPASVA-RLQ 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 519083138 247 RQGLVVTKTLGEGLWSRLYAAVRDGEQRqPITEAFIRSA 285
Cdd:cd08414  160 RPGVVYRPLADPPPRSELALAWRRDNAS-PALRAFLELA 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
103-283 1.82e-18

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: 81.77  E-value: 1.82e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPE 182
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAE 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 183 ELASETLLIypvqR-----SRlDVWRHFLQPAGVSPS-LKSV---DNTLLLIQMVAARMGIAALPHWVVE-SFERQGLVV 252
Cdd:cd08420   94 ELAAEPWIL----RepgsgTR-EVFERALAEAGLDGLdLNIVmelGSTEAIKEAVEAGLGISILSRLAVRkELELGRLVA 168
                        170       180       190
                 ....*....|....*....|....*....|.
gi 519083138 253 TKTLGEGLWSRLYAAVRDGEQRQPITEAFIR 283
Cdd:cd08420  169 LPVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
103-283 3.39e-18

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: 81.03  E-value: 3.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPE 182
Cdd:cd08440   14 LLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 183 ELASETL-LIYPVQRSRLDVWRHFLQpAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESFERQGLVVTKTLGEGL 260
Cdd:cd08440   94 ELAGYPLiALGRGSGVRALIDRALAA-AGLTLRPAyEVSHMSTALGMVAAGLGVAVLPALALPLADHPGLVARPLTEPVV 172
                        170       180
                 ....*....|....*....|...
gi 519083138 261 WSRLYAAVRDGEQRQPITEAFIR 283
Cdd:cd08440  173 TRTVGLIRRRGRSLSPAAQAFLD 195
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
102-284 5.19e-18

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: 80.72  E-value: 5.19e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 102 QWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSD--ILPRS---GLHYSPMFDYEVRLVLAPDHPLAAK 176
Cdd:cd08423   13 ALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypVTPPPddpGLTRVPLLDDPLDLVLPADHPLAGR 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 177 TRITPEELASETlLIYPVQRSR-LDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVeSFERQGLVVTK 254
Cdd:cd08423   93 EEVALADLADEP-WIAGCPGSPcHRWLVRACRAAGFTPRIAhEADDYATVLALVAAGLGVALVPRLAL-GARPPGVVVRP 170
                        170       180       190
                 ....*....|....*....|....*....|
gi 519083138 255 tLGEGLWSRLYAAVRDGEQRQPITEAFIRS 284
Cdd:cd08423  171 -LRPPPTRRIYAAVRAGAARRPAVAAALEA 199
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
90-252 2.00e-17

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: 78.75  E-value: 2.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTsdILP--RSGLHYSPMFDYEVRLVL 167
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGIT--VLPvdEEEFDSQPLCNEPLVAVL 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 168 APDHPLAAKTRITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTL-LLIQMVAARMGIAALPHWVVESFE 246
Cdd:cd08438   79 PRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWdFIAELVAAGLGVALLPRSIAQRLD 158

                 ....*.
gi 519083138 247 RQGLVV 252
Cdd:cd08438  159 NAGVKV 164
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
2-200 2.85e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 80.81  E-value: 2.85e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPL-RFTPQGEILLQLANQVLPQISQA 79
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  80 LQACNE---PQQTRLRIAIEcHSCIQWLTP-ALENFHKNWPQVEMDFKSGvtfDPQPA---LQQGELDLVM-TSDILPRS 151
Cdd:PRK12682  81 KRIGDDfsnQDSGTLTIATT-HTQARYVLPrVVAAFRKRYPKVNLSLHQG---SPDEIarmVISGEADIGIaTESLADDP 156
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 519083138 152 GLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELASETLLIYP---VQRSRLD 200
Cdd:PRK12682 157 DLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHpgfTGRSRID 208
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-63 6.56e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.57  E-value: 6.56e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 519083138    5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGE 63
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
98-282 2.35e-16

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: 76.04  E-value: 2.35e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  98 HSCIQWLTPAL-ENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAK 176
Cdd:cd08434    8 HSLGTSLVPDLiRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGR 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 177 TRITPEELASETLLIYPvQRS--RLDVWRHFLQpAGVSP--SLKSVDNTlLLIQMVAARMGIAALPHWVVESFERqglVV 252
Cdd:cd08434   88 DSVDLAELADEPFVLLS-PGFglRPIVDELCAA-AGFTPkiAFEGEEDS-TIAGLVAAGLGVAILPEMTLLNPPG---VK 161
                        170       180       190
                 ....*....|....*....|....*....|.
gi 519083138 253 TKTLGEGLWSR-LYAAVRDGEQRQPITEAFI 282
Cdd:cd08434  162 KIPIKDPDAERtIGLAWLKDRYLSPAARRFK 192
rbcR CHL00180
LysR transcriptional regulator; Provisional
7-184 4.97e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 76.98  E-value: 4.97e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEP 86
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  87 QQtrlriaIECHSCI--------QWLTPAL-ENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILP---RSGLH 154
Cdd:CHL00180  90 KN------LQRGTLIigasqttgTYLMPRLiGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPtelKKILE 163
                        170       180       190
                 ....*....|....*....|....*....|
gi 519083138 155 YSPMFDYEVRLVLAPDHPLAAKTRITPEEL 184
Cdd:CHL00180 164 ITPYVEDELALIIPKSHPFAKLKKIQKEDL 193
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
1-235 8.21e-15

