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Conserved domains on  [gi|2198236249|ref|WP_239509324|]
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MULTISPECIES: LysR family transcriptional regulator [Citrobacter]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-155 2.82e-37

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 2.82e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAE 80
Cdd:COG0583    13 AEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGT 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2198236249  81 LRIGLTHLYQNYF-KALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAV 155
Cdd:COG0583    93 LRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 80-277 6.21e-17

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: 76.87  E-value: 6.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTH-LYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVINK 158
Cdd:cd05466     1 TLRIGASPsIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 159 KclpDPPANPYNYT--ALAEMPLVLLHRakDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSSEV 236
Cdd:cd05466    81 D---HPLAKRKSVTlaDLADEPLILFER--GSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGL-GIALLPESAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2198236249 237 DADKLSQCYVVDVFPSPQIFYPALVKLPSMPYLPALMDIIA 277
Cdd:cd05466   155 EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-155 2.82e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 2.82e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAE 80
Cdd:COG0583    13 AEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGT 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2198236249  81 LRIGLTHLYQNYF-KALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAV 155
Cdd:COG0583    93 LRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 2-234 3.47e-22

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 93.48  E-value: 3.47e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAG--FFLYRKGCeiLRQVEDTARETTDIAQKNRA 79
Cdd:PRK11242   14 EHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGevYLRYARRA--LQDLEAGRRAIHDVADLSRG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTHLYQNYFKALLME-VYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVINK 158
Cdd:PRK11242   92 SLRLAMTPTFTAYLIGPLIDaFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVVGR 171

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2198236249 159 KclpDPPA---NPYNYTALAEMPLVLLhrAKDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGlEAATLLPSS 234
Cdd:PRK11242  172 H---HPLAarrKALTLDELADEPLVLL--SAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG-RLATLLPAA 244
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-49 5.00e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.88  E-value: 5.00e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAG 49
Cdd:pfam00126  11 AETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 80-277 6.21e-17

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: 76.87  E-value: 6.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTH-LYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVINK 158
Cdd:cd05466     1 TLRIGASPsIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 159 KclpDPPANPYNYT--ALAEMPLVLLHRakDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSSEV 236
Cdd:cd05466    81 D---HPLAKRKSVTlaDLADEPLILFER--GSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGL-GIALLPESAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2198236249 237 DADKLSQCYVVDVFPSPQIFYPALVKLPSMPYLPALMDIIA 277
Cdd:cd05466   155 EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 78-239 3.61e-14

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: 69.63  E-value: 3.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  78 RAELRIGLTHLYQNYFKA-LLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVi 156
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPpLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLV- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 157 nkkCLPDPP---ANPYNYTALAEMPLVLLHRakDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPS 233
Cdd:pfam03466  80 ---APPDHPlarGEPVSLEDLADEPLILLPP--GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGL-GIALLPR 153


                  ....*.
gi 2198236249 234 SEVDAD 239
Cdd:pfam03466 154 SAVARE 159
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 80-225 9.80e-07

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 48.26  E-value: 9.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTHLYQNYF-KALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSF--DPIKLVavi 156
Cdd:cd08420     1 TLRIGASTTIGEYLlPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFaeDELVLV--- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249 157 nkkCLPD-PPANPYNYTA--LAEMPLVLlhRAKDSGTYEMLMDLFRKSGVS---AKVIMHITQPGVILDWLESGL 225
Cdd:cd08420    78 ---VPPDhPLAGRKEVTAeeLAAEPWIL--REPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGL 147
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-155 2.82e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 2.82e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAE 80
Cdd:COG0583    13 AEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGT 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2198236249  81 LRIGLTHLYQNYF-KALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAV 155
Cdd:COG0583    93 LRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 2-234 3.47e-22

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 93.48  E-value: 3.47e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAG--FFLYRKGCeiLRQVEDTARETTDIAQKNRA 79
Cdd:PRK11242   14 EHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGevYLRYARRA--LQDLEAGRRAIHDVADLSRG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTHLYQNYFKALLME-VYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVINK 158
Cdd:PRK11242   92 SLRLAMTPTFTAYLIGPLIDaFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVVGR 171

