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Conserved domains on  [gi|490589123|ref|WP_004454143|]
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LysR family transcriptional regulator [Clostridioides difficile]

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];
1-287 2.36e-42

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKILSP--AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITL 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPpsLARYLLPPLLARFRARHPGVRLELregnSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 155 TCEEILLGVSINHPLSLKDEVylsevsdenfivitkgenyrevidilcesanfkpkiafeSDSPYTIYALIKSLQGVGFI 234
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123 235 CgkSWGLSQDPE---IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFK 287
Cdd:COG0583  202 P--RFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 2.36e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKILSP--AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITL 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPpsLARYLLPPLLARFRARHPGVRLELregnSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 155 TCEEILLGVSINHPLSLKDEVylsevsdenfivitkgenyrevidilcesanfkpkiafeSDSPYTIYALIKSLQGVGFI 234
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123 235 CgkSWGLSQDPE---IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFK 287
Cdd:COG0583  202 P--RFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-282 2.42e-31

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: 115.39  E-value: 2.42e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  95 ILSPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLS 170
Cdd:cd05466    6 ASPSIAAYLLPPLLAAFRQRYPGVELSLveggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 171 LKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICGKSWGLSQDPEIKLL 250
Cdd:cd05466   86 KRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVL 165

                        170       180       190
                 ....*....|....*....|....*....|..
gi 490589123 251 HIKDIEFKRYLNLSWFSENYESKAVLLFKNFL 282
Cdd:cd05466  166 PLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
1-234 3.36e-29

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 112.51  E-value: 3.36e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSG--EVKILSPAAANVLPSLLSNFRKLYPNITFNVSHTLPS----SYKKSDFDLYI--------SSSFTkl 146
Cdd:PRK09986  87 RVEQIGRGEAGriEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSmqmaALERRELDAGIwrmadlepNPGFT-- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 147 nsenSITLTCEEILLGVSINHPLSLKDEVYLSEVSDENFIVITKGE-NYREVIDILCESANFKPKIAFESDSPYTIYALI 225
Cdd:PRK09986 165 ----SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHsDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMV 240


                 ....*....
gi 490589123 226 KSLQGVGFI 234
Cdd:PRK09986 241 SMGIGITLL 249
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 7.54e-29

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 111.55  E-value: 7.54e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKIlspAAANV-----LPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSsfTKLNSEN- 150
Cdd:NF040786  81 EFDRYGKESKGVLRI---GASTIpgqylLPELLKKFKEKYPNVRFKLmisdSIKVIELLLEGEVDIGFTG--TKLEKKRl 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 151 -SITLTCEEILLGVSINHPLS--LKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPK---IAFESDSPYTIYAL 224
Cdd:NF040786 156 vYTPFYKDRLVLITPNGTEKYrmLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVASLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490589123 225 IKSLQGVGFIcgKSWGLS---QDPEIKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYF 286
Cdd:NF040786 236 VEAGLGISVI--SELAAEkevERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKERY 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-287 2.27e-22

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: 91.97  E-value: 2.27e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   90 SGEVKI--LSPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGV 163
Cdd:pfam03466   1 SGRLRIgaPPTLASYLLPPLLARFRERYPDVELELtegnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  164 SINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICgkSWGLSQ 243
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLP--RSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 490589123  244 DPE---IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFK 287
Cdd:pfam03466 159 ELAdgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 2.36e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKILSP--AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITL 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPpsLARYLLPPLLARFRARHPGVRLELregnSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 155 TCEEILLGVSINHPLSLKDEVylsevsdenfivitkgenyrevidilcesanfkpkiafeSDSPYTIYALIKSLQGVGFI 234
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123 235 CgkSWGLSQDPE---IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFK 287
Cdd:COG0583  202 P--RFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-282 2.42e-31

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: 115.39  E-value: 2.42e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  95 ILSPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLS 170
Cdd:cd05466    6 ASPSIAAYLLPPLLAAFRQRYPGVELSLveggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 171 LKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICGKSWGLSQDPEIKLL 250
Cdd:cd05466   86 KRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVL 165

                        170       180       190
                 ....*....|....*....|....*....|..
gi 490589123 251 HIKDIEFKRYLNLSWFSENYESKAVLLFKNFL 282
Cdd:cd05466  166 PLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 100-282 1.82e-29