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 73.49  E-value: 8.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILL---QLANQVLPQIS 77
Cdd:PRK11013   3 AVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFeevQRSYYGLDRIV 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  78 QALQACNEPQQTRLRIAiechsCI----QWLTP-ALENFHKNWPQVemdfksGVTFDPQ--PALQQ----GELDLVMTSD 146
Cdd:PRK11013  83 SAAESLREFRQGQLSIA-----CLpvfsQSLLPgLCQPFLARYPDV------SLNIVPQesPLLEEwlsaQRHDLGLTET 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 147 ILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELASETLliypVQRSRLDVWRHFL----QPAGVS-------PSL 215
Cdd:PRK11013 152 LHTPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENF----ISLSRTDSYRQLLdqlfAEHGVKrrmvvetHSA 227
                        250       260
                 ....*....|....*....|
gi 519083138 216 KSVdntlllIQMVAARMGIA 235
Cdd:PRK11013 228 ASV------CAMVRAGVGVS 241
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
18-235 1.00e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 73.34  E-value: 1.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA---LQACNEPQqtRLRIA 94
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAtrkLRARSAKG--ALTVS 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  95 IECHSCIQWLTPALENFHKNWPQVEMDFKSgVTFDPQPAlqQGELDLVMtsdilpRSG------LHYSPMFDYEVRLVLA 168
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKA-VDRLEDFL--RDDVDVAI------RYGrgnwpgLRVEKLLDEYLLPVCS 170
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 519083138 169 PDHPLAAKTRITPEELASETLLiypvQRSRLDVWRHFLQPAGVS----PSLKSVDNTLLLIQMVAARMGIA 235
Cdd:PRK11139 171 PALLNGGKPLKTPEDLARHTLL----HDDSREDWRAWFRAAGLDdlnvQQGPIFSHSSMALQAAIHGQGVA 237
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
101-241 3.87e-14

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: 69.71  E-value: 3.87e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRIT 180
Cdd:cd08450   12 VQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIP 91
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 519083138 181 PEELASETLLIY-PVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWV 241
Cdd:cd08450   92 PQDLAGENFISPaPTAPVLQQVIENYAAQHNIQPNIIqEADNLLSAMSLVASTLGCALLPLYA 154
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-121 9.15e-14

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 70.19  E-value: 9.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGfRLFVRKSQPLRFTPQGEILLQLANQVLpQISQAL 80
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVG-QVLLVRTQPCRPTEAGQRLLRHARQVR-LLEAEL 78
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 519083138  81 QAC---NEPQQTRLRIAIECHSCIQWLTPALENFHKnWPQVEMD 121
Cdd:PRK03635  79 LGElpaLDGTPLTLSIAVNADSLATWFLPALAPVLA-RSGVLLD 121
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
12-190 1.19e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 70.42  E-value: 1.19e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  12 ALRNCgSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ--ACNEPQQT 89
Cdd:PRK10086  25 AARHQ-SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILdiKNQELSGT 103
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 -----RLRIAiEChsciqWLTPALENFHKNWPQVEMDFKSG---VTFdpqpalQQGELDLVMTSDILPRSGLHYSPMFDY 161
Cdd:PRK10086 104 ltvysRPSIA-QC-----WLVPRLADFTRRYPSISLTILTGnenVNF------QRAGIDLAIYFDDAPSAQLTHHFLMDE 171
                        170       180       190
                 ....*....|....*....|....*....|...
gi 519083138 162 EVRLVLAPD----HPLAAKtritPEELASETLL 190
Cdd:PRK10086 172 EILPVCSPEyaerHALTGN----PDNLRHCTLL 200
PRK12680 PRK12680
LysR family transcriptional regulator;
22-246 2.32e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 69.65  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  22 AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLANQVLPQISQA-LQACNEPQQTRLRIA-IECH 98
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIrTYAANQRRESQGQLTlTTTH 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  99 SCIQW-LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL--VMTSDILPRSGLHYsPMFDYEvRLVLAP-DHPLA 174
Cdd:PRK12680 102 TQARFvLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIaiVSTAGGEPSAGIAV-PLYRWR-RLVVVPrGHALD 179
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 519083138 175 AKTRiTPE--ELASETLLIYPVQ-RSRLDVWRHFLQpAGVSPS--LKSVDNTLLLiQMVAARMGIAALPHWVVESFE 246
Cdd:PRK12680 180 TPRR-APDmaALAEHPLISYESStRPGSSLQRAFAQ-LGLEPSiaLTALDADLIK-TYVRAGLGVGLLAEMAVNAND 253
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
17-193 3.62e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 68.82  E-value: 3.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI----SQALQACNEPQQTrLR 92
Cdd:PRK11074  17 GSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMqetrRQCQQVANGWRGQ-LS 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  93 IAIECHSCIQWLTPALENFHKNWPQVE----MDFKSGVtFDpqpALQQGELDLVM--TSDIlPRSG-LHYSPMFDYEVRL 165
Cdd:PRK11074  96 IAVDNIVRPDRTRQLIVDFYRHFDDVEliirQEVFNGV-WD---ALADGRVDIAIgaTRAI-PVGGrFAFRDMGMLSWAC 170
                        170       180
                 ....*....|....*....|....*...
gi 519083138 166 VLAPDHPLAAKTRitpeELASETLLIYP 193
Cdd:PRK11074 171 VVSSDHPLASMDG----PLSDDELRPYP 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
133-283 1.83e-12

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: 65.24  E-value: 1.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 133 ALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELASETLL--------------IYPVQRSR 198
Cdd:cd08411   45 KLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAGERLLlleeghclrdqaleLCRLAGAR 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 199 LDVWRHflqpAGvspSLksvdNTllLIQMVAARMGIAALPHWVVESFERQG-LVVTKTLGEGLWSR-LYAAVRDGEQRQP 276
Cdd:cd08411  125 EQTDFE----AT---SL----ET--LRQMVAAGLGITLLPELAVPSEELRGdRLVVRPFAEPAPSRtIGLVWRRSSPRAA 191

                 ....*..
gi 519083138 277 ITEAFIR 283
Cdd:cd08411  192 AFEALAE 198
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
5-213 2.15e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 66.52  E-value: 2.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN 84
Cdd:PRK11242   4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIH 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  85 ---EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDY 161
Cdd:PRK11242  84 dvaDLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTE 163
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 519083138 162 EVRLVLAPDHPLAAKTR-ITPEELASETL-LIYPVQRSRLDVWRHFLQpAGVSP 213
Cdd:PRK11242 164 TLALVVGRHHPLAARRKaLTLDELADEPLvLLSAEFATREQIDRYFRR-HGVTP 216
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-138 4.34e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 65.38  E-value: 4.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRkSQPLRFTPQGEILLQLANQVlpQISQA- 79
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV--ALLEAd 77
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 519083138  80 LQACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNwPQVEMDfksgVTFDPQ----PALQQGE 138
Cdd:PRK13348  78 LLSTLPAERGsppTLAIAVNADSLATWFLPALAAVLAG-ERILLE----LIVDDQdhtfALLERGE 138
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
104-283 9.28e-12