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2198236249 159 KclpDPPA---NPYNYTALAEMPLVLLhrAKDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGlEAATLLPSS 234
Cdd:PRK11242  172 H---HPLAarrKALTLDELADEPLVLL--SAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG-RLATLLPAA 244
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 4-234 4.56e-18

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 82.42  E-value: 4.56e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   4 GSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK11233   16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  84 GLT--HLYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIqrpYRSEGFDYVSFDPI---KLVAVink 158
Cdd:PRK11233   96 GLApgTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVI---YEHSPVAGLSSQPLlkeDLFLV--- 169

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2198236249 159 kCLPDPPANPYNYTALAEMPLVLlhrAKDSGTYEMLMD-LFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSS 234
Cdd:PRK11233  170 -GTQDCPGQSVDLAAVAQMNLFL---PRDYSAVRLRVDeAFSLRRLTAKVIGEIESIATLTAAIASGM-GVTVLPES 241
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-49 5.00e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.88  E-value: 5.00e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAG 49
Cdd:pfam00126  11 AETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-133 1.18e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.22  E-value: 1.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   3 QGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELR 82
Cdd:CHL00180   19 EGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRGTLI 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2198236249  83 IGLTHLYQNYFKALLMEVYRRN-PDTAINISVTDSSHLETLLTEGGIDIALI 133
Cdd:CHL00180   99 IGASQTTGTYLMPRLIGLFRQRyPQINVQLQVHSTRRIAWNVANGQIDIAIV 150
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 80-277 6.21e-17

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: 76.87  E-value: 6.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTH-LYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVINK 158
Cdd:cd05466     1 TLRIGASPsIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 159 KclpDPPANPYNYT--ALAEMPLVLLHRakDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSSEV 236
Cdd:cd05466    81 D---HPLAKRKSVTlaDLADEPLILFER--GSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGL-GIALLPESAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2198236249 237 DADKLSQCYVVDVFPSPQIFYPALVKLPSMPYLPALMDIIA 277
Cdd:cd05466   155 EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 78-239 3.61e-14

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: 69.63  E-value: 3.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  78 RAELRIGLTHLYQNYFKA-LLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVi 156
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPpLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLV- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 157 nkkCLPDPP---ANPYNYTALAEMPLVLLHRakDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPS 233
Cdd:pfam03466  80 ---APPDHPlarGEPVSLEDLADEPLILLPP--GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGL-GIALLPR 153


                  ....*.
gi 2198236249 234 SEVDAD 239
Cdd:pfam03466 154 SAVARE 159
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-132 3.27e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 68.46  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   3 QG-SVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRI-EPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAE 80
Cdd:PRK12684   15 QNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGN 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2198236249  81 LRIGLTHLYQNY-FKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIAL 132
Cdd:PRK12684   95 LTIATTHTQARYaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-194 2.23e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 65.86  E-value: 2.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQvedtARETTDIAQKNRAE 80
Cdd:PRK10837   15 LKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEIEQLFREDNGA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  81 LRIGLTHLYQNYFKALLMEVYRRN-PDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVinkk 159
Cdd:PRK10837   91 LRIYASSTIGNYILPAMIARYRRDyPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLEDELVVF---- 166

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2198236249 160 CLPDPP--ANPYNYTALAEMPLVLlhRAKDSGTYEML 194
Cdd:PRK10837  167 AAPDSPlaRGPVTLEQLAAAPWIL--RERGSGTREIV 201
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 2-278 5.22e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 64.79  E-value: 5.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRaEL 81
Cdd:PRK09906   14 EELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQEDR-QL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  82 RIGLTHLYQ-NYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVInkkc 160
Cdd:PRK09906   93 TIGFVPSAEvNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPLVVVL---- 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 161 lpdpPANpYNYTALAEMPLVLLH-------RAKDSGT-YEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLP 232
Cdd:PRK09906  169 ----PVD-HPLAHEKEITAAQLDgvnfistDPAYSGSlAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL-GCTIIP 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249 233 SsevdadklsqcYVVDVFPSPQIFYPALVKLPSMPYL---------PALMDIIAQ 278
Cdd:PRK09906  243 G-----------YMNNFNTGQVVFRPLAGNVPSIALLmawkkgemkPALRDFIAI 286
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 6-87 1.14e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 61.16  E-value: 1.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   6 VSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEP-TEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRIG 84
Cdd:PRK12682   19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIA 98