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: 110.32  E-value: 1.82e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 100 AANVLPSLLSNFRKLYPNITF----NVSHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLSLKDEV 175
Cdd:cd08434   11 GTSLVPDLIRAFRKEYPNVTFelhqGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 176 YLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFIcgKSWGLSQDPEIKLLHIKDI 255
Cdd:cd08434   91 DLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAIL--PEMTLLNPPGVKKIPIKDP 168

                        170       180
                 ....*....|....*....|....*..
gi 490589123 256 EFKRYLNLSWFSENYESKAVLLFKNFL 282
Cdd:cd08434  169 DAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK09986 PRK09986
LysR family transcriptional regulator;
1-234 3.36e-29

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 112.51  E-value: 3.36e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSG--EVKILSPAAANVLPSLLSNFRKLYPNITFNVSHTLPS----SYKKSDFDLYI--------SSSFTkl 146
Cdd:PRK09986  87 RVEQIGRGEAGriEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSmqmaALERRELDAGIwrmadlepNPGFT-- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 147 nsenSITLTCEEILLGVSINHPLSLKDEVYLSEVSDENFIVITKGE-NYREVIDILCESANFKPKIAFESDSPYTIYALI 225
Cdd:PRK09986 165 ----SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHsDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMV 240


                 ....*....
gi 490589123 226 KSLQGVGFI 234
Cdd:PRK09986 241 SMGIGITLL 249
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 7.54e-29

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 111.55  E-value: 7.54e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKIlspAAANV-----LPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSsfTKLNSEN- 150
Cdd:NF040786  81 EFDRYGKESKGVLRI---GASTIpgqylLPELLKKFKEKYPNVRFKLmisdSIKVIELLLEGEVDIGFTG--TKLEKKRl 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 151 -SITLTCEEILLGVSINHPLS--LKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPK---IAFESDSPYTIYAL 224
Cdd:NF040786 156 vYTPFYKDRLVLITPNGTEKYrmLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVASLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490589123 225 IKSLQGVGFIcgKSWGLS---QDPEIKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYF 286
Cdd:NF040786 236 VEAGLGISVI--SELAAEkevERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKERY 298
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-288 1.81e-24

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 100.09  E-value: 1.81e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   3 LLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKEL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  83 QDTSLENSGEVKILSP--AAANVLPSLLSNFRKLYPNIT--FNVSHTLPSSYK--KSDFDLYISSSFTKLNSENSITLTC 156
Cdd:CHL00180  87 EDLKNLQRGTLIIGASqtTGTYLMPRLIGLFRQRYPQINvqLQVHSTRRIAWNvaNGQIDIAIVGGEVPTELKKILEITP 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 157 ---EEILLGVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVID-IL----CESANFkpKIAFESDSPYTIYALIKSL 228
Cdd:CHL00180 167 yveDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDnILiqngIDSKRF--KIEMELNSIEAIKNAVQSG 244

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490589123 229 QGVGFIcgKSWGLSQDPEIKLLH---IKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFKN 288
Cdd:CHL00180 245 LGAAFV--SVSAIEKELELGLLHwikIENITIKRMLSIITNPNRYKSKASETFYNEILTLFNT 305
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-226 4.17e-24

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 98.88  E-value: 4.17e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKI-LSPA-AANVLPSLLSNFRKLYPNITFNVSHT----LPSSYKKSDFDLYISSSFTKLNSENSITL 154
Cdd:PRK11242  81 AIHDVADLSRGSLRLaMTPTfTAYLIGPLIDAFHARYPGITLTIREMsqerIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490589123 155 TCEEILLGVSINHPLSLK-DEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSpytIYALIK 226
Cdd:PRK11242 161 FTETLALVVGRHHPLAARrKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANS---ISAVLE 230
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-287 2.27e-22

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: 91.97  E-value: 2.27e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   90 SGEVKI--LSPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGV 163
Cdd:pfam03466   1 SGRLRIgaPPTLASYLLPPLLARFRERYPDVELELtegnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  164 SINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICgkSWGLSQ 243
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLP--RSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 490589123  244 DPE---IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFLINYFK 287
Cdd:pfam03466 159 ELAdgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-187 1.73e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 89.06  E-value: 1.73e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENS----GEVKIlspAAANVLPSLLSNFRKLYPNITFNVSHTLPS----SYKKSDFDLYISSSFTKLNSENSI 152
Cdd:PRK09906  81 RARKIVQEDRqltiGFVPS---AEVNLLPKVLPMFRLRHPDTLIELVSLITTqqeeKLRRGELDVGFMRHPVYSDEIDYL 157