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: 63.00  E-value: 9.28e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTS--DILPrSGLHYSPMFDYEVRLVLAPDHPLAAKTRITP 181
Cdd:cd08436   15 LPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGlpERRP-PGLASRELAREPLVAVVAPDHPLAGRRRVAL 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 182 EELASETLLIYPV---QRSRLDvwrHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESFERqglVVTKTLG 257
Cdd:cd08436   94 ADLADEPFVDFPPgtgARRQVD---RAFAAAGVRRRVAfEVSDVDLLLDLVARGLGVALLPASVAARLPG---LAALPLE 167
                        170       180
                 ....*....|....*....|....*.
gi 519083138 258 EGLWSRLYAAVRDGeQRQPITEAFIR 283
Cdd:cd08436  168 PAPRRRLYLAWSAP-PPSPAARAFLE 192
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
90-285 1.05e-11

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: 63.06  E-value: 1.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIEchSCIQW--LTPALENFHKNWPQVEMDFKSgvtFDPQ---PALQQGELDL--VMTSDILPRSGLHYSPMFDYE 162
Cdd:cd08449    1 HLNIGMV--GSVLWggLGPALRRFKRQYPNVTVRFHE---LSPEaqkAALLSKRIDLgfVRFADTLNDPPLASELLWREP 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 163 VRLVLAPDHPLAAKTRITPEELASETLLIYPVQRSRL--DVWRHFLQpAGVSPSL-KSVDNTLLLIQMVAARMGIAALPh 239
Cdd:cd08449   76 MVVALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRFadFLINCCLQ-AGFTPQItQEVVEPQTLMALVAAGFGVALVP- 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 519083138 240 wvvESFERQ---GLVVTKtLGEGLWSRLYaAVRDGEQRQPITEAFIRSA 285
Cdd:cd08449  154 ---ESYARLpwpGVRFIP-LKQAISADLY-AVYHPDSATPVIQAFLALL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
11-200 1.16e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 64.29  E-value: 1.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  11 QALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLANQVL---PQISQALQACNEP 86
Cdd:PRK12683  11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaENLRRLAEQFADR 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  87 QQTRLRIAIeCHSCIQW-LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRS-GLHYSPMFDYEVR 164
Cdd:PRK12683  91 DSGHLTVAT-THTQARYaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREpDLVSFPYYSWHHV 169
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 519083138 165 LVLAPDHPLAAKTRITPEELASETLLIYP---VQRSRLD 200
Cdd:PRK12683 170 VVVPKGHPLTGRENLTLEAIAEYPIITYDqgfTGRSRID 208
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
18-192 1.73e-11

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 63.84  E-value: 1.73e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLANQVLPQISQALQACNE---PQQTRLRI 93
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEfaaQDQGNLTI 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  94 AIeCHSCIQW-LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM-TSDILPRSGLHYSPMFDYEVRLVLAPDH 171
Cdd:PRK12684  98 AT-THTQARYaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIaTEAIADYKELVSLPCYQWNHCVVVPPDH 176
                        170       180
                 ....*....|....*....|.
gi 519083138 172 PLAAKTRITPEELASETLLIY 192
Cdd:PRK12684 177 PLLERKPLTLEDLAQYPLITY 197
PRK09791 PRK09791
LysR family transcriptional regulator;
17-179 1.82e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 63.63  E-value: 1.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLpqisQALQACNEPQQTRL----- 91
Cdd:PRK09791  20 GSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIL----EELRAAQEDIRQRQgqlag 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  92 RIAIECHSCI-QWLTPA-LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdILPRS---GLHYSPMFDYEVRLV 166
Cdd:PRK09791  96 QINIGMGASIaRSLMPAvISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINT-YYQGPydhEFTFEKLLEKQFAVF 174
                        170
                 ....*....|...
gi 519083138 167 LAPDHPLAAKTRI 179
Cdd:PRK09791 175 CRPGHPAIGARSL 187
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
27-243 1.84e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 63.30  E-value: 1.84e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  27 HQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQT---RLRI-----AIECH 98
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSlsgELSLfcsvtAAYSH 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  99 sciqwLTPALENFHKNWPQVEMDFKSGvtfDPQPAL---QQGELDLVMT--SDILPrSGLHYSPMfdYEVRLVL-APDHP 172
Cdd:PRK11716  82 -----LPPILDRFRAEHPLVEIKLTTG---DAADAVekvQSGEADLAIAakPETLP-ASVAFSPI--DEIPLVLiAPALP 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 173 LAAKTRITPEELA-SETLLIYPVQ---RSRLDVW--RHFLQP------AG----VSpslksvdntllliqMVAARMGIAA 236
Cdd:PRK11716 151 CPVRQQLSQEKPDwSRIPFILPEHgpaRRRIDLWfrRHKIKPniyatvSGheaiVS--------------MVALGCGVGL 216

                 ....*..
gi 519083138 237 LPHWVVE 243
Cdd:PRK11716 217 LPEVVLE 223
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
90-252 3.59e-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: 61.42  E-value: 3.59e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAieCHSCIQW--LTPALENFHKNWPQVemdfksGVTFDPQP------ALQQGELDLVMTSDILPRSGLHYSPMFDY 161
Cdd:cd08415    1 TLRIA--ALPALALslLPRAIARFRARHPDV------RISLHTLSsstvveAVLSGQADLGLASLPLDHPGLESEPLASG 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 162 EVRLVLAPDHPLAAKTRITPEELASETLLIYPVQ---RSRLDVWrhfLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAAL 237
Cdd:cd08415   73 RAVCVLPPGHPLARKDVVTPADLAGEPLISLGRGdplRQRVDAA---FERAGVEPRIViETQLSHTACALVAAGLGVAIV 149
                        170
                 ....*....|....*
gi 519083138 238 PHWVVESFERQGLVV 252
Cdd:cd08415  150 DPLTAAGYAGAGLVV 164
cbl PRK12679
HTH-type transcriptional regulator Cbl;
11-200 5.83e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 62.52  E-value: 5.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  11 QALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLANQVLPQISQ----ALQACNE 85
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNvrrlADLFTND 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  86 pQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPR-SGLHYSPMFDYEVR 164
Cdd:PRK12679  91 -TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNdPQLVAFPWFRWHHS 169
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 519083138 165 LVLAPDHPLAAKTRITPEELASETLLIYP---VQRSRLD 200
Cdd:PRK12679 170 LLVPHDHPLTQITPLTLESIAKWPLITYRqgiTGRSRID 208
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
104-283 7.48e-11