                  ...
gi 2198236249  85 LTH 87
Cdd:PRK12682   99 TTH 101
PRK09791 PRK09791
LysR family transcriptional regulator;
3-76 1.42e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 60.55  E-value: 1.42e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2198236249   3 QGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEdTAREttDIAQK 76
Cdd:PRK09791   19 QGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELR-AAQE--DIRQR 89
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 6-225 2.22e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 60.06  E-value: 2.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   6 VSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEP-TEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRIG 84
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  85 LTHLYQNYfkAL------LMEVYrrnPDTAINISVTDSSHLETLLTEGGIDI-----ALIQRPyrsegfDYVSFDPIKLV 153
Cdd:PRK12683   99 TTHTQARY--ALpkvvrqFKEVF---PKVHLALRQGSPQEIAEMLLNGEADIgiateALDREP------DLVSFPYYSWH 167

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2198236249 154 -AVINKKCLPDPPANPYNYTALAEMPLVLLH-----RAKDSGTyemlmdlFRKSGVSAKVIMHITQPGVILDWLESGL 225
Cdd:PRK12683  168 hVVVVPKGHPLTGRENLTLEAIAEYPIITYDqgftgRSRIDQA-------FAEAGLVPDIVLTALDADVIKTYVELGM 238
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 96-248 2.81e-10

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 58.38  E-value: 2.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  96 LLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGfdyVSFDPI---KLVAVINKKCLPDPPAnPYNYT 172
Cdd:cd08433    18 LLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPG---LSTEPLleeDLFLVGPADAPLPRGA-PVPLA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 173 ALAEMPLVLLHRAKdsGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSS----EVDADKLSQCYVVD 248
Cdd:cd08433    94 ELARLPLILPSRGH--GLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGL-GYTILPASavaaEVAAGRLVAAPIVD 170
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 4-106 9.03e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 58.41  E-value: 9.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   4 GSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK11074   17 GSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSI 96

                          90       100
                  ....*....|....*....|....
gi 2198236249  84 GLTHLYQ-NYFKALLMEVYRRNPD 106
Cdd:PRK11074   97 AVDNIVRpDRTRQLIVDFYRHFDD 120
PRK12680 PRK12680
LysR family transcriptional regulator;
5-238 2.16e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 57.32  E-value: 2.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   5 SVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEP-TEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK12680   18 NITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  84 GLTHLYQNY-FKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQ----RPyrSEGFDYVSFDPIKLVAVINK 158
Cdd:PRK12680   98 TTTHTQARFvLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVStaggEP--SAGIAVPLYRWRRLVVVPRG 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 159 KCLPDPPANPyNYTALAEMPLVllhrAKDSGTYEM--LMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSSEV 236
Cdd:PRK12680  176 HALDTPRRAP-DMAALAEHPLI----SYESSTRPGssLQRAFAQLGLEPSIALTALDADLIKTYVRAGL-GVGLLAEMAV 249


                  ..
gi 2198236249 237 DA 238
Cdd:PRK12680  250 NA 251
PRK09986 PRK09986
LysR family transcriptional regulator;
8-234 5.99e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 55.88  E-value: 5.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   8 QAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRIGL-- 85
Cdd:PRK09986   26 RAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEIGIvg 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  86 THLYqnyfkALLMEVYRR----NPDTAINISVTDSSHLETLLTEGGIDIAlIQR---PYRSEGFDYV-----SFdpikLV 153
Cdd:PRK09986  106 TALW-----GRLRPAMRHflkeNPNVEWLLRELSPSMQMAALERRELDAG-IWRmadLEPNPGFTSRrlhesAF----AV 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 154 AVINKKCLPDPPANPynYTALAEMPLVLLHRAKdSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPS 233
Cdd:PRK09986  176 AVPEEHPLASRSSVP--LKALRNEYFITLPFVH-SDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGI-GITLLPD 251