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490589123 153 TLTCEEILLGVSINHPLSLKDEVYLSEVSDENFIV 187
Cdd:PRK09906 158 ELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFIS 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-62 2.93e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.05  E-value: 2.93e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 490589123    5 HLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGR 62
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-217 4.82e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 85.04  E-value: 4.82e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARME-HITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIV-LNEYGRLFLKRVDSILDLVESS 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 KKELQDTSLENSGEVKILS--PAAANVLPSLLSNFRKLYPNITFNVSHTLPSS----YKKSDFDLYISSSfTKLNSENSI 152
Cdd:PRK12682  81 KRIGDDFSNQDSGTLTIATthTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEiarmVISGEADIGIATE-SLADDPDLA 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490589123 153 TLTCEE--ILLGVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFES-DS 217
Cdd:PRK12682 160 TLPCYDwqHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAiDS 227
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-201 1.00e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 83.97  E-value: 1.00e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   3 LLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDlvesSKKEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLE----QAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  83 QDTSLENSGEVKIL-SPAAAN-VLPSLLSNFRKLYPNI--TFNVSHTLPSSYKKSDFDLYI-----SSSFTKLNSENSIT 153
Cdd:PRK10837  81 EQLFREDNGALRIYaSSTIGNyILPAMIARYRRDYPQLplELSVGNSQDVINAVLDFRVDIgliegPCHSPELISEPWLE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 490589123 154 ltcEEILLGVSINHPLsLKDEVYLSEVSDENFIVITKGENYREVIDIL 201
Cdd:PRK10837 161 ---DELVVFAAPDSPL-ARGPVTLEQLAAAPWILRERGSGTREIVDYL 204
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-246 5.70e-17

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 79.25  E-value: 5.70e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARME-HITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIV-LNEYGRLFLKRVDSILDLVESS 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 KKELQDTSLENSGEVKILS--PAAANVLPSLLSNFRKLYPNITFNVSHTLPSS----YKKSDFDLYIS----SSFTKLns 148
Cdd:PRK12684  81 KRVGKEFAAQDQGNLTIATthTQARYALPAAIKEFKKRYPKVRLSILQGSPTQiaemVLHGQADLAIAteaiADYKEL-- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 149 ensITLTCEEI--LLGVSINHPLSLKDEVYLSEVSdeNFIVITKGENY--REVIDILCESANFKPKI---AFESDspyti 221
Cdd:PRK12684 159 ---VSLPCYQWnhCVVVPPDHPLLERKPLTLEDLA--QYPLITYDFAFagRSKINKAFALRGLKPDIvleAIDAD----- 228

                        250       260
                 ....*....|....*....|....*....
gi 490589123 222 yaLIKSL----QGVGFICgkswGLSQDPE 246
Cdd:PRK12684 229 --VIKTYvelgLGVGIVA----DMAFDPE 251
PRK09791 PRK09791
LysR family transcriptional regulator;
4-118 2.10e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 74.80  E-value: 2.10e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   4 LH-LKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKEL 82
Cdd:PRK09791   7 IHqIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490589123  83 QDTSLENSGEVKILSPA--AANVLPSLLSNFRKLYPNI 118
Cdd:PRK09791  87 RQRQGQLAGQINIGMGAsiARSLMPAVISRFHQQHPQV 124
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-118 8.08e-15

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.95  E-value: 8.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   6 LKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQDT 85
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                         90       100       110
                 ....*....|....*....|....*....|...
gi 490589123  86 SLENSGEVKILSPAAANVLPSLLSNFRKLYPNI 118
Cdd:PRK11139  91 SAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDI 123
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 96-282 2.14e-14

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: 70.28  E-value: 2.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  96 LSPAAANVL-PSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDL------YISSSFtklnseNSITLTCEEILLGVS 164
Cdd:cd08438    6 LPPLGGSLLfAPLLAAFRQRYPNIELELveygGKKVEQAVLNGELDVgitvlpVDEEEF------DSQPLCNEPLVAVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 165 INHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGF----ICGKswg 240
Cdd:cd08438   80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALlprsIAQR--- 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 490589123 241 lsQDPE-IKLLHIKDIEFKRYLNLSWFSENYESKAVLLFKNFL 282
Cdd:cd08438  157 --LDNAgVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-250 6.81e-14