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: 60.36  E-value: 7.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM--TSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITP 181
Cdd:cd08435   15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARPGHPLARRARLTL 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 182 EELASETLLIYP---VQRSRLDvwrHFLQPAGVSPSLKSVDNT--LLLIQMVAARMGIAALPHWVVESFERQG-LVVTKT 255
Cdd:cd08435   95 ADLADYPWVLPPpgtPLRQRLE---QLFAAAGLPLPRNVVETAsiSALLALLARSDMLAVLPRSVAEDELRAGvLRELPL 171
                        170       180
                 ....*....|....*....|....*...
gi 519083138 256 LGEGLWSRLYAAVRDGEQRQPITEAFIR 283
Cdd:cd08435  172 PLPTSRRPIGITTRRGGPLSPAARALLD 199
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-302 1.15e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 61.36  E-value: 1.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS--- 77
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLEsmp 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  78 QALQACNEPQQTRLRIAIE--------CHSCIQWLtpalenfHKNWPQVEMDFKSGVTFDPQPAL--QQGELDLVMTSDI 147
Cdd:PRK10094  81 SELQQVNDGVERQVNIVINnllynpqaVAQLLAWL-------NERYPFTQFHISRQIYMGVWDSLlyEGFSLAIGVTGTE 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 148 LPRSGLHYSPMFDYEVRLVLAPDHPLAAktriTPEELASETLLIYPV--------QRSRLDVWRHFLQPAGVSPSLKSvd 219
Cdd:PRK10094 154 ALANTFSLDPLGSVQWRFVMAADHPLAN----VEEPLTEAQLRRFPAvniedsarTLTKRVAWRLPGQKEIIVPDMET-- 227
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 220 ntllliqMVAARM---GIAALPHWVVESFERQGLVVTKTlgeglwsrlyaaVRDGEQRQPITEAFIRSARNHACDHLPFV 296
Cdd:PRK10094 228 -------KIAAHLagvGIGFLPKSLCQSMIDNQQLVSRV------------IPTMRPPSPLSLAWRKFGSGKAVEDIVTL 288

                 ....*.
gi 519083138 297 KSAERP 302
Cdd:PRK10094 289 FTQRRP 294
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-200 1.16e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 61.45  E-value: 1.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  21 AAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPL-RFTPQGEILLQLANQVLPQ---ISQALQACNEPQQTRLRIAIE 96
Cdd:PRK12681  21 ATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKvesIKSVAGEHTWPDKGSLYIATT 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  97 cHSCIQW-LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDilprsGLH-YS-----PMFDYEVRLVLAP 169
Cdd:PRK12681 101 -HTQARYaLPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATE-----ALHlYDdlimlPCYHWNRSVVVPP 174
                        170       180       190
                 ....*....|....*....|....*....|....
gi 519083138 170 DHPLAAKTRITPEELASETLLIYP---VQRSRLD 200
Cdd:PRK12681 175 DHPLAKKKKLTIEELAQYPLVTYVfgfTGRSELD 208
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-247 3.16e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.16  E-value: 3.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEI-------LLQLANQVL 73
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIyyqgcrrMLHEVQDVH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  74 PQisqaLQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVtfdPQPALQQGELDLVMTSDILPRSGL 153
Cdd:PRK10632  81 EQ----LYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGI---PAPDLIADGLDVVIRVGALQDSSL 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 154 hyspmfdYEVRLVLAPDHPLAAKTRI----TPE---ELASETLLIYPVqrsRLDVWRHFLQPAGVS----PSLKSVDN-T 221
Cdd:PRK10632 154 -------FSRRLGAMPMVVCAAKSYLaqygTPEkpaDLSSHSWLEYSV---RPDNEFELIAPEGIStrliPQGRFVTNdP 223
                        250       260
                 ....*....|....*....|....*..
gi 519083138 222 LLLIQMVAARMGIAALP-HWVVESFER 247
Cdd:PRK10632 224 QTLVRWLTAGAGIAYVPlMWVIDEINR 250
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
104-285 1.58e-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: 56.78  E-value: 1.58e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEE 183
Cdd:cd08412   15 LPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHPLAGKDEVSLAD 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 184 LASETLLIYPVQRSR---LDVWRHflqpAGVSP----SLKSVDntlLLIQMVAARMGIAALPHWVV--ESFERQGLvVTK 254
Cdd:cd08412   95 LAAEPLILLDLPHSReyfLSLFAA----AGLTPriayRTSSFE---AVRSLVANGLGYSLLNDRPYrpWSYDGKRL-VRR 166
                        170       180       190
                 ....*....|....*....|....*....|..
gi 519083138 255 TLGEGLWS-RLYAAVRDGEQRQPITEAFIRSA 285
Cdd:cd08412  167 PLADPVPPlRLGLAWRRGARLTRAARAFVDFA 198
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
90-251 3.97e-09

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: 55.52  E-value: 3.97e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAieCHSCI--QWLTPALENFHKNWPQVEMDfksgVTFDPQPA-LQQGELDLVMTSDILPRSGLHYSPMFDYEVRLV 166
Cdd:cd08422    2 RLRIS--APVSFgrLHLAPLLAEFLARYPDVRLE----LVLSDRLVdLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLV 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 167 LAPDHpLAAKTRI-TPEELASETLLIYPvQRSRLDVWRhFLQPAG-----VSPSLkSVDNTLLLIQMVAARMGIAALPHW 240
Cdd:cd08422   76 ASPAY-LARHGTPqTPEDLARHRCLGYR-LPGRPLRWR-FRRGGGevevrVRGRL-VVNDGEALRAAALAGLGIALLPDF 151
                        170
                 ....*....|..
gi 519083138 241 VVESFERQG-LV 251
Cdd:cd08422  152 LVAEDLASGrLV 163
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
104-282 4.57e-09