                  .
gi 2198236249 234 S 234
Cdd:PRK09986  252 S 252
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 80-234 9.64e-09

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: 54.05  E-value: 9.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTH-LYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVAVink 158
Cdd:cd08414     1 RLRIGFVGsALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVA--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 159 kcLPD----------PPAnpynytALAEMPLVLLHRAKDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAA 228
Cdd:cd08414    78 --LPAdhplaaresvSLA------DLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGL-GV 148


                  ....*.
gi 2198236249 229 TLLPSS 234
Cdd:cd08414   149 ALVPAS 154
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 80-234 1.17e-08

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: 53.71  E-value: 1.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGL-----THLyqnyFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSFDPIKLVA 154
Cdd:cd08438     1 HLRLGLpplggSLL----FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 155 VInkkclpdPPANPY------NYTALAEMPLVLLHraKDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAA 228
Cdd:cd08438    77 VL-------PRGHPLagrktvSLADLADEPFILFN--EDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGL-GV 146


                  ....*.
gi 2198236249 229 TLLPSS 234
Cdd:cd08438   147 ALLPRS 152
cysB PRK12681
HTH-type transcriptional regulator CysB;
6-87 1.42e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 54.90  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   6 VSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRI-EPTEAGFFLYRKGCEILRQVED---TARETTDiaqKNRAEL 81
Cdd:PRK12681   19 VSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESiksVAGEHTW---PDKGSL 95


                  ....*.
gi 2198236249  82 RIGLTH 87
Cdd:PRK12681   96 YIATTH 101
PRK09801 PRK09801
LysR family transcriptional regulator;
4-251 2.37e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 54.27  E-value: 2.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   4 GSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK09801   21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEGMIRI 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  84 GLTHLY-QNYFKALLMEVYRRNPDTAINISVTDSshlETLLTEGGIDIALiqrPYRSEGFDYVsfdpIKLVAVINKKCLP 162
Cdd:PRK09801  101 GCSFGFgRSHIAPAITELMRNYPELQVHFELFDR---QIDLVQDNIDLDI---RINDEIPDYY----IAHLLTKNKRILC 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 163 DPPANPYNYT---ALAEMP----LVLLHRAKDSGTYEMLMDLFRKsgvSAKVIMHITQPG--VILDWlesGLEAATLLPS 233
Cdd:PRK09801  171 AAPEYLQKYPqpqSLQELSrhdcLVTKERDMTHGIWELGNGQEKK---SVKVSGHLSSNSgeIVLQW---ALEGKGIMLR 244

                         250
                  ....*....|....*....
gi 2198236249 234 SEVDADK-LSQCYVVDVFP 251
Cdd:PRK09801  245 SEWDVLPfLESGKLVQVLP 263
PRK10341 PRK10341
transcriptional regulator TdcA;
4-132 1.19e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.17  E-value: 1.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   4 GSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK10341   22 GSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSF 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2198236249  84 GLTHLYQNYFKALLMEVYRR-NPDTAINISVTDSSHLETLLTEGGIDIAL 132
Cdd:PRK10341  102 GFPSLIGFTFMSDMINKFKEvFPKAQVSMYEAQLSSFLPAIRDGRLDFAI 151
cbl PRK12679
HTH-type transcriptional regulator Cbl;
5-132 2.96e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.96  E-value: 2.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   5 SVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNR-IEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI 83
Cdd:PRK12679   18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTI 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2198236249  84 GLTHLYQNYFKALLMEVYRRN-PDTAINISVTDSSHLETLLTEGGIDIAL 132
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELfPEVRLELIQGTPQEIATLLQNGEADIGI 147
nhaR PRK11062
transcriptional activator NhaR; Provisional
 3-54 5.13e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 50.01  E-value: 5.13e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2198236249   3 QGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYR 54
Cdd:PRK11062   18 EGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFR 69
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-126 6.57e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.58  E-value: 6.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVrRGNRIEPTEAGFFLYRKgceiLRQV---EDTARETTDIAQKNR 78
Cdd:PRK13348   15 ETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLV-RGRPCRPTPAGQRLLRH----LRQVallEADLLSTLPAERGSP 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2198236249  79 AELRIGLthlyqN------YFKALLMEVYRRnPDTAINISVTDSSHLETLLTEG 126
Cdd:PRK13348   90 PTLAIAV-----NadslatWFLPALAAVLAG-ERILLELIVDDQDHTFALLERG 137
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 80-225 9.80e-07