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 70.46  E-value: 6.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYF-QTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKG-RYIVLNEYGRLFLKRVDSILDLVESS 78
Cdd:PRK12683   1 MNFQQLRIIrEAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 KKELQDTSLENSGEVKILS--PAAANVLPSLLSNFRKLYPNITFNVSHTLPSS----YKKSDFDLYISSSftKLNSE-NS 151
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVATthTQARYALPKVVRQFKEVFPKVHLALRQGSPQEiaemLLNGEADIGIATE--ALDREpDL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 152 ITLTCEEI--LLGVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKI---AFESDspytiyaLIK 226
Cdd:PRK12683 159 VSFPYYSWhhVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIvltALDAD-------VIK 231

                        250       260
                 ....*....|....*....|....*...
gi 490589123 227 SL----QGVGFICGKSWGLSQDPEIKLL 250
Cdd:PRK12683 232 TYvelgMGVGIVAAMAYDPQRDTGLVAL 259
PRK10341 PRK10341
transcriptional regulator TdcA;
5-116 8.39e-14

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 70.28  E-value: 8.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   5 HLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQD 84
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEING 90

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490589123  85 TSLENSGEVKILSPA--AANVLPSLLSNFRKLYP 116
Cdd:PRK10341  91 MSSEAVVDVSFGFPSliGFTFMSDMINKFKEVFP 124
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-213 1.04e-12

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 67.23  E-value: 1.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARME-HITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIV-LNEYGRLFLKRVDSILDLVESS 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 KKELQDTSLENSGEVKILSP--AAANVLPSLLSNFRKLYPNITFNVSHTLPS----SYKKSDFDLYISSSFTKLnSENSI 152
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIATThtQARYALPPVIKGFIERYPRVSLHMHQGSPTqiaeAAAKGNADFAIATEALHL-YDDLI 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490589123 153 TLTC----EEILlgVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAF 213
Cdd:PRK12681 160 MLPCyhwnRSVV--VPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVF 222
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-231 3.71e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 65.47  E-value: 3.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLENSGEVKI-LSP--AAANVLPSLLSNFRKLYPNITF----NVSHTLPSSYKKSDFDLYISSSFTKLNSENSIT 153
Cdd:PRK11233  81 AVHNVGQALSGQVSIgLAPgtAASSLTMPLLQAVRAEFPGIVLylheNSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490589123 154 LTCEEILLGVSINHPlslKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGV 231
Cdd:PRK11233 161 LLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGV 235
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 103-282 8.36e-12

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: 62.89  E-value: 8.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 103 VLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDL-YISSSFT--KLNSEnsiTLTCEEILLGVSINHPLSLKDEV 175
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLtignTEEIAERVLDGEIDLgLVEGPVDhpDLIVE---PFAEDELVLVVPPDHPLAGRKEV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 176 YLSEVSDENFIVITKGENYREVIDILCESANF---KPKIAFESDSPYTIYALIKSLQGVGFICGkswgLSQDPEIKL--- 249
Cdd:cd08420   91 TAEELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEAVEAGLGISILSR----LAVRKELELgrl 166

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490589123 250 --LHIKDIEFKRYLNLSWFSENYESKAVLLFKNFL 282
Cdd:cd08420  167 vaLPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-244 1.76e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 63.68  E-value: 1.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARME-HITKASHKLNIAQPALSKTISSLEKELGVQLFDRKG-RYIVLNEYGRLFLKRVDSILDlvESS 78
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILN--EAS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 K-KELQDT-SLENSGEVKILS--PAAANVLPSLLSNFRKLYPNITFNVSHTLPSSykksdfdlyISSSFtkLNSENSITL 154
Cdd:PRK12679  79 NvRRLADLfTNDTSGVLTIATthTQARYSLPEVIKAFRELFPEVRLELIQGTPQE---------IATLL--QNGEADIGI 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 155 TCEEIL----------------LGVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSP 218
Cdd:PRK12679 148 ASERLSndpqlvafpwfrwhhsLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDS 227

                        250       260
                 ....*....|....*....|....*.
gi 490589123 219 YTIYALIKSLQGVGFICGKSWGLSQD 244
Cdd:PRK12679 228 DVIKTYVALGLGIGLVAEQSSGEQEE 253
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 97-234 2.54e-11

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: 61.37  E-value: 2.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  97 SPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLSLK 172
Cdd:cd08414    8 GSALYGLLPRLLRRFRARYPDVELELremtTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAAR 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490589123 173 DEVYLSEVSDENFIVITKGEN--YREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFI 234
Cdd:cd08414   88 ESVSLADLADEPFVLFPREPGpgLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALV 151
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-115 3.75e-11