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: 55.20  E-value: 4.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEE 183
Cdd:cd08452   15 LPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIED 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 184 LASETLLIYP--VQRSRLDVWRHFLQPAGVSPSL-KSVDNTLLLIQMVAARMGIAALPHwVVESFERQGLVVTKTLGEGL 260
Cdd:cd08452   95 LRDEPIITVAreAWPTLYDEIIQLCEQAGFRPKIvQEATEYQTVIGLVSAGIGVTFVPS-SAKKLFNLEVAYRKIDQINL 173
                        170       180
                 ....*....|....*....|..
gi 519083138 261 WSRLYAAVRDGEQRqPITEAFI 282
Cdd:cd08452  174 NAEWSIAYRKDNHN-PLLKHFI 194
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
101-212 8.57e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 54.63  E-value: 8.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPALENFHKNWPQVEMDFKS-GVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRI 179
Cdd:cd08463   12 ALFLPELVARFRREAPGARLEIHPlGPDFDYERALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRADHPLARRGLM 91
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 519083138 180 TPEELASETLL----IYPVQRSRLDVwrhFLQPAGVS 212
Cdd:cd08463   92 TLDDYLEAPHLaptpYSVGQRGVIDS---HLARLGLK 125
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
116-239 8.72e-09

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: 54.58  E-value: 8.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 116 PQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMfdYEVRLVLA--PDHPLAAKTRITPEELASETLLIYP 193
Cdd:cd08447   27 PDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPL--VREPLVAAvpAGHPLAGAERLTLEDLDGQPFIMYS 104
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 519083138 194 VQRSRL--D-VWRHFlQPAGVSPS-LKSVDNTLLLIQMVAARMGIAALPH 239
Cdd:cd08447  105 PTEARYfhDlVVRLF-ASAGVQPRyVQYLSQIHTMLALVRAGLGVALVPA 153
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
103-251 9.85e-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: 54.15  E-value: 9.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAaktrITPE 182
Cdd:cd08442   14 RLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPV----SRAE 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 519083138 183 ELASETLLIYP---VQRSRLdvwRHFLQPAGVSPS----LKSVDNtllLIQMVAARMGIAALPHWVVESFERQGLV 251
Cdd:cd08442   90 DLAGSTLLAFRagcSYRRRL---EDWLAEEGVSPGkimeFGSYHA---ILGCVAAGMGIALLPRSVLDSLQGRGSV 159
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
102-239 1.01e-08

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 54.12  E-value: 1.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 102 QWLTPALENFHKNWPQVEMDFK-SGVTFDpqpaLQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHpLAAKTRIT 180
Cdd:cd08432   13 RWLIPRLARFQARHPDIDLRLStSDRLVD----FAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPAL-LAGLPLLS 87
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 519083138 181 PEELASETLLiypVQRSRLDVWRHFLQPAGVSPSLKS----VDNTLLLIQMVAARMGIAALPH 239
Cdd:cd08432   88 PADLARHTLL---HDATRPEAWQWWLWAAGVADVDARrgprFDDSSLALQAAVAGLGVALAPR 147
PRK10341 PRK10341
transcriptional regulator TdcA;
5-187 1.60e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN 84
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  85 -EPQQTRLRIAIECHSCI--QWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL---VMTSDILPRSgLHYSPM 158
Cdd:PRK10341  90 gMSSEAVVDVSFGFPSLIgfTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFaigTLSNEMKLQD-LHVEPL 168
                        170       180
                 ....*....|....*....|....*....
gi 519083138 159 FDYEVRLVLAPDHPLAAKTRItpEELASE 187
Cdd:PRK10341 169 FESEFVLVASKSRTCTGTTTL--ESLKNE 195
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
103-288 2.87e-08

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: 53.13  E-value: 2.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALEN-FHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMT--SDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRI 179
Cdd:cd08418   13 TLMPAVINrFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGtlPDEMYLKELISEPLFESDFVVVARKDHPLQGARSL 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 180 TPEELASETLliyPVQR-SRLDVWRHFLQPAGVSPSLKSVDNTLLLIQ-MVAARMGIAALPHWVVESFERQGLVVTKTLG 257
Cdd:cd08418   93 EELLDASWVL---PGTRmGYYNNLLEALRRLGYNPRVAVRTDSIVSIInLVEKADFLTILSRDMGRGPLDSFRLITIPVE 169
                        170       180       190
                 ....*....|....*....|....*....|..
gi 519083138 258 EGLWSRLYAAV-RDGEQRQPITEAFIRSARNH 288
Cdd:cd08418  170 EPLPSADYYLIyRKKSRLTPLAEQLVELFRRY 201
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
17-238 3.69e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 53.92  E-value: 3.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQT---RLRI 93
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQAlsgQVSI 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  94 AIECHSCIQWLT-PALENFHKNWPQVEMDF--KSGVTFDPQpaLQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPD 170
Cdd:PRK11233  96 GLAPGTAASSLTmPLLQAVRAEFPGIVLYLheNSGATLNEK--LMNGQLDMAVIYEHSPVAGLSSQPLLKEDLFLVGTQD 173
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 519083138 171 HPlaaKTRITPEELASETLL---IYPVQRSRLDvwRHFLQpAGVSPSLKS-VDNTLLLIQMVAARMGIAALP 238
Cdd:PRK11233 174 CP---GQSVDLAAVAQMNLFlprDYSAVRLRVD--EAFSL-RRLTAKVIGeIESIATLTAAIASGMGVTVLP 239
PRK09801 PRK09801
LysR family transcriptional regulator;
5-204 4.50e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 53.50  E-value: 4.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ----ISQAL 80
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQyqrlVDDVT 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  81 QACNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKsgvTFDPQPALQQGELDL-VMTSDILPrsglhyspmf 159
Cdd:PRK09801  89 QIKTRPEGM-IRIGCSFGFGRSHIAPAITELMRNYPELQVHFE---LFDRQIDLVQDNIDLdIRINDEIP---------- 154
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 519083138 160 DYEVRlvlapdHPLAAKTRITPEelASETLLIYPVQRSRLDVWRH 204
Cdd:PRK09801 155 DYYIA------HLLTKNKRILCA--APEYLQKYPQPQSLQELSRH 191
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
22-190 8.70e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 52.72  E-value: 8.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  22 AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI-------SQALQACNEPqqtrLRIA 94
Cdd:PRK11151  21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkemaSQQGETMSGP----LHIG 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  95 IechscIQWLTPAL-----ENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:PRK11151  97 L-----IPTVGPYLlphiiPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLFDEPMLLAVYE 171
                        170       180
                 ....*....|....*....|.
gi 519083138 170 DHPLAAKTRITPEELASETLL 190
Cdd:PRK11151 172 DHPWANRDRVPMSDLAGEKLL 192
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
134-281 1.18e-07