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 48.26  E-value: 9.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTHLYQNYF-KALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRSEGFDYVSF--DPIKLVavi 156
Cdd:cd08420     1 TLRIGASTTIGEYLlPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFaeDELVLV--- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249 157 nkkCLPD-PPANPYNYTA--LAEMPLVLlhRAKDSGTYEMLMDLFRKSGVS---AKVIMHITQPGVILDWLESGL 225
Cdd:cd08420    78 ---VPPDhPLAGRKEVTAeeLAAEPWIL--REPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGL 147
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
7-87 3.11e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 47.74  E-value: 3.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   7 SQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARET---TDIAQKnraELRI 83
Cdd:PRK10082   29 SQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELrggSDYAQR---KIKI 105


                  ....
gi 2198236249  84 GLTH 87
Cdd:PRK10082  106 AAAH 109
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-145 4.36e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 47.29  E-value: 4.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAG--FFLYRKGCEILRQVEDTARETTDIAQKNR 78
Cdd:PRK14997   14 VEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGqtFYEHCKAMLVEAQAAQDAIAALQVEPRGI 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2198236249  79 AELRIGLTHLYQnYFKALLMEVYRRNPDTAINISVTDSshlETLLTEGGIDIALIQRPYRSEGFDYV 145
Cdd:PRK14997   94 VKLTCPVTLLHV-HIGPMLAKFMARYPDVSLQLEATNR---RVDVVGEGVDVAIRVRPRPFEDSDLV 156
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
1-55 5.82e-06

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 46.97  E-value: 5.82e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRK 55
Cdd:PRK15243   16 METGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRK 70
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-132 7.33e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 46.37  E-value: 7.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   5 SVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVedtaRETTD--IAQKNRAELR 82
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL----AEATRklRARSAKGALT 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249  83 IGLthlyQNYFKAL-----LMEVYRRNPDTAINISVTDSshLETLLTEgGIDIAL 132
Cdd:PRK11139   98 VSL----LPSFAIQwlvprLSSFNEAHPDIDVRLKAVDR--LEDFLRD-DVDVAI 145
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-111 1.14e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.91  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGfFLYRKGC-EILRQVEDTARETTDIAQKNRA 79
Cdd:PRK10632   14 VEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG-RIYYQGCrRMLHEVQDVHEQLYAFNNTPIG 92

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2198236249  80 ELRIGLTH-LYQNYFKALLMEVYRRNPDTAINI 111
Cdd:PRK10632   93 TLRIGCSStMAQNVLAGLTAKMLKEYPGLSVNL 125
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-132 1.56e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 45.37  E-value: 1.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRkgcEILRQ---VEDTARETTDIAQKN 77
Cdd:PRK11013   16 MTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFE---EVQRSyygLDRIVSAAESLREFR 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2198236249  78 RAELRIG-LTHLYQNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIAL 132
Cdd:PRK11013   93 QGQLSIAcLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGL 148
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 9-63 4.57e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 44.25  E-value: 4.57e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2198236249   9 AAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQV 63
Cdd:PRK11151   21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREV 75
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
2-112 5.46e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 44.03  E-value: 5.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEI----------LRQVEDTARETT 71
Cdd:PRK10094   15 ETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWlswlesmpseLQQVNDGVERQV 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2198236249  72 DIAQKNRaelriglthLYQNYFKA-LLMEVYRRNPDTAINIS 112
Cdd:PRK10094   95 NIVINNL---------LYNPQAVAqLLAWLNERYPFTQFHIS 127
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
2-64 1.04e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 42.84  E-value: 1.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2198236249   2 EQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLfVRRGNRIEPTEAGfflyRKGCEILRQVE 64
Cdd:PRK03635   15 REGSFERAAQKLHITQSAVSQRIKALEERVGQVL-LVRTQPCRPTEAG----QRLLRHARQVR 72
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-85 2.03e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   4 GSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVedtARETTDIAQKNRAELRI 83
Cdd:PRK15421   17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI---SQALQACNEPQQTRLRI 93