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 62.38  E-value: 3.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   9 FQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQDTSLE 88
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490589123  89 NSGEVKIlspAAAN-----VLPSLLSNFRKLY 115
Cdd:PRK10082  99 AQRKIKI---AAAHslslgLLPSIISQMPPLF 127
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-232 5.74e-11

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: 60.51  E-value: 5.74e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  93 VKILSPAAANVLPSLLSNFRKLYPNITFNVsHTLPSSY-----KKSDFDLYISSSFTKLNS-ENSITLTCEEILLgVSIN 166
Cdd:cd08456    4 IAVLPALSQSFLPRAIKAFLQRHPDVTISI-HTRDSPTveqwlSAQQCDLGLVSTLHEPPGiERERLLRIDGVCV-LPPG 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123 167 HPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKslQGVG 232
Cdd:cd08456   82 HRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVA--AGVG 145
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-118 7.92e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 60.99  E-value: 7.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  26 NIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQDTSLENSGEVKILSP--AAANV 103
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSvtAAYSH 81

                         90
                 ....*....|....*
gi 490589123 104 LPSLLSNFRKLYPNI 118
Cdd:PRK11716  82 LPPILDRFRAEHPLV 96
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-231 1.85e-10

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: 59.21  E-value: 1.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  92 EVKILSPAAANVLPSLLSNFRKLYPNITFNVSHTLPSSYKKSDFDLYISSSF---------TKLNSEnsiTLTCEEILLG 162
Cdd:cd08449    3 NIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFvrfadtlndPPLASE---LLWREPMVVA 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490589123 163 VSINHPLSLKDEVYLSEVSDENFIVITKgENYREVIDI--LCESANFKPKIAFESDSPYTIYALIKSLQGV 231
Cdd:cd08449   80 LPEEHPLAGRKSLTLADLRDEPFVFLRL-ANSRFADFLinCCLQAGFTPQITQEVVEPQTLMALVAAGFGV 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-196 2.04e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 60.43  E-value: 2.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGrlflkrvdsiLDLVESSKK 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG----------LLLVDQART 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQdtslensgEVKILSPAAAN--------------------VLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFD 136
Cdd:PRK11151  71 VLR--------EVKVLKEMASQqgetmsgplhigliptvgpyLLPHIIPMLHQTFPKLEMYLheaqTHQLLAQLDSGKLD 142

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 137 LYISSSFTKLNSENSITLTCEEILLGVSINHPLSLKDEVYLSEVSDENFIVITKGENYRE 196
Cdd:PRK11151 143 CAILALVKESEAFIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRD 202
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-170 3.92e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.43  E-value: 3.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   6 LKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQDT 85
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  86 sleNSG---EVKIL------SPAAanvLPSLLSNFRKLYPNITFNVSHTLP----SSYKKSDFDLYISSSFTKLNSENSI 152
Cdd:PRK10094  87 ---NDGverQVNIVinnllyNPQA---VAQLLAWLNERYPFTQFHISRQIYmgvwDSLLYEGFSLAIGVTGTEALANTFS 160

                        170       180
                 ....*....|....*....|
gi 490589123 153 TLTCEEI--LLGVSINHPLS 170
Cdd:PRK10094 161 LDPLGSVqwRFVMAADHPLA 180
PRK12680 PRK12680
LysR family transcriptional regulator;
1-142 4.02e-10

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 59.64  E-value: 4.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARME-HITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYI-VLNEYGRLFLKRVDSILDLVESS 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  79 KKELQDTSLENSGEVKILS--PAAANVLPSLLSNFRKLYPNITFNVSHTLPSS----YKKSDFDLYISSS 142
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTthTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAaldlLGQGDADIAIVST 150
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-187 4.47e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.26  E-value: 4.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ---ELQDTSLENSGE----VKILSPAaanvlpslLSNFRKLYPNITFN----VSHTLPSSYKKSDFDLYISSSFTKLNSE 149
Cdd:PRK15421  82 acnEPQQTRLRIAIEchscIQWLTPA--------LENFHKNWPQVEMDfksgVTFDPQPALQQGELDLVMTSDILPRSGL 153

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 490589123 150 NSITLTCEEILLGVSINHPLSLKDEVYLSEVSDENFIV 187
Cdd:PRK15421 154 HYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLI 191
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 101-263 4.65e-10