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: 51.35  E-value: 1.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 134 LQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELASETLLIypvqR-----SRLDVWRHFlQP 208
Cdd:cd08419   44 LADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREPFLL----RepgsgTRLAMERFF-AE 118
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 519083138 209 AGVSPSLKSVDNTLLLI-QMVAARMGIAALP-HWVVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPITEAF 281
Cdd:cd08419  119 HGVTLRVRMELGSNEAIkQAVMAGLGLSVLSlHTLALELATGRLAVLDVEGFPIRRQWYVVHRKGKRLSPAAQAF 193
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
7-173 2.04e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 51.57  E-value: 2.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLpQISQalQACN-- 84
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL-RFND--EACSsl 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  85 --EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDfksgVTFDPQP----ALQQGELDLVMTS---DILPRSGLHY 155
Cdd:PRK15092  93 mySNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALD----VRVKRNAfmmeMLESQEVDLAVTThrpSSFPALNLRT 168
                        170
                 ....*....|....*....
gi 519083138 156 SPMFDY-EVRLVLAPDHPL 173
Cdd:PRK15092 169 SPTLWYcAAEYVLQKGEPI 187
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
2-186 2.75e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 51.23  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ---ISQ 78
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQaveIEQ 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  79 ALQACNepqqTRLRIAieCHSCI-QWLTPA-LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYS 156
Cdd:PRK10837  83 LFREDN----GALRIY--ASSTIgNYILPAmIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156
                        170       180       190
                 ....*....|....*....|....*....|
gi 519083138 157 PMFDYEVRLVLAPDHPLAAKTrITPEELAS 186
Cdd:PRK10837 157 PWLEDELVVFAAPDSPLARGP-VTLEQLAA 185
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-108 7.94e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 49.67  E-value: 7.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ--- 78
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESnla 90
                         90       100       110
                 ....*....|....*....|....*....|
gi 519083138  79 ALQACNEPQQTRLRIAiECHSCIQWLTPAL 108
Cdd:PRK10082  91 ELRGGSDYAQRKIKIA-AAHSLSLGLLPSI 119
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
90-257 8.51e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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: 176158  Cd Length: 221  Bit Score: 48.94  E-value: 8.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMT--SDILPRsgLHYSPMFDYEVRLVL 167
Cdd:cd08469    1 SFVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGifEQIPPR--FRRRTLFDEDEVWVM 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 168 APDHPlAAKTRITPEELA---------------------SETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLI 225
Cdd:cd08469   79 RKDHP-AARGALTIETLAryphivvslggeeegavsgfiSERGLARQTEMFDRRALEEAFRESGLVPRVAvTVPHALAVP 157
                        170       180       190
                 ....*....|....*....|....*....|..
gi 519083138 226 QMVAARMGIAALPHWVVESFERQGLVVTKTLG 257
Cdd:cd08469  158 PLLADSDMLALLPRSLARAFAERGGLVMKEPP 189
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
107-283 8.57e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 48.80  E-value: 8.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 107 ALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELAS 186
Cdd:cd08448   18 ILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLRELAG 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 187 ETLLIYPvqrsrldvwRHF-----------LQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPhwvvESFERQGL--VV 252
Cdd:cd08448   98 EPFVLFS---------REVspdyydqiialCMDAGFHPKIRhEVRHWLTVVALVAAGMGVALVP----RSLARAGLagVR 164
                        170       180       190
                 ....*....|....*....|....*....|..
gi 519083138 253 TKTL-GEGLWSRLYAAVRDGEQrQPITEAFIR 283
Cdd:cd08448  165 FLPLkGATQRSELYAAWKASAP-NPALQAFLA 195
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
101-252 1.01e-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: 48.36  E-value: 1.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPAL-ENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLaAKTRI 179
Cdd:cd08417   11 EALLLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPL-AGGPL 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 519083138 180 TPEE-LASETLLIYPVQRSRLDVwRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWVVESF-ERQGLVV 252
Cdd:cd08417   90 TLEDyLAAPHVLVSPRGRGHGLV-DDALAELGLSRRVAlTVPHFLAAPALVAGTDLIATVPRRLAEALaERLGLRV 164
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-283 1.17e-06

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.46  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  90 RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAP 169
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 170 DHPLAAKTRITPEELASETLLIYPVQRSrldvWRHFLQPA----GVSPSLKSVDNTL-LLIQMVAARMGIAALPHWVVES 244
Cdd:cd08426   81 GHPLARQPSVTLAQLAGYPLALPPPSFS----LRQILDAAfaraGVQLEPVLISNSIeTLKQLVAAGGGISLLTELAVRR 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 519083138 245 FERQGLVVTKTLGE--GLWSRLYAAVRDGEQRQPITEAFIR 283
Cdd:cd08426  157 EIRRGQLVAVPLADphMNHRQLELQTRAGRQLPAAASAFLQ 197
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
91-193 1.56e-06

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


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 48.03  E-value: 1.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  91 LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGV---TFDpqpALQQGELDLVM-TSDILPRSGLHYSPMFDYEVRLV 166
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVlggTWD---ALASGRADLVIgATGELPPGGVKTRPLGEVEFVFA 78
                         90       100
                 ....*....|....*....|....*..
gi 519083138 167 LAPDHPLAAktriTPEELASETLLIYP 193
Cdd:cd08431   79 VAPNHPLAK----LDGPLDASAIKQYP 101
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
104-200 1.59e-06