                  ..
gi 2198236249  84 GL 85
Cdd:PRK15421   94 AI 95
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-109 2.37e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.93  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   9 AAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGfflyrkgcEILRQVEDTARETTDIAQKNRA------ELR 82
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG--------ERLLPYAETLMNTWQAAKKEVAhtsqhnELS 92

                          90       100
                  ....*....|....*....|....*...
gi 2198236249  83 IGLT-HLYQNYFKALLMEVYRRNPDTAI 109
Cdd:PRK03601   93 IGASaSLWECMLTPWLGRLYQNQEALQF 120
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-132 3.65e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 41.53  E-value: 3.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249   3 QGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKgceILRQVEDTARETTDIaqKNrAELR 82
Cdd:PRK10086   28 HQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA---LKSSLDTLNQEILDI--KN-QELS 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2198236249  83 IGLThLY------QNYFKALLMEVYRRNPDTAINISV-TDSSHLETllteGGIDIAL 132
Cdd:PRK10086  102 GTLT-VYsrpsiaQCWLVPRLADFTRRYPSISLTILTgNENVNFQR----AGIDLAI 153
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 80-177 8.45e-04

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 39.62  E-value: 8.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  80 ELRIGLTHLY-QNYFKALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRP----------------YRSEGF 142
Cdd:cd08439     1 TLRIGCPDDYaDTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPppgasatilrrsptvwYCAAGY 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2198236249 143 DYVSFDPIKLVavinkkcLPDPPaNPYNYTALAEM 177
Cdd:cd08439    81 ILAPGEPLPLA-------LLDEP-TLDRRAALAAL 107
leuO PRK09508
leucine transcriptional activator; Reviewed
 1-46 2.13e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 38.85  E-value: 2.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2198236249   1 MEQGSVSQAAKSLNMAQPPLSKRIQELEEELQVSLFVRRGNRIEPT 46
Cdd:PRK09508   34 MQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT 79
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-253 2.60e-03

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: 37.97  E-value: 2.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  95 ALLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYRS-EGFDYVSFDPIKLVAVinkkCLPDPP---ANPYN 170
Cdd:cd08436    17 ELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAV----VAPDHPlagRRRVA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249 171 YTALAEMPLVLLHraKDSGTYEMLMDLFRKSGVSAKVIMHITQPGVILDWLESGLeAATLLPSSEVDADklSQCYVVDVF 250
Cdd:cd08436    93 LADLADEPFVDFP--PGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGL-GVALLPASVAARL--PGLAALPLE 167


                  ...
gi 2198236249 251 PSP 253
Cdd:cd08436   168 PAP 170
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
20-153 3.31e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 38.26  E-value: 3.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2198236249  20 LSKRIQELEEELQVSLFVRRGNRIEPTEAGFFLYRKGCEILRQVEDTARETTDIAQKNRAELRI------GLTHLYQnyf 93
Cdd:PRK11716    8 LSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvtaAYSHLPP--- 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2198236249  94 kaLLMEVYRRNPDTAINISVTDSSHLETLLTEGGIDIALIQRPYR-SEGFDYVSFDPIKLV 153
Cdd:PRK11716   85 --ILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETlPASVAFSPIDEIPLV 143
 
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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