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: 58.11  E-value: 4.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 101 ANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSE--NSITLTCEEILLGVSINHPLSLKDE 174
Cdd:cd08437   12 NYYFPKLAKDLIKTGLMIQIDTyeggSAELLEQLLQGDLDIALLGSLTPLENSalHSKIIKTQHFMIIVSKDHPLAKAKK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 175 VYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICGKSwgLSQDPEIKLLHIKD 254
Cdd:cd08437   92 VNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIA--VKPDDHLVAIPLLD 169

                        170
                 ....*....|
gi 490589123 255 IE-FKRYLNL 263
Cdd:cd08437  170 NEqPTFYISL 179
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-122 6.17e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 58.86  E-value: 6.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   9 FQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYG-RLFLKRVDSILDLvessKKELQD-TS 86
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkRVFWALKSSLDTL----NQEILDiKN 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 490589123  87 LENSGEVKILSPaaanvlPSL--------LSNFRKLYPNITFNV 122
Cdd:PRK10086  98 QELSGTLTVYSR------PSIaqcwlvprLADFTRRYPSISLTI 135
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-232 6.20e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 58.85  E-value: 6.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   3 LLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDR-KGRYIVLNEYGRLF---------LKRVDSIL 72
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvRGRLHPTVQGLRLFeevqrsyygLDRIVSAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  73 DlvesSKKELQDtslensGEVKI--LSPAAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYIS-SSFTK 145
Cdd:PRK11013  86 E----SLREFRQ------GQLSIacLPVFSQSLLPGLCQPFLARYPDVSLNIvpqeSPLLEEWLSAQRHDLGLTeTLHTP 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 146 LNSENSITLTCEEILLgVSINHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALI 225
Cdd:PRK11013 156 AGTERTELLTLDEVCV-LPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMV 234


                 ....*..
gi 490589123 226 KslQGVG 232
Cdd:PRK11013 235 R--AGVG 239
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 99-234 5.80e-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: 54.82  E-value: 5.80e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  99 AAANVLPSLLSNFRKLYPNITFNVSHTLPSSYKKSDFDLYISSSF-------TKLNSENSITLTCeeiLLGVSINHPLSL 171
Cdd:cd08452   10 AIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFlhppiqhTALHIETVQSSPC---VLALPKQHPLAS 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123 172 KDEVYLSEVSDENFIVITKGEN---YREVIDiLCESANFKPKIAFESDSPYTIYALIKSLQGVGFI 234
Cdd:cd08452   87 KEEITIEDLRDEPIITVAREAWptlYDEIIQ-LCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFV 151
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-234 1.17e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 53.76  E-value: 1.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  99 AAANVLPSLLSNFRKLYPNITFNVSHTLPSS----YKKSDFDLYI--SSSFTKLNSENSITLT--CEEIL-LGVSINHPL 169
Cdd:cd08423   10 AAAALLPPALAALRARHPGLEVRLREAEPPEsldaLRAGELDLAVvfDYPVTPPPDDPGLTRVplLDDPLdLVLPADHPL 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490589123 170 SLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFI 234
Cdd:cd08423   90 AGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALV 154
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 97-232 2.31e-08

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: 52.95  E-value: 2.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  97 SPA-AANVLPSLLSNFRKLYPNITFNVsHTLPSS-----YKKSDFDLYISSsftkLNSENSiTLTCEEILLG--VSI--- 165
Cdd:cd08415    7 LPAlALSLLPRAIARFRARHPDVRISL-HTLSSStvveaVLSGQADLGLAS----LPLDHP-GLESEPLASGraVCVlpp 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490589123 166 NHPLSLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKslQGVG 232
Cdd:cd08415   81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVA--AGLG 145
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-125 9.08e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.30  E-value: 9.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 490589123  81 ELQDTSLENSGEVKILSPAA---ANVLPsLLSNFRKLYPNITFNVSHT 125
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTllhVHIGP-MLAKFMARYPDVSLQLEAT 128
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 96-233 1.15e-07