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like 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. 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 48.00  E-value: 1.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPR-SGLHYSPMFDYEvRLVLAP-DHPLAAKTRITP 181
Cdd:cd08413   15 LPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDhPDLVTLPCYRWN-HCVIVPpGHPLADLGPLTL 93
                         90       100
                 ....*....|....*....|..
gi 519083138 182 EELASETLLIYP---VQRSRLD 200
Cdd:cd08413   94 EDLAQYPLITYDfgfTGRSSID 115
leuO PRK09508
leucine transcriptional activator; Reviewed
22-248 1.87e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 48.87  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  22 AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTpqgeillQLANQVLPQISQALQ--------ACNEPQQ-TRL- 91
Cdd:PRK09508  42 AAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT-------ARARQLFGPVRQALQlvqnelpgSGFEPESsERVf 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  92 RIAIeCHSCIQWLTPALEN-FHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPD 170
Cdd:PRK09508 115 NLCI-CSPLDIRLTSQIYNrIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTSVPLFKDELVLVASKN 193
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 171 HPLAAKTrITPEELASETLLIYpvqrsRLDVWRHFLQPAGVSP-----------SLKSVDNTLLLIQMVAarmgIAalPH 239
Cdd:PRK09508 194 HPRIKGP-ITEEQLYNEQHAVV-----SLDRFASFSQPWYDTVdkqasiayqgtALSSVLNVVSQTHLVA----IA--PR 261

                 ....*....
gi 519083138 240 WVVESFERQ 248
Cdd:PRK09508 262 WLAEEFAES 270
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
107-283 3.86e-06

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: 46.79  E-value: 3.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 107 ALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLV-MTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEELA 185
Cdd:cd08451   19 LIRRFREAYPDVELTLEEANTAELLEALREGRLDAAfVRPPVARSDGLVLELLLEEPMLVALPAGHPLARERSIPLAALA 98
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 186 SETLLIYPVQRSRL---DVWRHFLQpAGVSPSLKSVDNTLL-LIQMVAARMGIAALPHwVVESFERQGLVVTKTLGEGLW 261
Cdd:cd08451   99 DEPFILFPRPVGPGlydAIIAACRR-AGFTPRIGQEAPQMAsAINLVAAGLGVSIVPA-SMRQLQAPGVVYRPLAGAPLT 176
                        170       180
                 ....*....|....*....|..
gi 519083138 262 SRLYAAVRDGEqRQPITEAFIR 283
Cdd:cd08451  177 APLALAYRRGE-RSPAVRNFIA 197
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
101-252 8.37e-06

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 45.75  E-value: 8.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPALENFHKNWPQVEMDFKSGVT-FDpqpaLQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDhpLAAKTRI 179
Cdd:cd08481   12 TRWLIPRLPDFLARHPDITVNLVTRDEpFD----FSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPA--LLAGRAL 85
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 519083138 180 -TPEELASETLLiypVQRSRLDVWRHFLQPAGVS----PSLKSVDNTLLLIQMVAARMGIAALPHWVVE-SFERQGLVV 252
Cdd:cd08481   86 aAPADLAHLPLL---QQTTRPEAWRDWFEEVGLEvptaYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEeELARGRLVV 161
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
102-283 1.62e-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: 176113  Cd Length: 198  Bit Score: 44.82  E-value: 1.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 102 QWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITP 181
Cdd:cd08421   13 EFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAF 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 182 EELASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK----SVDNtllLIQMVAARMGIAALPHWVVESFERQGLVVTKTLG 257
Cdd:cd08421   93 ADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRvqvsSFDA---VCRMVAAGLGIGIVPESAARRYARALGLRVVPLD 169
                        170       180
                 ....*....|....*....|....*...
gi 519083138 258 EGlWS--RLYAAVRDGEQRQPITEAFIR 283
Cdd:cd08421  170 DA-WArrRLLLCVRSFDALPPAARALVD 196
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
104-251 4.84e-05

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: 43.50  E-value: 4.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGvTFDPQ-PALQQGELD--LVMTSDI--LPrSGLHYSPMFDYEVRLVLAPDHPLAAKTR 178
Cdd:cd08453   15 LPELVRRFREAYPDVELQLREA-TSDVQlEALLAGEIDagIVIPPPGasAP-PALAYRPLLSEPLVLAVPAAWAAEGGAP 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 179 ITPEELASETLLIYP--VQRSRLDVWRHFLQPAGVSPSLKSVdntllLIQM------VAARMGIAalphWVVES---FER 247
Cdd:cd08453   93 LALAAVAAEPLVIFPrrIAPAFHDAVTGYYRAAGQTPRIAQE-----AIQMqtiislVSAGMGVA----LVPASlrnLAR 163

                 ....
gi 519083138 248 QGLV 251
Cdd:cd08453  164 PGVV 167
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
103-252 5.87e-05

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 43.13  E-value: 5.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALENFHKNWPQVEMDFKSgvtfdpqpalQQGELDLVmtsdilpRSGLHYSPMFD-------YEVRLVLAPDHPL-- 173
Cdd:cd08484   14 WLLPRLAEFRQLHPFIDLRLST----------NNNRVDIA-------AEGLDFAIRFGegawpgtDATRLFEAPLSPLct 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 174 --AAKTRITPEELASETLLiypvqRS-RLDVWRHFLQPAGVSPSLKS---VDNTLLLIQMVAARMGIAALPHWVVESFER 247
Cdd:cd08484   77 peLARRLSEPADLANETLL-----RSyRADEWPQWFEAAGVPPPPINgpvFDSSLLMVEAALQGAGVALAPPSMFSRELA 151

                 ....*
gi 519083138 248 QGLVV 252
Cdd:cd08484  152 SGALV 156
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-116 7.20e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 43.47  E-value: 7.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  22 AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQ-TRLRIAI----- 95
Cdd:PRK03601  21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQhNELSIGAsaslw 100
                         90       100
                 ....*....|....*....|.
gi 519083138  96 EChsciqWLTPALENFHKNWP 116
Cdd:PRK03601 101 EC-----MLTPWLGRLYQNQE 116
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
101-238 9.75e-05

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


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 42.53  E-value: 9.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPALENFHKNWPQVEMDFKsgvTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDhplAAKTRIT 180
Cdd:cd08487   12 VGWLLPRLAEFRQLHPFIELRLR---TNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPE---IAKRLSH 85
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 519083138 181 PEELASETLLiypvqRS-RLDVWRHFLQPAGVSPSLKS---VDNTLLLIQMVAARMGIAALP 238
Cdd:cd08487   86 PADLINETLL-----RSyRTDEWLQWFEAANMPPIKIRgpvFDSSRLMVEAAMQGAGVALAP 142
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
104-215 2.47e-04

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: 41.39  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILP-RSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPE 182
Cdd:cd08443   15 LPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHdYDDLITLPCYHWNRCVVVKRDHPLADKQSISIE 94
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 519083138 183 ELASETLLIYP---VQRSRLDvwrHFLQPAGVSPSL 215
Cdd:cd08443   95 ELATYPIVTYTfgfTGRSELD---TAFNRAGLTPNI 127
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
162-272 2.50e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 41.44  E-value: 2.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 162 EVRLVLA--PDHPLAA-KTRITPEELASETLLIYPVQR--SRLDVWRHFLQPAGVSPS-LKSVDNTLLLIQMVAARMGIA 235
Cdd:cd08445   72 EEPLVVAlpAGHPLAQeKAPLTLAQLADEPLILYPASPrpSFADQVLSLFRDHGLRPRvIQEVRELQTALGLVAAGEGVT 151
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 519083138 236 ALPHwVVESFERQGLVVTKTLGEGLWSRLYAAVRDGE 272
Cdd:cd08445  152 LVPA-SVQRLRRDDVVYRPLLDPDATSPIIMSVRAGD 187
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
17-124 5.58e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 41.13  E-value: 5.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQ-QTRLRIAI 95
Cdd:PRK14997  17 GGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQvEPRGIVKL 96
                         90       100       110
                 ....*....|....*....|....*....|.
gi 519083138  96 ECHSCIQ--WLTPALENFHKNWPQVEMDFKS 124
Cdd:PRK14997  97 TCPVTLLhvHIGPMLAKFMARYPDVSLQLEA 127
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
101-237 8.42e-04

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 39.62  E-value: 8.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 101 IQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILP--RSGLHYSPMFDYEVRLVLAPDHPLAAKTR 178
Cdd:cd08437   12 NYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPleNSALHSKIIKTQHFMIIVSKDHPLAKAKK 91
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 179 ITPEELASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIAAL 237
Cdd:cd08437   92 VNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPnIVYRTNDIHILKSMVRENVGIGFL 151
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
166-252 8.97e-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: 39.71  E-value: 8.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 166 VLAPDHPLAAKTRITPEELASETLLIYPVQ---RSRLDvwRHFlQPAGVSPSLK-SVDNTLLLIQMVAARMGIAALPHWV 241
Cdd:cd08456   77 VLPPGHRLAVKKVLTPSDLEGEPFISLARTdgtRQRVD--ALF-EQAGVKRRIVvETSYAATICALVAAGVGVSVVNPLT 153
                         90
                 ....*....|.
gi 519083138 242 VESFERQGLVV 252
Cdd:cd08456  154 ALDYAAAGLVV 164
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
5-56 1.16e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 40.04  E-value: 1.16e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 519083138   5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPL 56
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTL 58
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
103-252 1.28e-03

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 39.31  E-value: 1.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 103 WLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLVMTSDILP-RSGLHYSPMFDYEVRLVLAPDHPLAAKTRITP 181
Cdd:cd08482   14 WLIPRLPAFQAALPDIDLQLSAS---DGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSLAPTVPLRQAP 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 519083138 182 EE-LASETLLiypVQRSRLDVWRHFLQPAGVSPSL----KSVDNTLLLIQMVAARMGIAALPHWVVESFERQGLVV 252
Cdd:cd08482   91 AAaLLGAPLL---HTRSRPQAWPDWAAAQGLAPEKlgtgQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLV 163
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
104-253 2.01e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 38.76  E-value: 2.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDfksgVTFDPQPALQQGE-LDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPE 182
Cdd:cd08476   14 LLPVLAAFMQRYPEIELD----LDFSDRLVDVIDEgFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHGTPETPA 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 519083138 183 ELASETLLIYPVQRS-RLDVWRHFLQPAGVSPSLKSV---DNTLLLIQMVAARMGIAALPHWVVESFERQGLVVT 253
Cdd:cd08476   90 DLAEHACLRYRFPTTgKLEPWPLRGDGGDPELRLPTAlvcNNIEALIEFALQGLGIACLPDFSVREALADGRLVT 164
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
104-243 2.40e-03

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 38.33  E-value: 2.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFKSGvtfDPQPALQQ---GELDLVMTS--DILPrSGLHYSPMFDyeVRLVL-APDHPLAAKT 177
Cdd:cd08430   15 LPPILERFRAQHPQVEIKLHTG---DPADAIDKvlnGEADIAIAArpDKLP-ARLAFLPLAT--SPLVFiAPNIACAVTQ 88
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 519083138 178 RITPEELASETL-LIYP---VQRSRLDVWrhfLQPAGVSPSLKS-VDNTLLLIQMVAARMGIAALPHWVVE 243
Cdd:cd08430   89 QLSQGEIDWSRLpFILPergLARERLDQW---FRRRGIKPNIYAqVAGHEAIVSMVALGCGVGIVPELVLD 156
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
104-238 9.66e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 36.44  E-value: 9.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519083138 104 LTPALENFHKNWPQVEMDFksgVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHpLAAKTR-ITPE 182
Cdd:cd08477   16 LTPALAEYLARYPDVRVDL---VLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY-LARHGTpTTPE 91
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 519083138 183 ELASETLLIYPVQRSRlDVWrHFLQPAG-----VSPSLkSVDNTLLLIQMVAARMGIAALP 238
Cdd:cd08477   92 DLARHECLGFSYWRAR-NRW-RLEGPGGevkvpVSGRL-TVNSGQALRVAALAGLGIVLQP 149
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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