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.01  E-value: 1.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  96 LSPAAANVLPSLLSNFRKLYPNITFNVS----HTLPSSYKKSDFDLYISssftkLNSENSITLTCEEIL-----LGVSIN 166
Cdd:cd08412    7 FSTLAPYYLPGLLRRFREAYPGVEVRVVegnqEELEEGLRSGELDLALT-----YDLDLPEDIAFEPLArlppyVWLPAD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490589123 167 HPLSLKDEVYLSEVSDENFIVITKGENYREVIDiLCESANFKPKIAFESDSpytiYALIKSL--QGVGF 233
Cdd:cd08412   82 HPLAGKDEVSLADLAAEPLILLDLPHSREYFLS-LFAAAGLTPRIAYRTSS----FEAVRSLvaNGLGY 145
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-265 2.06e-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: 50.34  E-value: 2.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 103 VLPSLLSNFRKLYPNITFNVsHTLPSS-----YKKSDFDLYISSSfTKLNSENSITLTCEE-ILLGVSINHPLSLKDEVY 176
Cdd:cd08448   14 GLPRILRAFRAEYPGIEVAL-HEMSSAeqieaLLRGELDLGFVHS-RRLPAGLSARLLHREpFVCCLPAGHPLAARRRID 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 177 LSEVSDENFIVITKG---ENYREVIDiLCESANFKPKIAFESDSPYTIYALIKSLQGVGfICGKSWGLSQDPEIKLLHIK 253
Cdd:cd08448   92 LRELAGEPFVLFSREvspDYYDQIIA-LCMDAGFHPKIRHEVRHWLTVVALVAAGMGVA-LVPRSLARAGLAGVRFLPLK 169

                        170
                 ....*....|..
gi 490589123 254 DIEFKRYLNLSW 265
Cdd:cd08448  170 GATQRSELYAAW 181
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-233 2.19e-07

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 50.29  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  95 ILSPAAANvLPSLLSNFRKLYP--NITFNV--SHTLPSSYKKSDFDL-YISSSFTKLNSENSITLTCEEILLGVSINHPL 169
Cdd:cd08436    7 ITSLAAVD-LPELLARFHRRHPgvDIRLRQagSDDLLAAVREGRLDLaFVGLPERRPPGLASRELAREPLVAVVAPDHPL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490589123 170 SLKDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGF 233
Cdd:cd08436   86 AGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVAL 149
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-128 2.37e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.30  E-value: 2.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   3 LLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKEL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 490589123  83 QDTSLENSGEVKILSPA--AANVLPSLLSNFRKLYPNITFNVSHTLPS 128
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSStmAQNVLAGLTAKMLKEYPGLSVNLVTGIPA 131
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-83 3.29e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 50.71  E-value: 3.29e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490589123  11 TVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKKELQ 83
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQ 84
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-232 1.13e-06

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: 47.91  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  99 AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSftkLNSENSIT---LTCEEILLGVSINHPLSL 171
Cdd:cd08440   10 LAATLLPPVLAAFRRRHPGIRVRLrdvsAEQVIEAVRSGEVDFGIGSE---PEADPDLEfepLLRDPFVLVCPKDHPLAR 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490589123 172 KDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKslQGVG 232
Cdd:cd08440   87 RRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVA--AGLG 145
leuO PRK09508
leucine transcriptional activator; Reviewed
 2-168 1.48e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 48.87  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   2 DLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVessKKE 81
Cdd:PRK09508  23 DLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLV---QNE 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  82 LQDTSLE--NSGEV---KILSPAAANVLPSLLSNFRKLYPNITF--------NVSHTLpsSYKKSDFDLyissSFTKLNS 148
Cdd:PRK09508 100 LPGSGFEpeSSERVfnlCICSPLDIRLTSQIYNRIEQIAPNIHVvfksslnqNIEHQL--RYQETEFVI----SYEEFDR 173

                        170       180
                 ....*....|....*....|..
gi 490589123 149 E--NSITLTCEEILLGVSINHP 168
Cdd:PRK09508 174 PefTSVPLFKDELVLVASKNHP 195
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-154 1.02e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.17  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  81 ELQDTSLEnsGEVKILSP--AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSS----FTKLNSEN 150
Cdd:PRK15092  91 SLMYSNLQ--GVLTIGASddTADTILPFLLNRVSSVYPKLALDVrvkrNAFMMEMLESQEVDLAVTTHrpssFPALNLRT 168


                 ....
gi 490589123 151 SITL 154
Cdd:PRK15092 169 SPTL 172
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 102-231 1.26e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 44.96  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 102 NVLPSLLSNFRKLYPNITFNVSHTLPSSYKKSDFDLYISSSFTKLNS-ENSIT---LTCEEILLGVSINHPLSLKDEVYL 177
Cdd:cd08446   14 DTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPvEPDIAvenVAQERLYLAVPKSHPLAARPAVSL 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490589123 178 SEVSDENFIVITKGEN---YREVIDiLCESANFKPKIAFESDSPYTIYALIKSLQGV 231
Cdd:cd08446   94 ADLRNEPLILFPRGGRpsfADEVLG-LFRRAGVEPRVAQEVEDVVAALALVAAGFGV 149
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-99 1.77e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.39  E-value: 1.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVESSKK 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90
                 ....*....|....*....
gi 490589123  81 ELQDTSLENsgEVKILSPA 99
Cdd:PRK03601  81 EVAHTSQHN--ELSIGASA 97
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-81 1.86e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 45.38  E-value: 1.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   5 HLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDS-------ILDLVES 77
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKmftlsqeMLDIVNY 87


                 ....
gi 490589123  78 SKKE 81
Cdd:PRK11062  88 RKES 91
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 103-221 5.92e-05

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: 42.90  E-value: 5.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 103 VLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSsfTKLNSEN--SITLTCEEILLGVSINHPLSLKDEVY 176
Cdd:cd08411   15 LLPRLLPALRQAYPKLRLYLredqTERLLEKLRSGELDAALLA--LPVDEPGleEEPLFDEPFLLAVPKDHPLAKRKSVT 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 490589123 177 LSEVSDENFIVITKGENYRE-VIDIlCESANFKPKIAFESDSPYTI 221
Cdd:cd08411   93 PEDLAGERLLLLEEGHCLRDqALEL-CRLAGAREQTDFEATSLETL 137
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 100-255 2.48e-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: 2.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 100 AANVLPSLLSNFRKLYPNITFNVS----HTLPSSYKKSDFDLYISSSFTKLNSeNSITLTCEEI--LLGVSINHPLSLKD 173
Cdd:cd08443   11 ARYVLPPVIKGFIERYPRVSLQMHqgspTQIAEMVSKGLVDFAIATEALHDYD-DLITLPCYHWnrCVVVKRDHPLADKQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 174 EVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFICGKSWGLSQDPEIKLLHIK 253
Cdd:cd08443   90 SISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDAR 169


                 ..
gi 490589123 254 DI 255
Cdd:cd08443  170 DL 171
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 106-226 4.24e-04

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 40.39  E-value: 4.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 106 SLLSNFRKLYPNITFNVSHT----LPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLSLK-DEVYLSEV 180
Cdd:cd08425   18 PLIDRFHARYPGIALSLREMpqerIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRrTALTLDDL 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 490589123 181 SDENFIVITKGENYREVIDILCESANFKPKIAFESDSpytIYALIK 226
Cdd:cd08425   98 AAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANS---ISAVLE 140
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 98-232 4.41e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 40.55  E-value: 4.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  98 PAAAN-VLPSLLSNFRKLYPNITFNVShTLPSS-----YKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPLSL 171
Cdd:cd08457    8 PALANgFLPRFLAAFLRLRPNLHLSLM-GLSSSqvleaVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQ 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490589123 172 KDEVYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKslQGVG 232
Cdd:cd08457   87 LDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVR--EGLG 145
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
1-111 9.90e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 40.04  E-value: 9.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123   1 MDLL---HLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRKGRYIVLNEYGRLFLKRVDSILDLVES 77
Cdd:PRK15243   1 MDFLinkKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHA 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490589123  78 SKKELQDTslensGEVKILSPAAANVLPSLLSNF 111
Cdd:PRK15243  81 LEQEIGPT-----GKTKQLEIIFDEIYPESLKNL 109
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 99-234 1.32e-03

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: 39.13  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123  99 AAANVLPSLLSNFRKLYPNITFNV----SHTLPSSYKKSDFDLYISSSFTKLNSENSITLTCEEILLGVSINHPlslkDE 174
Cdd:cd08442   10 TAAVRLPPLLAAYHARYPKVDLSLstgtTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP----PV 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490589123 175 VYLSEVSDENFIVITKGENYREVIDILCESANFKPKIAFESDSPYTIYALIKSLQGVGFI 234
Cdd:cd08442   86 SRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALL 145
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-77 3.73e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.41  E-value: 3.73e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490589123   2 DLLHLKYFQTVARMEHITKASHKLNIAQPALSKTISSLEKELGVQLFDRkGRYIVLNEYGRLFLKRVDSIlDLVES 77
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-ALLEA 76
 
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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